d3panels.js

!function() { // encapsulate d3panels functions
    var d3panels = {
        version: "1.8.4"
    };
"use strict";

// Generated by CoffeeScript 2.6.1
// A variety of utility functions used by the different panel functions
// determine rounding of axis labels
d3panels.formatAxis = function (d) {
  var extra_digits = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : 0;
  var gap, i, ndig, x; // determine typical gap between values
  //# remove nulls and sort

  d = function () {
    var k, len, results;
    results = [];

    for (k = 0, len = d.length; k < len; k++) {
      x = d[k];

      if (x != null) {
        results.push(x);
      }
    }

    return results;
  }();

  d.sort();

  if (d.length <= 1) {
    gap = 1;
  } else {
    // take differences
    d = function () {
      var k, ref, results;
      results = [];

      for (i = k = 1, ref = d.length - 1; 1 <= ref ? k <= ref : k >= ref; i = 1 <= ref ? ++k : --k) {
        results.push(d[i] - d[i - 1]);
      }

      return results;
    }(); // get mean


    gap = d3.mean(d);
  } // turn gap into number of digits


  ndig = Math.round(d3panels.log10(Math.abs(gap)));

  if (ndig < -8) {
    ndig = -8;
  }

  if (ndig > 0) {
    ndig = 0;
  }

  ndig = Math.abs(ndig) + extra_digits; // function to return

  return function (val) {
    if (val != null && val !== "NA") {
      return d3.format("." + ndig + "f")(val);
    }

    return "NA";
  };
}; // unique values of array (ignore nulls)


d3panels.unique = function (x) {
  var k, len, output, v;
  output = {};

  for (k = 0, len = x.length; k < len; k++) {
    v = x[k];

    if (v != null) {
      output[v] = v;
    }
  }

  output = function () {
    var results;
    results = [];

    for (v in output) {
      results.push(output[v]);
    }

    return results;
  }();

  return d3panels.forceAsArray(output);
}; // Pull out a variable (column) from a two-dimensional array
// [NO LONGER USED]


d3panels.pullVarAsArray = function (data, variable) {
  var i, results;
  results = [];

  for (i in data) {
    results.push(data[i][variable]);
  }

  return results;
}; // reorganize lod/pos by chromosome
//    uniquechr = vector of unique chromosome IDs
//    chr = vector of chromosome IDs


d3panels.reorgByChr = function (uniquechr, chr, vector) {
  var c, i, k, len, result;

  if (chr.length !== vector.length) {
    d3panels.displayError("reorgByChr: chr.length (" + chr.length + ") != vector.length (" + vector.length + ")");
  }

  result = {};

  for (i = k = 0, len = uniquechr.length; k < len; i = ++k) {
    c = uniquechr[i];

    result[c] = function () {
      var results;
      results = [];

      for (i in vector) {
        if (chr[i] === c) {
          results.push(vector[i]);
        }
      }

      return results;
    }();
  }

  return result;
}; // reorganize lod and position by chromosome
// also, add markerinfo object


d3panels.reorgLodData = function (data) {
  var i;
  data.posByChr = d3panels.reorgByChr(data.chrname, data.chr, data.pos);
  data.lodByChr = d3panels.reorgByChr(data.chrname, data.chr, data.lod);

  if (data.poslabel != null) {
    data.poslabelByChr = d3panels.reorgByChr(data.chrname, data.chr, data.poslabel);
  }

  if (data.marker != null) {
    data.markerinfo = function () {
      var results;
      results = [];

      for (i in data.marker) {
        if (data.marker[i] !== "") {
          results.push({
            name: data.marker[i],
            chr: data.chr[i],
            pos: data.pos[i],
            lod: data.lod[i]
          });
        }
      }

      return results;
    }();
  }

  return data;
}; // calculate chromosome scales for chrpanelframe (and so lodchart)
// type = "xaxis"     normal x-axis scale
//      = "yaxis"     y-axis scale
//      = "revyaxis"  reversed y-axis scale


d3panels.calc_chrscales = function (plot_width, left_margin, gap, chr, start, end) {
  var reverse = arguments.length > 6 && arguments[6] !== undefined ? arguments[6] : false;
  var chr_end_pixels, chr_length, chr_start_pixels, domain, i, k, n_chr, range, ref, right, tot_chr_length, tot_pixels, xscale; // calculate chromosome lengths, start and end in pixels

  n_chr = chr.length;

  chr_length = function () {
    var results;
    results = [];

    for (i in end) {
      results.push(end[i] - start[i]);
    }

    return results;
  }();

  tot_chr_length = chr_length.reduce(function (t, s) {
    return t + s;
  });
  tot_pixels = plot_width - gap * n_chr;
  chr_start_pixels = [left_margin + gap / 2];
  chr_end_pixels = [left_margin + gap / 2 + tot_pixels / tot_chr_length * chr_length[0]];

  for (i = k = 1, ref = n_chr - 1; 1 <= ref ? k <= ref : k >= ref; i = 1 <= ref ? ++k : --k) {
    chr_start_pixels.push(chr_end_pixels[i - 1] + gap);
    chr_end_pixels.push(chr_start_pixels[i] + tot_pixels / tot_chr_length * chr_length[i]);
  }

  right = plot_width + left_margin * 2;
  xscale = {};

  for (i in chr) {
    domain = [start[i], end[i]];
    range = [chr_start_pixels[i], chr_end_pixels[i]];

    if (reverse) {
      // for y-axis
      domain.reverse();
      range = [right - range[1], right - range[0]];
    }

    xscale[chr[i]] = d3.scaleLinear().domain(domain).range(range);
  } // return the scale


  return xscale;
}; // Select a set of categorical colors
// ngroup is positive integer
// palette = "dark" or "pastel"


d3panels.selectGroupColors = function (ngroup, palette) {
  var cat20, pastel1, pastel20, set1;

  if (ngroup === 0) {
    return [];
  } // ColorBrewer, now in D3 v5


  set1 = ["#e41a1c", "#377eb8", "#4daf4a", "#984ea3", "#ff7f00", "#ffff33", "#a65628", "#f781bf", "#999999"]; // ColorBrewer, now in D3 v5

  pastel1 = ["#fbb4ae", "#b3cde3", "#ccebc5", "#decbe4", "#fed9a6", "#ffffcc", "#e5d8bd", "#fddaec", "#f2f2f2"]; // from D3 v4

  cat20 = ["#1f77b4", "#aec7e8", "#ff7f0e", "#ffbb78", "#2ca02c", "#98df8a", "#d62728", "#ff9896", "#9467bd", "#c5b0d5", "#8c564b", "#c49c94", "#e377c2", "#f7b6d2", "#7f7f7f", "#c7c7c7", "#bcbd22", "#dbdb8d", "#17becf", "#9edae5"]; // my own rough attempt to make a _big_ pastel palette

  pastel20 = ["#8fc7f4", "#fed7f8", "#ffbf8e", "#fffbb8", "#8ce08c", "#d8ffca", "#f68788", "#ffd8d6", "#d4a7fd", "#f5f0f5", "#cc968b", "#f4dcd4", "#f3b7f2", "#f7f6f2", "#bfbfbf", "#f7f7f7", "#fcfd82", "#fbfbcd", "#87feff", "#defaf5"];

  if (palette === "dark") {
    if (ngroup === 1) {
      return ["slateblue"];
    }

    if (ngroup === 2) {
      return ["MediumVioletRed", "slateblue"];
    }

    if (ngroup === 3) {
      return ["MediumVioletRed", "MediumSeaGreen", "slateblue"];
    }

    if (ngroup <= 9) {
      return set1.slice(0, ngroup);
    }

    return cat20.slice(0, ngroup);
  } else {
    if (ngroup === 1) {
      return ["#bebebe"];
    }

    if (ngroup === 2) {
      return ["lightpink", "lightblue"];
    }

    if (ngroup <= 9) {
      return pastel1.slice(0, ngroup);
    }

    return pastel20.slice(0, ngroup);
  }
}; // expand element/array (e.g., of colors) to a given length
//     single elment -> array, then repeated to length n


d3panels.expand2vector = function (input, n) {
  var i;

  if (input == null) {
    return input; // return null if null
  }

  if (Array.isArray(input) && input.length >= n) {
    return input;
  }

  if (!Array.isArray(input)) {
    input = [input];
  }

  if (input.length > 1 && n > 1) {
    input = function () {
      var results;
      results = [];

      for (i in d3.range(n)) {
        results.push(input[i % input.length]);
      }

      return results;
    }();
  }

  if (input.length === 1 && n > 1) {
    input = function () {
      var results;
      results = [];

      for (i in d3.range(n)) {
        results.push(input[0]);
      }

      return results;
    }();
  }

  return input;
}; // median of a vector


d3panels.median = function (x) {
  var n, xv;

  if (x == null) {
    return null;
  }

  x = function () {
    var k, len, results;
    results = [];

    for (k = 0, len = x.length; k < len; k++) {
      xv = x[k];

      if (xv != null) {
        results.push(xv);
      }
    }

    return results;
  }();

  n = x.length;

  if (!(n > 0)) {
    return null;
  }

  x.sort(function (a, b) {
    return a - b;
  });

  if (n % 2 === 1) {
    return x[(n - 1) / 2];
  }

  return (x[n / 2] + x[n / 2 - 1]) / 2;
}; // pad a vector to left and right


d3panels.pad_vector = function (x) {
  var pad = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : null;

  // x should be sorted
  if (pad == null) {
    return [x[0] - (x[1] - x[0])].concat(x).concat([x[x.length - 1] + (x[x.length - 1] - x[x.length - 2])]);
  }

  return [x[0] - pad].concat(x).concat(x[x.length - 1] + pad);
}; // calculate midpoints


d3panels.calc_midpoints = function (x) {
  // x should be sorted
  var i, k, ref, results;
  results = [];

  for (i = k = 0, ref = x.length - 2; 0 <= ref ? k <= ref : k >= ref; i = 0 <= ref ? ++k : --k) {
    results.push((x[i] + x[i + 1]) / 2);
  }

  return results;
}; // calc cell rectangles (left, right, top, bottom)


d3panels.calc_cell_rect = function (cells, xmid, ymid) {
  var bottom, cell, k, left, len, results, right, top;
  results = [];

  for (k = 0, len = cells.length; k < len; k++) {
    cell = cells[k];
    left = xmid[cell.xindex];
    right = xmid[1 + cell.xindex];
    top = ymid[cell.yindex];
    bottom = ymid[1 + cell.yindex];
    cell.left = d3.min([left, right]);
    cell.width = Math.abs(right - left);
    cell.top = d3.min([top, bottom]);
    results.push(cell.height = Math.abs(bottom - top));
  }

  return results;
}; // calc chr cell rectangles (left, right, top, bottom)


d3panels.calc_chrcell_rect = function (cells, xmid, ymid) {
  var bottom, cell, k, left, len, results, right, top;
  results = [];

  for (k = 0, len = cells.length; k < len; k++) {
    cell = cells[k];
    left = xmid[cell.chr][cell.posindex];
    right = xmid[cell.chr][1 + cell.posindex];
    top = ymid[cell.lodindex];
    bottom = ymid[1 + cell.lodindex];
    cell.left = d3.min([left, right]);
    cell.width = Math.abs(right - left);
    cell.top = d3.min([top, bottom]);
    results.push(cell.height = Math.abs(bottom - top));
  }

  return results;
}; // calc chr cell rectangles (left, right, top, bottom)


d3panels.calc_2dchrcell_rect = function (cells, xmid, ymid) {
  var bottom, cell, k, left, len, results, right, top;
  results = [];

  for (k = 0, len = cells.length; k < len; k++) {
    cell = cells[k];
    left = xmid[cell.chrx][cell.xindexByChr];
    right = xmid[cell.chrx][1 + cell.xindexByChr];
    top = ymid[cell.chry][cell.yindexByChr];
    bottom = ymid[cell.chry][1 + cell.yindexByChr];
    cell.left = d3.min([left, right]);
    cell.width = Math.abs(right - left);
    cell.top = d3.min([top, bottom]);
    results.push(cell.height = Math.abs(bottom - top));
  }

  return results;
}; // maximum difference between adjacent values in a vector
// [NO LONGER USED]


d3panels.maxdiff = function (x) {
  var d, i, k, ref, result;

  if (x.length < 2) {
    return null;
  }

  result = x[1] - x[0];

  if (x.length < 3) {
    return result;
  }

  for (i = k = 2, ref = x.length; 2 <= ref ? k < ref : k > ref; i = 2 <= ref ? ++k : --k) {
    d = x[i] - x[i - 1];

    if (d > result) {
      result = d;
    }
  }

  return result;
}; // matrix extent, min, max, and max of absolute values


d3panels.matrixMin = function (mat) {
  var i, j, result;
  result = mat[0][0];

  for (i in mat) {
    for (j in mat[i]) {
      if (!(result != null) || result > mat[i][j] && mat[i][j] != null) {
        result = mat[i][j];
      }
    }
  }

  return result;
};

d3panels.matrixMax = function (mat) {
  var i, j, result;
  result = mat[0][0];

  for (i in mat) {
    for (j in mat[i]) {
      if (!(result != null) || result < mat[i][j] && mat[i][j] != null) {
        result = mat[i][j];
      }
    }
  }

  return result;
};

d3panels.matrixMaxAbs = function (mat) {
  var i, j, result;
  result = Math.abs(mat[0][0]);

  for (i in mat) {
    for (j in mat[i]) {
      if (!(result != null) || result < Math.abs(mat[i][j]) && mat[i][j] != null) {
        result = Math.abs(mat[i][j]);
      }
    }
  }

  return result;
};

d3panels.matrixExtent = function (mat) {
  return [d3panels.matrixMin(mat), d3panels.matrixMax(mat)];
}; // force an object to be an array (rather than a scalar)


d3panels.forceAsArray = function (x) {
  if (x == null) {
    return x; // if null, return null
  }

  if (Array.isArray(x)) {
    return x;
  }

  return [x];
}; // any values in vec that appear in missing are made null


d3panels.missing2null = function (vec) {
  var missingvalues = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : ['NA', ''];
  return vec.map(function (value) {
    if (missingvalues.indexOf(value) > -1) {
      return null;
    } else {
      return value;
    }
  });
}; // display error at top of page


d3panels.displayError = function (message) {
  var divid = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : null;
  var div;
  div = "div.error";

  if (divid != null) {
    div += "#" + divid;
  }

  if (d3.select(div).empty()) {
    // no errors yet
    d3.select("body").insert("div", ":first-child").attr("class", "error");
  }

  return d3.select(div).append("p").text(message);
}; // sum values in an array


d3panels.sumArray = function (vec) {
  var x;

  vec = function () {
    var k, len, results;
    results = [];

    for (k = 0, len = vec.length; k < len; k++) {
      x = vec[k];

      if (x != null) {
        results.push(x);
      }
    }

    return results;
  }();

  if (!(vec.length > 0)) {
    return null;
  }

  return vec.reduce(function (a, b) {
    return a * 1 + b * 1;
  });
}; // calculate cross-tabulation


d3panels.calc_crosstab = function (data) {
  var col, cs, i, k, l, ncol, nrow, ref, ref1, result, row, rs;
  nrow = data.ycat.length;
  ncol = data.xcat.length;

  result = function () {
    var k, ref, results; // matrix of 0's

    results = [];

    for (row = k = 0, ref = nrow; 0 <= ref ? k <= ref : k >= ref; row = 0 <= ref ? ++k : --k) {
      results.push(function () {
        var l, ref1, results1;
        results1 = [];

        for (col = l = 0, ref1 = ncol; 0 <= ref1 ? l <= ref1 : l >= ref1; col = 0 <= ref1 ? ++l : --l) {
          results1.push(0);
        }

        return results1;
      }());
    }

    return results;
  }(); // count things up


  for (i in data.x) {
    result[data.y[i]][data.x[i]] += 1;
  } // row and column sums


  rs = d3panels.rowSums(result);
  cs = d3panels.colSums(result); // fill in column sums

  for (i = k = 0, ref = ncol; 0 <= ref ? k < ref : k > ref; i = 0 <= ref ? ++k : --k) {
    result[nrow][i] = cs[i];
  } // fill in row sums


  for (i = l = 0, ref1 = nrow; 0 <= ref1 ? l < ref1 : l > ref1; i = 0 <= ref1 ? ++l : --l) {
    result[i][ncol] = rs[i];
  } // fill in total


  result[nrow][ncol] = d3panels.sumArray(rs);
  return result;
}; // rowSums: the sums for each row


d3panels.rowSums = function (mat) {
  var k, len, results, x;
  results = [];

  for (k = 0, len = mat.length; k < len; k++) {
    x = mat[k];
    results.push(d3panels.sumArray(x));
  }

  return results;
}; // transpose: matrix transpose


d3panels.transpose = function (mat) {
  var i, j, k, ref, results;
  results = [];

  for (j = k = 0, ref = mat[0].length; 0 <= ref ? k < ref : k > ref; j = 0 <= ref ? ++k : --k) {
    results.push(function () {
      var l, ref1, results1;
      results1 = [];

      for (i = l = 0, ref1 = mat.length; 0 <= ref1 ? l < ref1 : l > ref1; i = 0 <= ref1 ? ++l : --l) {
        results1.push(mat[i][j]);
      }

      return results1;
    }());
  }

  return results;
}; // colSums = the sums for each column


d3panels.colSums = function (mat) {
  return d3panels.rowSums(d3panels.transpose(mat));
}; // log base 2


d3panels.log2 = function (x) {
  if (x == null) {
    return x;
  }

  return Math.log(x) / Math.log(2.0);
}; // log base 10


d3panels.log10 = function (x) {
  if (x == null) {
    return x;
  }

  return Math.log(x) / Math.log(10.0);
}; // absolute value, preserving nulls


d3panels.abs = function (x) {
  if (x == null) {
    return x;
  }

  return Math.abs(x);
}; // mean of y for each possible value of g


d3panels.mean_by_group = function (g, y) {
  var i, means, n;
  means = {};
  n = {};

  for (i in g) {
    if (n[g[i]] != null) {
      if (y[i] != null) {
        means[g[i]] += y[i];
      }

      if (y[i] != null) {
        n[g[i]] += 1;
      }
    } else {
      if (y[i] != null) {
        means[g[i]] = y[i];
      }

      if (y[i] != null) {
        n[g[i]] = 1;
      }
    }
  }

  for (i in means) {
    means[i] /= n[i];
  }

  return means;
}; // SD of y for each possible value of g


d3panels.sd_by_group = function (g, y) {
  var dev, i, means, n, sds;
  means = d3panels.mean_by_group(g, y);
  sds = {};
  n = {};

  for (i in g) {
    dev = y[i] - means[g[i]];

    if (n[g[i]] != null) {
      if (y[i] != null) {
        sds[g[i]] += dev * dev;
      }

      if (y[i] != null) {
        n[g[i]] += 1;
      }
    } else {
      if (y[i] != null) {
        sds[g[i]] = dev * dev;
      }

      if (y[i] != null) {
        n[g[i]] = 1;
      }
    }
  }

  for (i in sds) {
    sds[i] = n[i] < 2 ? null : Math.sqrt(sds[i] / (n[i] - 1));
  }

  return sds;
}; // count groups


d3panels.count_groups = function (g, y) {
  var i, n;
  n = {};

  for (i in g) {
    if (n[g[i]] != null) {
      if (y[i] != null) {
        n[g[i]] += 1;
      }
    } else {
      if (y[i] != null) {
        n[g[i]] = 1;
      }
    }
  }

  return n;
}; // CI for mean(y) for each possible value of g
//  (as mean +/- m*SD)


d3panels.ci_by_group = function (g, y) {
  var m = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : 2;
  var ci, dev, i, means, n, sds;
  means = d3panels.mean_by_group(g, y); // repeat the code for the SD, so I do two passes but not three

  sds = {};
  n = {};

  for (i in g) {
    dev = y[i] - means[g[i]];

    if (n[g[i]] != null) {
      if (y[i] != null) {
        sds[g[i]] += dev * dev;
      }

      if (y[i] != null) {
        n[g[i]] += 1;
      }
    } else {
      if (y[i] != null) {
        sds[g[i]] = dev * dev;
      }

      if (y[i] != null) {
        n[g[i]] = 1;
      }
    }
  }

  for (i in sds) {
    sds[i] = n[i] < 2 ? null : Math.sqrt(sds[i] / (n[i] - 1));
  }

  ci = {};

  for (i in means) {
    ci[i] = {
      mean: means[i],
      low: n[i] > 0 ? means[i] - m * sds[i] / Math.sqrt(n[i]) : means[i],
      high: n[i] > 0 ? means[i] + m * sds[i] / Math.sqrt(n[i]) : means[i]
    };
  }

  return ci;
}; // pad y-axis limits a bit


d3panels.pad_ylim = function (ylim) {
  var p = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : 0.025;
  var d;
  d = ylim[1] - ylim[0];
  return [ylim[0] - d * p, ylim[1] + d * p];
}; // add to data: unique chromosome names, chr starting values, chr end values


d3panels.add_chrname_start_end = function (data) {
  var c, i, k, l, len, len1, ref, ref1, these_pos;

  if (data.chrname == null) {
    data.chrname = d3panels.unique(data.chr);
  }

  data.chrname = d3panels.forceAsArray(data.chrname);

  if (data.chrstart == null) {
    data.chrstart = [];
    ref = data.chrname;

    for (k = 0, len = ref.length; k < len; k++) {
      c = ref[k];

      these_pos = function () {
        var results;
        results = [];

        for (i in data.chr) {
          if (data.chr[i] === c) {
            results.push(data.pos[i]);
          }
        }

        return results;
      }();

      data.chrstart.push(d3.min(these_pos));
    }
  }

  if (data.chrend == null) {
    data.chrend = [];
    ref1 = data.chrname;

    for (l = 0, len1 = ref1.length; l < len1; l++) {
      c = ref1[l];

      these_pos = function () {
        var results;
        results = [];

        for (i in data.chr) {
          if (data.chr[i] === c) {
            results.push(data.pos[i]);
          }
        }

        return results;
      }();

      data.chrend.push(d3.max(these_pos));
    }
  }

  data.start = d3panels.forceAsArray(data.start);
  data.end = d3panels.forceAsArray(data.end);
  return data;
}; // calculate breakpoints in prepara


d3panels.calc_breaks = function (number, low, high) {
  var d, i, results;

  if (low >= high) {
    d3panels.displayError("calc_breaks: should have low < high");

    if (low > high) {
      var _ref = [high, low];
      low = _ref[0];
      high = _ref[1];
    }

    if (low === high) {
      low -= 0.5;
      high += 0.5;
    }
  }

  if (number < 2) {
    d3panels.displayError("calc_breaks: number should be >= 2");
    number = 2;
  }

  d = (high - low) / (number - 1);
  results = [];

  for (i in d3.range(number)) {
    results.push(low + d * i);
  }

  return results;
}; // calculate frequencies for histogram


d3panels.calc_freq = function (values, breaks) {
  var return_counts = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : false;
  var br, i, k, len, n, ref, result, v, z; // clone and sort

  v = values.slice(0);
  v.sort(function (a, b) {
    return +a - b;
  });
  br = breaks.slice(0);
  br.sort(function (a, b) {
    return +a - b;
  });
  br[0] -= 1e-6;
  br[br.length - 1] += 1e-6;

  result = function () {
    var k, len, ref, results;
    ref = d3.range(br.length - 1);
    results = [];

    for (k = 0, len = ref.length; k < len; k++) {
      i = ref[k];
      results.push(0);
    }

    return results;
  }();

  n = v.length;

  v = function () {
    var k, len, results;
    results = [];

    for (k = 0, len = v.length; k < len; k++) {
      z = v[k];

      if (z > br[0] && z < br[br.length - 1]) {
        results.push(z);
      }
    }

    return results;
  }();

  if (v.length < n) {
    d3panels.displayError("calc_freq: values out of range of breaks");
  }

  n = v.length;
  ref = d3.range(br.length - 1);

  for (k = 0, len = ref.length; k < len; k++) {
    i = ref[k];

    result[i] = function () {
      var l, len1, results;
      results = [];

      for (l = 0, len1 = v.length; l < len1; l++) {
        z = v[l];

        if (z >= br[i] && z < br[i + 1]) {
          results.push(z);
        }
      }

      return results;
    }().length;

    if (!return_counts) {
      // convert to density?
      result[i] /= n * (br[i + 1] - br[i]);
    }
  }

  return result;
}; // calculate points on path to draw histogram


d3panels.calc_hist_path = function (freq, breaks) {
  var i, result;

  if (freq.length !== breaks.length - 1) {
    d3panels.displayError("freq.length (" + freq.length + ") should be breaks.length - 1 (" + (breaks.length - 1) + ")");
  }

  result = [{
    x: breaks[0],
    y: 0
  }];

  for (i in freq) {
    result.push({
      x: breaks[i],
      y: freq[i]
    });
    result.push({
      x: breaks[+i + 1],
      y: freq[i]
    });
  }

  result.push({
    x: breaks[breaks.length - 1],
    y: 0
  });
  return result;
}; // find index of nearest value in a vector


d3panels.index_of_nearest = function (d, vec) {
  var abs_diff;
  abs_diff = vec.map(function (val) {
    return Math.abs(val - d);
  });
  return abs_diff.indexOf(d3.min(abs_diff));
}; // ensure that arguments that are named lists (ie objects) have all the required components


d3panels.check_listarg_v_default = function (arg, defaults) {
  var key;

  for (key in defaults) {
    if (arg[key] == null) {
      arg[key] = defaults[key];
    }
  }

  return arg;
}; // get x,y client position of an object


d3panels.object_position = function (object) {
  var obj, x, y;
  obj = object.node().getBoundingClientRect();
  x = obj.left / 2.0 + obj.right / 2.0;
  y = obj.top / 2.0 + obj.bottom / 2.0;
  return {
    x: x,
    y: y
  };
};"use strict";

// Generated by CoffeeScript 2.6.1
// lod2dheatmap: heat map panel, with the two dimensions broken into chromosomes
d3panels.lod2dheatmap = function (chartOpts) {
  var cellSelect, cells, celltip, chart, chrGap, colors, equalCells, height, hilitcolor, margin, nullcolor, oneAtTop, ref, ref1, ref10, ref11, ref2, ref3, ref4, ref5, ref6, ref7, ref8, ref9, svg, tipclass, width, xscale, yscale, zlim, zscale, zthresh;

  if (chartOpts == null) {
    chartOpts = {}; // make sure it's defined
  } // chartOpts start


  width = (ref = chartOpts != null ? chartOpts.width : void 0) != null ? ref : 800; // overall height of chart in pixels

  height = (ref1 = chartOpts != null ? chartOpts.height : void 0) != null ? ref1 : 800; // overall width of chart in pixels

  margin = (ref2 = chartOpts != null ? chartOpts.margin : void 0) != null ? ref2 : {
    left: 60,
    top: 40,
    right: 40,
    bottom: 60 // margins in pixels (left, top, right, bottom)

  };
  chrGap = (ref3 = chartOpts != null ? chartOpts.chrGap : void 0) != null ? ref3 : 6; // gap between chromosomes in pixels

  equalCells = (ref4 = chartOpts != null ? chartOpts.equalCells : void 0) != null ? ref4 : false; // if true, make all cells equal-sized; in this case, chartOpts.chrGap is ignored

  oneAtTop = (ref5 = chartOpts != null ? chartOpts.oneAtTop : void 0) != null ? ref5 : false; // if true, put chromosome 1 at the top rather than bottom

  colors = (ref6 = chartOpts != null ? chartOpts.colors : void 0) != null ? ref6 : ["slateblue", "white", "crimson" // vector of three colors for the color scale (negative - zero - positive)
  ];
  nullcolor = (ref7 = chartOpts != null ? chartOpts.nullcolor : void 0) != null ? ref7 : "#e6e6e6"; // color for empty cells

  zlim = (ref8 = chartOpts != null ? chartOpts.zlim : void 0) != null ? ref8 : null; // z-axis limits (if null take from data, symmetric about 0)

  zthresh = (ref9 = chartOpts != null ? chartOpts.zthresh : void 0) != null ? ref9 : null; // z threshold; if |z| < zthresh, not shown

  hilitcolor = (ref10 = chartOpts != null ? chartOpts.hilitcolor : void 0) != null ? ref10 : "black"; // color of box around highlighted cell

  tipclass = (ref11 = chartOpts != null ? chartOpts.tipclass : void 0) != null ? ref11 : "tooltip"; // class name for tool tips
  // chartOpts end
  // further chartOpts: chr2dpanelframe
  // accessors start

  xscale = null; // x-axis scale (vector by chromosome)

  yscale = null; // y-axis scale (vector by chromosome)

  zscale = null; // z-axis scale

  celltip = null; // cell tooltip selection

  cells = null; // cell selection

  svg = null; // SVG selection
  // accessors end

  cellSelect = null; // actual name for the cell selection
  //# the main function

  chart = function chart(selection, data) {
    // (chr, pos, lod[chrx][chry])  optionally poslabel (e.g., marker names)
    var cellg, chr, i, indexWithinChr, j, k, l, len, len1, len2, m, myframe, n_pos, posByChr, ref12, ref13, ref14, tooltipfunc, x, xmid_scaled, y, ymid_scaled, zmax, zmin; // args that are lists: check that they have all the pieces

    margin = d3panels.check_listarg_v_default(margin, {
      left: 60,
      top: 40,
      right: 40,
      bottom: 60
    });

    if (data.chr == null) {
      d3panels.displayError("lod2dheatmap: data.chr is missing");
    }

    if (data.pos == null) {
      d3panels.displayError("lod2dheatmap: data.pos is missing");
    }

    if (data.lod == null) {
      d3panels.displayError("lod2dheatmap: data.lod is missing");
    }

    n_pos = data.chr.length;

    if (data.pos.length !== n_pos) {
      d3panels.displayError("lod2dheatmap: data.pos.length (" + data.pos.length + ") != data.chr.length (" + n_pos + ")");
    }

    if (data.lod.length !== n_pos) {
      d3panels.displayError("lod2dheatmap: data.lod.length (" + data.lod.length + ") != data.chr.length (" + n_pos + ")");
    }

    for (i in data.lod) {
      if (data.lod[i].length !== n_pos) {
        d3panels.displayError("lod2dheatmap: data.lod[" + i + "].length (" + data.lod[i].length + ") != data.chr.length (" + n_pos + ")");
      }
    }

    if (data.poslabel != null) {
      if (data.poslabel.length !== n_pos) {
        d3panels.displayError("lod2dheatmap: data.poslabel.length (" + data.poslabel.length + ") != data.chr.length (" + n_pos + ")");
      }
    } else {
      // create position labels
      data.poslabel = function () {
        var results;
        results = [];

        for (i in data.chr) {
          results.push(data.chr[i] + "@" + d3panels.formatAxis(data.pos)(data.pos[i]));
        }

        return results;
      }();
    }

    if (data.chrname == null) {
      // create chrname if missing
      data.chrname = d3panels.unique(data.chr);
    }

    data.chrname = d3panels.forceAsArray(data.chrname); // if equalCells, change positions to dummy values

    if (equalCells) {
      data.pos = [];
      ref12 = data.chrname;

      for (k = 0, len = ref12.length; k < len; k++) {
        chr = ref12[k];
        data.pos = data.pos.concat(function () {
          var results;
          results = [];

          for (i in data.chr) {
            if (data.chr[i] === chr) {
              results.push(+i);
            }
          }

          return results;
        }());
      }
    } // create chrstart, chrend if missing


    data = d3panels.add_chrname_start_end(data); // if equalCells, adjust chrGap to make chromosome ends equal

    if (equalCells) {
      chrGap = (width - margin.left - margin.right - 2 * data.chrname.length) / data.chr.length + 2;
    } // create frame


    chartOpts.chrGap = chrGap;
    chartOpts.width = width;
    chartOpts.height = height;
    chartOpts.margin = margin;
    myframe = d3panels.chr2dpanelframe(chartOpts); // create SVG

    myframe(selection, {
      chr: data.chrname,
      start: data.chrstart,
      end: data.chrend
    });
    svg = myframe.svg(); // scales

    xscale = myframe.xscale();
    yscale = myframe.yscale(); // split position by chromosome

    posByChr = d3panels.reorgByChr(data.chrname, data.chr, data.pos); // scaled midpoints

    xmid_scaled = {};
    ymid_scaled = {};
    ref13 = data.chrname;

    for (l = 0, len1 = ref13.length; l < len1; l++) {
      chr = ref13[l];
      xmid_scaled[chr] = d3panels.calc_midpoints(d3panels.pad_vector(function () {
        var len2, m, ref14, results;
        ref14 = posByChr[chr];
        results = [];

        for (m = 0, len2 = ref14.length; m < len2; m++) {
          x = ref14[m];
          results.push(xscale[chr](x));
        }

        return results;
      }(), chrGap - 2));
      ymid_scaled[chr] = d3panels.calc_midpoints(d3panels.pad_vector(function () {
        var len2, m, ref14, results;
        ref14 = posByChr[chr];
        results = [];

        for (m = 0, len2 = ref14.length; m < len2; m++) {
          y = ref14[m];
          results.push(yscale[chr](y));
        }

        return results;
      }(), oneAtTop ? chrGap - 2 : 2 - chrGap));
    } // z-axis (color) limits; if not provided, make symmetric about 0


    zmin = d3panels.matrixMin(data.lod);
    zmax = d3panels.matrixMaxAbs(data.lod);
    zlim = zlim != null ? zlim : [-zmax, 0, zmax];

    if (zlim.length !== colors.length) {
      d3panels.displayError("lod2dheatmap: zlim.length (" + zlim.length + ") != colors.length (" + colors.length + ")");
    }

    zscale = d3.scaleLinear().domain(zlim).range(colors);
    zthresh = zthresh != null ? zthresh : zmin - 1; // create within-chromosome index

    indexWithinChr = [];
    ref14 = data.chrname;

    for (m = 0, len2 = ref14.length; m < len2; m++) {
      chr = ref14[m];
      indexWithinChr = indexWithinChr.concat(function () {
        var results;
        results = [];

        for (i in posByChr[chr]) {
          results.push(+i);
        }

        return results;
      }());
    } // create cells for plotting


    cells = [];

    for (i in data.chr) {
      for (j in data.chr) {
        if (Math.abs(data.lod[i][j]) >= zthresh) {
          cells.push({
            lod: data.lod[i][j],
            chrx: data.chr[i],
            chry: data.chr[j],
            poslabelx: data.poslabel[i],
            poslabely: data.poslabel[j],
            xindex: i,
            yindex: j,
            xindexByChr: indexWithinChr[i],
            yindexByChr: indexWithinChr[j]
          });
        }
      }
    } // calc cell height, width


    d3panels.calc_2dchrcell_rect(cells, xmid_scaled, ymid_scaled);
    cellg = svg.append("g").attr("id", "cells");
    cellSelect = cellg.selectAll("empty").data(cells).enter().append("rect").attr("x", function (d) {
      return d.left;
    }).attr("y", function (d) {
      return d.top;
    }).attr("width", function (d) {
      return d.width;
    }).attr("height", function (d) {
      return d.height;
    }).attr("class", function (d, i) {
      return "cell" + i;
    }).attr("fill", function (d) {
      if (d.lod != null) {
        return zscale(d.lod);
      } else {
        return nullcolor;
      }
    }).attr("stroke", "none").attr("stroke-width", "1").on("mouseover", function () {
      return d3.select(this).attr("stroke", hilitcolor).raise();
    }).on("mouseout", function () {
      return d3.select(this).attr("stroke", "none");
    }); // tool tip

    tooltipfunc = function tooltipfunc(d) {
      var z;
      z = d3.format(".2f")(Math.abs(d.lod));
      return "(" + d.poslabelx + "," + d.poslabely + ") &rarr; " + z;
    };

    return celltip = d3panels.tooltip_create(d3.select("body"), cellg.selectAll("rect"), {
      tipclass: tipclass
    }, tooltipfunc);
  }; // functions to grab stuff


  chart.xscale = function () {
    return xscale;
  };

  chart.yscale = function () {
    return yscale;
  };

  chart.zscale = function () {
    return zscale;
  };

  chart.cells = function () {
    return cellSelect;
  };

  chart.celltip = function () {
    return celltip;
  };

  chart.svg = function () {
    return svg;
  }; // function to remove chart


  chart.remove = function () {
    svg.remove();
    d3panels.tooltip_destroy(celltip);
    return null;
  }; // return the chart function


  return chart;
};"use strict";

// Generated by CoffeeScript 2.5.1
// panelframe: create a frame for a plot (rectangle + axes + labels)
d3panels.panelframe = function (chartOpts) {
  var axispos, box, boxcolor, boxwidth, chart, height, margin, nxticks, nyticks, plot_height, plot_width, rectcolor, ref, ref1, ref10, ref11, ref12, ref13, ref14, ref15, ref16, ref17, ref18, ref19, ref2, ref20, ref21, ref22, ref23, ref24, ref25, ref26, ref3, ref4, ref5, ref6, ref7, ref8, ref9, rotate_ylab, svg, title, titlepos, v_over_h, width, xNA, xNA_size, xlab, xlabels, xlim, xlineOpts, xlines, xscale, xscale_wnull, xticklab, xticks, yNA, yNA_size, ylab, ylabels, ylim, ylineOpts, ylines, yscale, yscale_wnull, yticklab, yticks;

  if (chartOpts == null) {
    chartOpts = {}; // make sure it's defined
  } // chartOpts start


  width = (ref = chartOpts != null ? chartOpts.width : void 0) != null ? ref : 800; // overall width of chart in pixels

  height = (ref1 = chartOpts != null ? chartOpts.height : void 0) != null ? ref1 : 500; // overall height of chart in pixels

  margin = (ref2 = chartOpts != null ? chartOpts.margin : void 0) != null ? ref2 : {
    left: 60,
    top: 40,
    right: 40,
    bottom: 40,
    inner: 3 // margins in pixels (left, top, right, bottom, inner)

  };
  axispos = (ref3 = chartOpts != null ? chartOpts.axispos : void 0) != null ? ref3 : {
    xtitle: 25,
    ytitle: 45,
    xlabel: 5,
    ylabel: 5 // position of axis labels in pixels (xtitle, ytitle, xlabel, ylabel)

  };
  titlepos = (ref4 = chartOpts != null ? chartOpts.titlepos : void 0) != null ? ref4 : 20; // position of chart title in pixels

  title = (ref5 = chartOpts != null ? chartOpts.title : void 0) != null ? ref5 : ""; // chart title

  xlab = (ref6 = chartOpts != null ? chartOpts.xlab : void 0) != null ? ref6 : "X"; // x-axis label

  ylab = (ref7 = chartOpts != null ? chartOpts.ylab : void 0) != null ? ref7 : "Y"; // y-axis label

  rotate_ylab = (ref8 = chartOpts != null ? chartOpts.rotate_ylab : void 0) != null ? ref8 : null; // whether to rotate the y-axis label

  xNA = (ref9 = chartOpts != null ? chartOpts.xNA : void 0) != null ? ref9 : false; // include box for x=NA values

  yNA = (ref10 = chartOpts != null ? chartOpts.yNA : void 0) != null ? ref10 : false; // include box for y=NA values

  xNA_size = (ref11 = chartOpts != null ? chartOpts.xNA_size : void 0) != null ? ref11 : {
    width: 20,
    gap: 10 // width and gap for x=NA box

  };
  yNA_size = (ref12 = chartOpts != null ? chartOpts.yNA_size : void 0) != null ? ref12 : {
    width: 20,
    gap: 10 // width and gap for y=NA box

  };
  xlim = (ref13 = chartOpts != null ? chartOpts.xlim : void 0) != null ? ref13 : [0, 1 // x-axis limits
  ];
  ylim = (ref14 = chartOpts != null ? chartOpts.ylim : void 0) != null ? ref14 : [0, 1 // y-axis limits
  ];
  nxticks = (ref15 = chartOpts != null ? chartOpts.nxticks : void 0) != null ? ref15 : 5; // no. ticks on x-axis

  xticks = (ref16 = chartOpts != null ? chartOpts.xticks : void 0) != null ? ref16 : null; // vector of tick positions on x-axis

  xticklab = (ref17 = chartOpts != null ? chartOpts.xticklab : void 0) != null ? ref17 : null; // vector of x-axis tick labels

  nyticks = (ref18 = chartOpts != null ? chartOpts.nyticks : void 0) != null ? ref18 : 5; // no. ticks on y-axis

  yticks = (ref19 = chartOpts != null ? chartOpts.yticks : void 0) != null ? ref19 : null; // vector of tick positions on y-axis

  yticklab = (ref20 = chartOpts != null ? chartOpts.yticklab : void 0) != null ? ref20 : null; // vector of y-axis tick labels

  rectcolor = (ref21 = chartOpts != null ? chartOpts.rectcolor : void 0) != null ? ref21 : "#e6e6e6"; // color of background rectangle

  boxcolor = (ref22 = chartOpts != null ? chartOpts.boxcolor : void 0) != null ? ref22 : "black"; // color of outer rectangle box

  boxwidth = (ref23 = chartOpts != null ? chartOpts.boxwidth : void 0) != null ? ref23 : 2; // width of outer box in pixels

  xlineOpts = (ref24 = chartOpts != null ? chartOpts.xlineOpts : void 0) != null ? ref24 : {
    color: "white",
    width: 2 // color and width of vertical lines

  };
  ylineOpts = (ref25 = chartOpts != null ? chartOpts.ylineOpts : void 0) != null ? ref25 : {
    color: "white",
    width: 2 // color and width of horizontal lines

  };
  v_over_h = (ref26 = chartOpts != null ? chartOpts.v_over_h : void 0) != null ? ref26 : false; // whether the vertical grid lines should be on top of the horizontal lines
  // chartOpts end
  // accessors start

  xscale = null; // x-axis scale

  yscale = null; // y-axis scale

  xNA = xNA; // true if x-axis NAs are handled in a separate box

  yNA = yNA; // true if y-axis NAs are handled in a separate box

  xlines = null; // xlines selection

  ylines = null; // ylines selection

  xlabels = null; // x-axis labels selection

  ylabels = null; // y-axis labels selection

  plot_width = null; // plot width (in pixels)

  plot_height = null; // plot height (in pixels)

  box = null; // outer box selection

  svg = null; // SVG selection
  // accessors end

  xscale_wnull = null;
  yscale_wnull = null; //# the main function

  chart = function chart(selection) {
    var boxes, boxes2include, d, g, i, inner_height, inner_width, xNA_xpos, xaxis, xrange, yNA_ypos, yaxis, ylabpos_x, ylabpos_y, yrange; // args that are lists: check that they have all the pieces

    margin = d3panels.check_listarg_v_default(margin, {
      left: 60,
      top: 40,
      right: 40,
      bottom: 40,
      inner: 3
    });
    axispos = d3panels.check_listarg_v_default(axispos, {
      xtitle: 25,
      ytitle: 45,
      xlabel: 5,
      ylabel: 5
    });
    xNA_size = d3panels.check_listarg_v_default(xNA_size, {
      width: 20,
      gap: 10
    });
    yNA_size = d3panels.check_listarg_v_default(yNA_size, {
      width: 20,
      gap: 10
    });
    xlineOpts = d3panels.check_listarg_v_default(xlineOpts, {
      color: "white",
      width: 2
    });
    ylineOpts = d3panels.check_listarg_v_default(ylineOpts, {
      color: "white",
      width: 2
    }); // Create SVG

    svg = selection.append("svg"); // Update the dimensions

    svg.attr("width", width).attr("height", height).attr("class", "d3panels"); // put all of this stuff in a group

    g = svg.append("g").attr("id", "frame");

    if (!xNA) {
      // if no x-axis NA box
      xNA_size = {
        width: 0,
        gap: 0
      };
    }

    if (!yNA) {
      // if no y-axis NA box
      yNA_size = {
        width: 0,
        gap: 0
      };
    } // placement of boxes according to whether NAs will be treated specially


    plot_width = width - (margin.left + margin.right);
    plot_height = height - (margin.top + margin.bottom);
    inner_width = width - (margin.right + margin.left + xNA_size.width + xNA_size.gap);
    inner_height = height - (margin.top + margin.bottom + yNA_size.width + yNA_size.gap);
    boxes = {
      left: [margin.left + xNA_size.width + xNA_size.gap, margin.left, margin.left, margin.left + xNA_size.width + xNA_size.gap],
      width: [inner_width, xNA_size.width, xNA_size.width, inner_width],
      top: [margin.top, margin.top, height - (margin.bottom + yNA_size.width), height - (margin.bottom + yNA_size.width)],
      height: [inner_height, inner_height, yNA_size.width, yNA_size.width]
    };
    xNA_xpos = xNA ? margin.left + xNA_size.width / 2 : -50000;
    yNA_ypos = yNA ? height - margin.bottom - yNA_size.width / 2 : -50000;
    xrange = [boxes.left[0], boxes.left[0] + boxes.width[0]];
    yrange = [boxes.top[0] + boxes.height[0], boxes.top[0]]; // background rectangles

    for (i in boxes.left) {
      if (boxes.width[i] > 0 && boxes.height[i] > 0) {
        g.append("rect").attr("x", boxes.left[i]).attr("y", boxes.top[i]).attr("height", boxes.height[i]).attr("width", boxes.width[i]).attr("fill", rectcolor).attr("stroke", "none").attr("shape-rendering", "crispEdges");
      }
    } // add title


    g.append("g").attr("class", "title").append("text").text(title).attr("x", (width - margin.left - margin.right) / 2 + margin.left).attr("y", titlepos); // rotate y-axis title?

    rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1;

    if (v_over_h) {
      // xlines on top
      yaxis = g.append("g").attr("class", "y axis");
      xaxis = g.append("g").attr("class", "x axis"); // xlines on bottom
    } else {
      xaxis = g.append("g").attr("class", "x axis");
      yaxis = g.append("g").attr("class", "y axis");
    }

    xaxis.append("text").attr("class", "title").text(xlab).attr("x", (width - margin.left - margin.right) / 2 + margin.left).attr("y", plot_height + margin.top + axispos.xtitle);
    ylabpos_y = (height - margin.top - margin.bottom) / 2 + margin.top;
    ylabpos_x = margin.left - axispos.ytitle;
    yaxis.append("text").attr("class", "title").text(ylab).attr("y", ylabpos_y).attr("x", ylabpos_x).attr("transform", rotate_ylab ? "rotate(270," + ylabpos_x + "," + ylabpos_y + ")" : ""); // scales (ignoring NA business)

    xscale = d3.scaleLinear().domain(xlim).range([xrange[0] + margin.inner, xrange[1] - margin.inner]);
    yscale = d3.scaleLinear().domain(ylim).range([yrange[0] - margin.inner, yrange[1] + margin.inner]); // scales (handling nulls)

    xscale_wnull = function xscale_wnull(val) {
      if (val == null) {
        return xNA_xpos;
      }

      return xscale(val);
    };

    yscale_wnull = function yscale_wnull(val) {
      if (val == null) {
        return yNA_ypos;
      }

      return yscale(val);
    }; // add X axis values + xlines
    // if xticks not provided, use nxticks to choose pretty ones


    xticks = xticks != null ? xticks : xscale.ticks(nxticks);

    if (xticklab != null && xticklab.length !== xticks.length) {
      d3panels.displayError("panelframe: xticklab.length (" + xticklab.length + ") != xticks.length (" + xticks.length + ")");
    }

    if (!(xticklab != null && xticklab.length === xticks.length)) {
      xticklab = function () {
        var j, len, results;
        results = [];

        for (j = 0, len = xticks.length; j < len; j++) {
          d = xticks[j];
          results.push(d3panels.formatAxis(xticks)(d));
        }

        return results;
      }();
    }

    if (xNA) {
      xticks = [null].concat(xticks);
    }

    if (xNA) {
      xticklab = ["NA"].concat(xticklab);
    } // add Y axis values + ylines
    // if yticks not provided, use nyticks to choose pretty ones


    yticks = yticks != null ? yticks : yscale.ticks(nyticks);

    if (yticklab != null && yticklab.length !== yticks.length) {
      d3panels.displayError("panelframe: yticklab.length (" + yticklab.length + ") != yticks.length (" + yticks.length + ")");
    }

    if (!(yticklab != null && yticklab.length === yticks.length)) {
      yticklab = function () {
        var j, len, results;
        results = [];

        for (j = 0, len = yticks.length; j < len; j++) {
          d = yticks[j];
          results.push(d3panels.formatAxis(yticks)(d));
        }

        return results;
      }();
    }

    if (yNA) {
      yticks = [null].concat(yticks);
    }

    if (yNA) {
      yticklab = ["NA"].concat(yticklab);
    } // do ylines first


    ylines = yaxis.append("g").attr("id", "ylines").selectAll("empty").data(yticks.concat(yticks)).enter().append("line").attr("y1", function (d) {
      return yscale_wnull(d);
    }).attr("y2", function (d) {
      return yscale_wnull(d);
    }).attr("x1", function (d, i) {
      if (i < yticks.length) {
        return xrange[0];
      }

      return margin.left;
    }).attr("x2", function (d, i) {
      if (i < yticks.length) {
        return xrange[1];
      }

      return margin.left + xNA_size.width;
    }).attr("fill", "none").attr("stroke", ylineOpts.color).attr("stroke-width", ylineOpts.width).attr("shape-rendering", "crispEdges").style("pointer-events", "none"); // xlines

    xlines = xaxis.append("g").attr("id", "xlines").selectAll("empty").data(xticks.concat(xticks)).enter().append("line").attr("x1", function (d) {
      return xscale_wnull(d);
    }).attr("x2", function (d) {
      return xscale_wnull(d);
    }).attr("y1", function (d, i) {
      if (i < xticks.length) {
        return yrange[0];
      }

      return height - margin.bottom;
    }).attr("y2", function (d, i) {
      if (i < xticks.length) {
        return yrange[1];
      }

      return height - margin.bottom - yNA_size.width;
    }).attr("fill", "none").attr("stroke", xlineOpts.color).attr("stroke-width", xlineOpts.width).attr("shape-rendering", "crispEdges").style("pointer-events", "none"); // axis labels

    xlabels = xaxis.append("g").attr("id", "xlabels").selectAll("empty").data(xticklab).enter().append("text").attr("x", function (d, i) {
      return xscale_wnull(xticks[i]);
    }).attr("y", height - margin.bottom + axispos.xlabel).text(function (d) {
      return d;
    });
    ylabels = yaxis.append("g").attr("id", "ylabels").selectAll("empty").data(yticklab).enter().append("text").attr("y", function (d, i) {
      return yscale_wnull(yticks[i]);
    }).attr("x", margin.left - axispos.ylabel).text(function (d) {
      return d;
    }); // background rectangle boxes

    boxes2include = function () {
      var results;
      results = [];

      for (i in boxes.left) {
        if (boxes.width[i] > 0 && boxes.height[i] > 0) {
          results.push(i);
        }
      }

      return results;
    }();

    box = svg.append("g").attr("id", "box");
    return box.selectAll("empty").data(boxes2include).enter().append("rect").attr("x", function (i) {
      return boxes.left[i];
    }).attr("y", function (i) {
      return boxes.top[i];
    }).attr("height", function (i) {
      return boxes.height[i];
    }).attr("width", function (i) {
      return boxes.width[i];
    }).attr("fill", "none").attr("stroke", boxcolor).attr("stroke-width", boxwidth).attr("shape-rendering", "crispEdges");
  }; // functions to grab stuff


  chart.xscale = function () {
    return xscale_wnull;
  };

  chart.yscale = function () {
    return yscale_wnull;
  };

  chart.xNA = function () {
    return xNA;
  };

  chart.yNA = function () {
    return yNA;
  };

  chart.xlines = function () {
    return xlines;
  };

  chart.ylines = function () {
    return ylines;
  };

  chart.xlabels = function () {
    return xlabels;
  };

  chart.ylabels = function () {
    return ylabels;
  };

  chart.plot_width = function () {
    return plot_width;
  };

  chart.plot_height = function () {
    return plot_height;
  };

  chart.width = function () {
    return width;
  };

  chart.height = function () {
    return height;
  };

  chart.margin = function () {
    return margin;
  };

  chart.box = function () {
    return box;
  };

  chart.svg = function () {
    return svg;
  }; // function to remove chart


  chart.remove = function () {
    svg.remove();
    return null;
  }; // return the chart function


  return chart;
};"use strict";

// Generated by CoffeeScript 2.5.1
// chrpanelframe: create a frame for a lod curve plot (rectangle + axes + labels)
d3panels.chrpanelframe = function (chartOpts) {
  var altrectcolor, axispos, box, boxcolor, boxwidth, chart, chrGap, chrSelect, chrlinecolor, chrlines, chrlinewidth, height, horizontal, margin, nyticks, rectcolor, ref, ref1, ref10, ref11, ref12, ref13, ref14, ref15, ref16, ref17, ref18, ref19, ref2, ref20, ref21, ref22, ref3, ref4, ref5, ref6, ref7, ref8, ref9, rotate_ylab, svg, title, titlepos, width, xlab, xlabels, xlineOpts, xscale, ylab, ylabels, ylim, ylineOpts, yscale, yticklab, yticks;

  if (chartOpts == null) {
    chartOpts = {}; // make sure it's defined
  } // chartOpts start


  width = (ref = chartOpts != null ? chartOpts.width : void 0) != null ? ref : 800; // overall height of chart in pixels

  height = (ref1 = chartOpts != null ? chartOpts.height : void 0) != null ? ref1 : 500; // overall width of chart in pixels

  margin = (ref2 = chartOpts != null ? chartOpts.margin : void 0) != null ? ref2 : {
    left: 60,
    top: 40,
    right: 40,
    bottom: 40 // margins in pixels (left, top, right, bottom)

  };
  axispos = (ref3 = chartOpts != null ? chartOpts.axispos : void 0) != null ? ref3 : {
    xtitle: 25,
    ytitle: 45,
    xlabel: 5,
    ylabel: 5 // position of axis labels in pixels (xtitle, ytitle, xlabel, ylabel)

  };
  titlepos = (ref4 = chartOpts != null ? chartOpts.titlepos : void 0) != null ? ref4 : 20; // position of chart title in pixels

  title = (ref5 = chartOpts != null ? chartOpts.title : void 0) != null ? ref5 : ""; // chart title

  xlab = (ref6 = chartOpts != null ? chartOpts.xlab : void 0) != null ? ref6 : null; // x-axis label

  ylab = (ref7 = chartOpts != null ? chartOpts.ylab : void 0) != null ? ref7 : "LOD score"; // y-axis label

  rotate_ylab = (ref8 = chartOpts != null ? chartOpts.rotate_ylab : void 0) != null ? ref8 : null; // whether to rotate the y-axis label

  ylim = (ref9 = chartOpts != null ? chartOpts.ylim : void 0) != null ? ref9 : [0, 1 // y-axis limits
  ];
  nyticks = (ref10 = chartOpts != null ? chartOpts.nyticks : void 0) != null ? ref10 : 5; // no. ticks on y-axis

  yticks = (ref11 = chartOpts != null ? chartOpts.yticks : void 0) != null ? ref11 : null; // vector of tick positions on y-axis

  yticklab = (ref12 = chartOpts != null ? chartOpts.yticklab : void 0) != null ? ref12 : null; // vector of y-axis tick labels

  rectcolor = (ref13 = chartOpts != null ? chartOpts.rectcolor : void 0) != null ? ref13 : "#e6e6e6"; // color of background rectangle

  altrectcolor = (ref14 = chartOpts != null ? chartOpts.altrectcolor : void 0) != null ? ref14 : "#d4d4d4"; // color of background rectangle for alternate chromosomes (if "", not created)

  chrlinecolor = (ref15 = chartOpts != null ? chartOpts.chrlinecolor : void 0) != null ? ref15 : ""; // color of lines between chromosomes (if "", leave off)

  chrlinewidth = (ref16 = chartOpts != null ? chartOpts.chrlinewidth : void 0) != null ? ref16 : 2; // width of lines between chromosomes

  boxcolor = (ref17 = chartOpts != null ? chartOpts.boxcolor : void 0) != null ? ref17 : "black"; // color of outer rectangle box

  boxwidth = (ref18 = chartOpts != null ? chartOpts.boxwidth : void 0) != null ? ref18 : 2; // width of outer box in pixels

  xlineOpts = (ref19 = chartOpts != null ? chartOpts.xlineOpts : void 0) != null ? ref19 : {
    color: "#d4d4d4",
    width: 2 // color and width of vertical lines (if one chromosome)

  };
  ylineOpts = (ref20 = chartOpts != null ? chartOpts.ylineOpts : void 0) != null ? ref20 : {
    color: "white",
    width: 2 // color and width of horizontal lines

  };
  chrGap = (ref21 = chartOpts != null ? chartOpts.chrGap : void 0) != null ? ref21 : 6; // gap between chromosomes in pixels

  horizontal = (ref22 = chartOpts.horizontal) != null ? ref22 : false; // if true, chromosomes on vertical axis (xlab, ylab, etc stay the same)
  // chartOpts end
  // accessors start

  xscale = null; // x-axis scale (vector by chromosome)

  yscale = null; // y-axis scale

  xlabels = null; // x-axis labels selection

  ylabels = null; // y-axis labels selection

  chrSelect = null; // chromosome rectangle selection

  chrlines = null; // chromosome lines selection

  box = null; // outer box selection

  svg = null; // SVG selection
  // accessors end
  //# the main function

  chart = function chart(selection, data) {
    // data = chr, start, end  (vectors with chromosome IDs, start positions, and end positions)
    var c, d, g, plot_height, plot_width, thechr, xaxis, xlines, xticks, yaxis, ylabpos_x, ylabpos_y, ylines; // args that are lists: check that they have all the pieces

    margin = d3panels.check_listarg_v_default(margin, {
      left: 60,
      top: 40,
      right: 40,
      bottom: 60
    });
    axispos = d3panels.check_listarg_v_default(axispos, {
      xtitle: 25,
      ytitle: 45,
      xlabel: 5,
      ylabel: 5
    });
    xlineOpts = d3panels.check_listarg_v_default(xlineOpts, {
      color: "white",
      width: 2
    });
    ylineOpts = d3panels.check_listarg_v_default(ylineOpts, {
      color: "white",
      width: 2
    });

    if (data.chr == null) {
      d3panels.displayError("chrpanelframe: data.chr is missing");
    }

    if (data.end == null) {
      d3panels.displayError("chrpanelframe: data.end is missing");
    }

    if (xlab == null) {
      xlab = data.chr.length === 1 ? "Position" : "Chromosome"; // "Chromosome" or "Position" depending on whether >1 or ==1 chr
    } // Create SVG


    svg = selection.append("svg"); // Update the dimensions

    svg.attr("width", width).attr("height", height).attr("class", "d3panels");
    g = svg.append("g").attr("id", "frame"); // placement of boxes according to whether NAs will be treated specially

    plot_width = width - (margin.left + margin.right);
    plot_height = height - (margin.top + margin.bottom);

    if (!(data != null ? data.start : void 0)) {
      // if start missing, use 0
      data.start = function () {
        var j, len, ref23, results;
        ref23 = data.chr;
        results = [];

        for (j = 0, len = ref23.length; j < len; j++) {
          c = ref23[j];
          results.push(0);
        }

        return results;
      }();
    }

    if (data.chr.length !== data.start.length) {
      d3panels.displayError("chrpanelframe: data.start.length (" + data.start.length + ") != data.chr.length (" + data.chr.length + ")");
    }

    if (data.chr.length !== data.end.length) {
      d3panels.displayError("chrpanelframe: data.end.length (" + data.end.length + ") != data.chr.length (" + data.chr.length + ")");
    } // scales (x-axis scale has by chromosome ID)


    if (horizontal) {
      // when horizontal, vertical is x-axis and horizontal is y-axis
      xscale = d3panels.calc_chrscales(plot_height, margin.top, chrGap, data.chr, data.start, data.end);
      yscale = d3.scaleLinear().domain(ylim.reverse()).range([plot_width + margin.left, margin.left]);
    } else {
      xscale = d3panels.calc_chrscales(plot_width, margin.left, chrGap, data.chr, data.start, data.end);
      yscale = d3.scaleLinear().domain(ylim).range([plot_height + margin.top, margin.top]);
    } // solid background


    g.append("rect").attr("x", margin.left).attr("width", plot_width).attr("y", margin.top).attr("height", plot_height).attr("fill", rectcolor).attr("shape-rendering", "crispEdges"); // background rectangles, alternating colors

    if (altrectcolor !== "") {
      chrSelect = g.append("g").selectAll("empty").data(data.chr).enter().append("rect").attr("x", function (d, i) {
        if (horizontal) {
          return margin.left;
        }

        return xscale[d](data.start[i]) - chrGap / 2;
      }).attr("width", function (d, i) {
        if (horizontal) {
          return plot_width;
        }

        return xscale[d](data.end[i]) - xscale[d](data.start[i]) + chrGap;
      }).attr("y", function (d, i) {
        if (horizontal) {
          return xscale[d](data.start[i]) - chrGap / 2;
        }

        return margin.top;
      }).attr("height", function (d, i) {
        if (horizontal) {
          return xscale[d](data.end[i]) - xscale[d](data.start[i]) + chrGap;
        }

        return plot_height;
      }).attr("fill", function (d, i) {
        if (i % 2 === 0) {
          return rectcolor;
        }

        return altrectcolor;
      }).attr("shape-rendering", "crispEdges");
    } // add title


    g.append("g").attr("class", "title").append("text").text(title).attr("x", (width - margin.left - margin.right) / 2 + margin.left).attr("y", titlepos); // rotate y-axis title?

    if (horizontal) {
      rotate_ylab = rotate_ylab != null ? rotate_ylab : xlab.length > 1;
    } else {
      rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1;
    }

    xaxis = g.append("g").attr("class", function () {
      if (horizontal) {
        return "y axis";
      }

      return "x axis";
    });
    yaxis = g.append("g").attr("class", function () {
      if (horizontal) {
        return "x axis";
      }

      return "y axis";
    });
    xaxis.append("text").attr("class", "title").text(function () {
      if (horizontal) {
        return ylab;
      }

      return xlab;
    }).attr("x", (width - margin.left - margin.right) / 2 + margin.left).attr("y", plot_height + margin.top + axispos.xtitle);
    ylabpos_y = (height - margin.top - margin.bottom) / 2 + margin.top;
    ylabpos_x = margin.left - axispos.ytitle;
    yaxis.append("text").attr("class", "title").text(function () {
      if (horizontal) {
        return xlab;
      }

      return ylab;
    }).attr("y", ylabpos_y).attr("x", ylabpos_x).attr("transform", rotate_ylab ? "rotate(270," + ylabpos_x + "," + ylabpos_y + ")" : ""); // axis labels

    if (data.chr.length > 1) {
      xlabels = xaxis.append("g").attr("id", "xlabels").selectAll("empty").data(data.chr).enter().append("text").attr("x", function (d, i) {
        if (horizontal) {
          return margin.left - axispos.ylabel;
        }

        return (xscale[d](data.start[i]) + xscale[d](data.end[i])) / 2;
      }).attr("y", function (d, i) {
        if (horizontal) {
          return (xscale[d](data.start[i]) + xscale[d](data.end[i])) / 2;
        }

        return height - margin.bottom + axispos.xlabel;
      }).text(function (d) {
        return d;
      });
    } else {
      thechr = data.chr[0];
      xticks = xscale[thechr].ticks(5);
      xlabels = xaxis.append("g").attr("id", "xlabels").selectAll("empty").data(xticks).enter().append("text").attr("x", function (d) {
        if (horizontal) {
          return margin.left - axispos.ylabel;
        }

        return xscale[thechr](d);
      }).attr("y", function (d, i) {
        if (horizontal) {
          return xscale[thechr](d);
        }

        return height - margin.bottom + axispos.xlabel;
      }).text(function (d) {
        return d;
      }); // vertical grid lines

      xlines = xaxis.append("g").attr("id", "xlines").selectAll("empty").data(xticks).enter().append("line").attr("x1", function (d) {
        if (horizontal) {
          return margin.left;
        }

        return xscale[thechr](d);
      }).attr("x2", function (d) {
        if (horizontal) {
          return margin.left + plot_width;
        }

        return xscale[thechr](d);
      }).attr("y1", function (d, i) {
        if (horizontal) {
          return xscale[thechr](d);
        }

        return margin.top;
      }).attr("y2", function (d, i) {
        if (horizontal) {
          return xscale[thechr](d);
        }

        return plot_height + margin.top;
      }).attr("fill", "none").attr("stroke", xlineOpts.color).attr("stroke-width", xlineOpts.width).attr("shape-rendering", "crispEdges").style("pointer-events", "none");
    } // add Y axis values + ylines
    // if yticks not provided, use nyticks to choose pretty ones


    yticks = yticks != null ? yticks : yscale.ticks(nyticks);

    if (yticklab != null && yticklab.length !== yticks.length) {
      displayError("chrpanelframe: yticklab.length (" + yticklab.length + ") != yticks.length (" + yticks.length + ")");
    }

    if (!(yticklab != null && yticklab.length === yticks.length)) {
      yticklab = function () {
        var j, len, results;
        results = [];

        for (j = 0, len = yticks.length; j < len; j++) {
          d = yticks[j];
          results.push(d3panels.formatAxis(yticks)(d));
        }

        return results;
      }();
    } // horizontal grid lines


    ylines = yaxis.append("g").attr("id", "ylines").selectAll("empty").data(yticks.concat(yticks)).enter().append("line").attr("y1", function (d) {
      if (horizontal) {
        return margin.top;
      }

      return yscale(d);
    }).attr("y2", function (d) {
      if (horizontal) {
        return margin.top + plot_height;
      }

      return yscale(d);
    }).attr("x1", function (d, i) {
      if (horizontal) {
        return yscale(d);
      }

      return margin.left;
    }).attr("x2", function (d, i) {
      if (horizontal) {
        return yscale(d);
      }

      return plot_width + margin.left;
    }).attr("fill", "none").attr("stroke", ylineOpts.color).attr("stroke-width", ylineOpts.width).attr("shape-rendering", "crispEdges").style("pointer-events", "none");
    ylabels = yaxis.append("g").attr("id", "ylabels").selectAll("empty").data(yticklab).enter().append("text").attr("y", function (d, i) {
      if (horizontal) {
        return height - margin.bottom + axispos.xlabel;
      }

      return yscale(yticks[i]);
    }).attr("x", function (d, i) {
      if (horizontal) {
        return yscale(yticks[i]);
      }

      return margin.left - axispos.ylabel;
    }).text(function (d) {
      return d;
    }); // chrlines

    if (chrlinecolor !== "" && data.chr.length > 1) {
      chrlines = svg.append("g").attr("id", "chrlines");
      chrlines.selectAll("empty").data(data.chr.slice(0, +(data.chr.length - 2) + 1 || 9e9)).enter().append("line").attr("x1", function (d, i) {
        if (horizontal) {
          return margin.left;
        }

        return xscale[d](data.end[i]) + chrGap / 2;
      }).attr("x2", function (d, i) {
        if (horizontal) {
          return margin.left + plot_width;
        }

        return xscale[d](data.end[i]) + chrGap / 2;
      }).attr("y1", function (d, i) {
        if (horizontal) {
          return xscale[d](data.end[i]) + chrGap / 2;
        }

        return margin.top;
      }).attr("y2", function (d, i) {
        if (horizontal) {
          return xscale[d](data.end[i]) + chrGap / 2;
        }

        return margin.top + plot_height;
      }).attr("stroke", chrlinecolor).attr("stroke-width", chrlinewidth).attr("shape-rendering", "crispEdges");
    } // background rectangle box


    return box = svg.append("rect").attr("class", "box").attr("x", margin.left).attr("y", margin.top).attr("height", plot_height).attr("width", plot_width).attr("fill", "none").attr("stroke", boxcolor).attr("stroke-width", boxwidth).attr("shape-rendering", "crispEdges");
  }; // functions to grab stuff


  chart.xscale = function () {
    return xscale;
  };

  chart.yscale = function () {
    return yscale;
  };

  chart.xlabels = function () {
    return xlabels;
  };

  chart.ylabels = function () {
    return ylabels;
  };

  chart.chrSelect = function () {
    return chrSelect;
  };

  chart.chrlines = function () {
    return chrlines;
  };

  chart.plot_width = function () {
    return plot_width;
  };

  chart.plot_height = function () {
    return plot_height;
  };

  chart.width = function () {
    return width;
  };

  chart.height = function () {
    return height;
  };

  chart.margin = function () {
    return margin;
  };

  chart.box = function () {
    return box;
  };

  chart.svg = function () {
    return svg;
  }; // function to remove chart


  chart.remove = function () {
    svg.remove();
    return null;
  }; // return the chart function


  return chart;
};"use strict";

// Generated by CoffeeScript 2.5.1
// chr2dpanelframe: create a frame for a 2d LOD heatmap
d3panels.chr2dpanelframe = function (chartOpts) {
  var altrectcolor, axispos, box, boxcolor, boxwidth, chart, chrGap, chrSelect, chrlinecolor, chrlines, chrlinewidth, height, margin, oneAtTop, rectcolor, ref, ref1, ref10, ref11, ref12, ref13, ref14, ref15, ref16, ref2, ref3, ref4, ref5, ref6, ref7, ref8, ref9, rotate_ylab, svg, title, titlepos, width, xlab, xlabels, xscale, ylab, ylabels, yscale;

  if (chartOpts == null) {
    chartOpts = {}; // make sure it's defined
  } // chartOpts start


  width = (ref = chartOpts != null ? chartOpts.width : void 0) != null ? ref : 800; // overall height of chart in pixels

  height = (ref1 = chartOpts != null ? chartOpts.height : void 0) != null ? ref1 : 800; // overall width of chart in pixels

  margin = (ref2 = chartOpts != null ? chartOpts.margin : void 0) != null ? ref2 : {
    left: 60,
    top: 40,
    right: 40,
    bottom: 60 // margins in pixels (left, top, right, bottom)

  };
  axispos = (ref3 = chartOpts != null ? chartOpts.axispos : void 0) != null ? ref3 : {
    xtitle: 25,
    ytitle: 45,
    xlabel: 5,
    ylabel: 5 // position of axis labels in pixels (xtitle, ytitle, xlabel, ylabel)

  };
  titlepos = (ref4 = chartOpts != null ? chartOpts.titlepos : void 0) != null ? ref4 : 20; // position of chart title in pixels

  title = (ref5 = chartOpts != null ? chartOpts.title : void 0) != null ? ref5 : ""; // chart title

  xlab = (ref6 = chartOpts != null ? chartOpts.xlab : void 0) != null ? ref6 : "Chromosome"; // x-axis label

  ylab = (ref7 = chartOpts != null ? chartOpts.ylab : void 0) != null ? ref7 : "Chromosome"; // y-axis label

  rotate_ylab = (ref8 = chartOpts != null ? chartOpts.rotate_ylab : void 0) != null ? ref8 : null; // whether to rotate the y-axis label

  rectcolor = (ref9 = chartOpts != null ? chartOpts.rectcolor : void 0) != null ? ref9 : "#e6e6e6"; // color of background rectangle

  altrectcolor = (ref10 = chartOpts != null ? chartOpts.altrectcolor : void 0) != null ? ref10 : "#d4d4d4"; // color of background rectangle for alternate chromosomes (if "", not created)

  chrlinecolor = (ref11 = chartOpts != null ? chartOpts.chrlinecolor : void 0) != null ? ref11 : ""; // color of lines between chromosomes (if "", leave off)

  chrlinewidth = (ref12 = chartOpts != null ? chartOpts.chrlinewidth : void 0) != null ? ref12 : 2; // width of lines between chromosomes

  boxcolor = (ref13 = chartOpts != null ? chartOpts.boxcolor : void 0) != null ? ref13 : "black"; // color of outer rectangle box

  boxwidth = (ref14 = chartOpts != null ? chartOpts.boxwidth : void 0) != null ? ref14 : 2; // width of outer box in pixels

  chrGap = (ref15 = chartOpts != null ? chartOpts.chrGap : void 0) != null ? ref15 : 6; // gap between chromosomes in pixels

  oneAtTop = (ref16 = chartOpts != null ? chartOpts.oneAtTop : void 0) != null ? ref16 : false; // if true, put chromosome 1 at the top rather than bottom
  // chartOpts end
  // accessors start

  xscale = null; // x-axis scale (vector by chromosome)

  yscale = null; // y-axis scale (vector by chromosome)

  xlabels = null; // x-axis labels selection

  ylabels = null; // y-axis labels selection

  chrSelect = null; // chromosome rectangle selection

  chrlines = null; // chromosome lines selection

  box = null; // outer box selection

  svg = null; // SVG selection
  // accessors end
  //# the main function

  chart = function chart(selection, data) {
    // data = chr, start, end  (vectors with chromosome IDs, start positions, and end positions)
    var c, chrRect, chrx, chry, g, j, k, len, len1, plot_height, plot_width, ref17, ref18, x, xaxis, y, yaxis, ylabpos_x, ylabpos_y; // args that are lists: check that they have all the pieces

    margin = d3panels.check_listarg_v_default(margin, {
      left: 60,
      top: 40,
      right: 40,
      bottom: 60
    });
    axispos = d3panels.check_listarg_v_default(axispos, {
      xtitle: 25,
      ytitle: 45,
      xlabel: 5,
      ylabel: 5
    });

    if (data.chr == null) {
      d3panels.displayError("chr2dpanelframe: data.chr is missing");
    }

    if (data.end == null) {
      d3panels.displayError("chr2dpanelframe: data.end is missing");
    } // Create SVG


    svg = selection.append("svg"); // Update the dimensions

    svg.attr("width", width).attr("height", height).attr("class", "d3panels");
    g = svg.append("g").attr("id", "frame"); // placement of boxes according to whether NAs will be treated specially

    plot_width = width - (margin.left + margin.right);
    plot_height = height - (margin.top + margin.bottom);

    if (!(data != null ? data.start : void 0)) {
      // if start missing, use 0
      data.start = function () {
        var j, len, ref17, results;
        ref17 = data.chr;
        results = [];

        for (j = 0, len = ref17.length; j < len; j++) {
          c = ref17[j];
          results.push(0);
        }

        return results;
      }();
    }

    if (data.chr.length !== data.start.length) {
      d3panels.displayError("chr2dpanelframe: data.start.length (" + data.start.length + ") != data.chr.length (" + data.chr.length + ")");
    }

    if (data.chr.length !== data.end.length) {
      d3panels.displayError("chr2dpanelframe: data.end.length (" + data.end.length + ") != data.chr.length (" + data.chr.length + ")");
    } // scales


    xscale = d3panels.calc_chrscales(plot_width, margin.left, chrGap, data.chr, data.start, data.end);
    yscale = d3panels.calc_chrscales(plot_height, margin.top, chrGap, data.chr, data.start, data.end, !oneAtTop); // last arg is for reverse scale
    // solid background

    g.append("rect").attr("x", margin.left).attr("width", plot_width).attr("y", margin.top).attr("height", plot_height).attr("fill", rectcolor).attr("shape-rendering", "crispEdges");
    chrRect = [];
    ref17 = data.chr;

    for (x = j = 0, len = ref17.length; j < len; x = ++j) {
      chrx = ref17[x];
      ref18 = data.chr;

      for (y = k = 0, len1 = ref18.length; k < len1; y = ++k) {
        chry = ref18[y];
        chrRect.push({
          chrx: chrx,
          xi: x,
          chry: chry,
          yi: y,
          odd: (x + y) % 2
        });
      }
    } // background rectangles, alternating colors


    if (altrectcolor !== "") {
      chrSelect = g.append("g").selectAll("empty").data(chrRect).enter().append("rect").attr("x", function (d) {
        return xscale[d.chrx](data.start[d.xi]) - chrGap / 2;
      }).attr("width", function (d) {
        return xscale[d.chrx](data.end[d.xi]) - xscale[d.chrx](data.start[d.xi]) + chrGap;
      }).attr("y", function (d) {
        if (oneAtTop) {
          return yscale[d.chry](data.start[d.yi]) - chrGap / 2;
        }

        return yscale[d.chry](data.end[d.yi]) - chrGap / 2;
      }).attr("height", function (d) {
        if (oneAtTop) {
          return yscale[d.chry](data.end[d.yi]) - yscale[d.chry](data.start[d.yi]) + chrGap;
        }

        return yscale[d.chry](data.start[d.yi]) - yscale[d.chry](data.end[d.yi]) + chrGap;
      }).attr("fill", function (d, i) {
        if (!d.odd) {
          return rectcolor;
        }

        return altrectcolor;
      }).attr("shape-rendering", "crispEdges");
    } // add title


    g.append("g").attr("class", "title").append("text").text(title).attr("x", (width - margin.left - margin.right) / 2 + margin.left).attr("y", titlepos); // rotate y-axis title?

    rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1;
    xaxis = g.append("g").attr("class", "x axis");
    yaxis = g.append("g").attr("class", "y axis");
    xaxis.append("text").attr("class", "title").text(function () {
      return xlab;
    }).attr("x", (width - margin.left - margin.right) / 2 + margin.left).attr("y", plot_height + margin.top + axispos.xtitle);
    ylabpos_y = (height - margin.top - margin.bottom) / 2 + margin.top;
    ylabpos_x = margin.left - axispos.ytitle;
    yaxis.append("text").attr("class", "title").text(function () {
      return ylab;
    }).attr("y", ylabpos_y).attr("x", ylabpos_x).attr("transform", rotate_ylab ? "rotate(270," + ylabpos_x + "," + ylabpos_y + ")" : ""); // axis labels

    xlabels = xaxis.append("g").attr("id", "xlabels").selectAll("empty").data(data.chr).enter().append("text").attr("x", function (d, i) {
      return (xscale[d](data.start[i]) + xscale[d](data.end[i])) / 2;
    }).attr("y", height - margin.bottom + axispos.xlabel).text(function (d) {
      return d;
    });
    ylabels = yaxis.append("g").attr("id", "ylabels").selectAll("empty").data(data.chr).enter().append("text").attr("y", function (d, i) {
      return (yscale[d](data.start[i]) + yscale[d](data.end[i])) / 2;
    }).attr("x", margin.left - axispos.ylabel).text(function (d) {
      return d;
    }); // chrlines

    if (chrlinecolor !== "" && data.chr.length > 1) {
      chrlines = svg.append("g").attr("id", "chrlines");
      chrlines.selectAll("empty").data(data.chr.slice(0, +(data.chr.length - 2) + 1 || 9e9)).enter().append("line").attr("x1", function (d, i) {
        return xscale[d](data.end[i]) + chrGap / 2;
      }).attr("x2", function (d, i) {
        return xscale[d](data.end[i]) + chrGap / 2;
      }).attr("y1", margin.top).attr("y2", margin.top + plot_height).attr("stroke", chrlinecolor).attr("stroke-width", chrlinewidth).attr("shape-rendering", "crispEdges");
      chrlines.selectAll("empty").data(data.chr.slice(0, +(data.chr.length - 2) + 1 || 9e9)).enter().append("line").attr("y1", function (d, i) {
        if (oneAtTop) {
          return yscale[d](data.end[i]) + chrGap / 2;
        }

        return yscale[d](data.end[i]) - chrGap / 2;
      }).attr("y2", function (d, i) {
        if (oneAtTop) {
          return yscale[d](data.end[i]) + chrGap / 2;
        }

        return yscale[d](data.end[i]) - chrGap / 2;
      }).attr("x1", margin.left).attr("x2", margin.left + plot_width).attr("stroke", chrlinecolor).attr("stroke-width", chrlinewidth).attr("shape-rendering", "crispEdges");
    } // background rectangle box


    return box = svg.append("rect").attr("class", "box").attr("x", margin.left).attr("y", margin.top).attr("height", plot_height).attr("width", plot_width).attr("fill", "none").attr("stroke", boxcolor).attr("stroke-width", boxwidth).attr("shape-rendering", "crispEdges");
  }; // functions to grab stuff


  chart.xscale = function () {
    return xscale;
  };

  chart.yscale = function () {
    return yscale;
  };

  chart.xlabels = function () {
    return xlabels;
  };

  chart.ylabels = function () {
    return ylabels;
  };

  chart.chrSelect = function () {
    return chrSelect;
  };

  chart.chrlines = function () {
    return chrlines;
  };

  chart.plot_width = function () {
    return plot_width;
  };

  chart.plot_height = function () {
    return plot_height;
  };

  chart.width = function () {
    return width;
  };

  chart.height = function () {
    return height;
  };

  chart.margin = function () {
    return margin;
  };

  chart.box = function () {
    return box;
  };

  chart.svg = function () {
    return svg;
  }; // function to remove chart


  chart.remove = function () {
    svg.remove();
    return null;
  }; // return the chart function


  return chart;
};"use strict";

// Generated by CoffeeScript 2.5.1
// cichart: plot of estimates and confidence intervals for a set of categories
d3panels.cichart = function (chartOpts) {
  var chart, horizontal, ref, ref1, ref10, ref11, ref2, ref3, ref4, ref5, ref6, ref7, ref8, ref9, segcolor, segments, segstrokewidth, segwidth, svg, tip, tipclass, v_over_h, vertsegcolor, xcatlabels, xlab, xlineOpts, xscale, ylab, ylim, yscale;

  if (chartOpts == null) {
    chartOpts = {}; // make sure it's defined
  } // chartOpts start


  xcatlabels = (ref = chartOpts != null ? chartOpts.xcatlabels : void 0) != null ? ref : null; // category labels

  segwidth = (ref1 = chartOpts != null ? chartOpts.segwidth : void 0) != null ? ref1 : 0.4; // segment width as proportion of distance between categories

  segcolor = (ref2 = chartOpts != null ? chartOpts.segcolor : void 0) != null ? ref2 : "slateblue"; // color for segments

  segstrokewidth = (ref3 = chartOpts != null ? chartOpts.segstrokewidth : void 0) != null ? ref3 : "3"; // stroke width for segments

  vertsegcolor = (ref4 = chartOpts != null ? chartOpts.vertsegcolor : void 0) != null ? ref4 : "slateblue"; // color for vertical segments

  xlab = (ref5 = chartOpts != null ? chartOpts.xlab : void 0) != null ? ref5 : "Group"; // x-axis label

  ylab = (ref6 = chartOpts != null ? chartOpts.ylab : void 0) != null ? ref6 : "Response"; // y-axis label

  ylim = (ref7 = chartOpts != null ? chartOpts.ylim : void 0) != null ? ref7 : null; // y-axis limits

  xlineOpts = (ref8 = chartOpts != null ? chartOpts.xlineOpts : void 0) != null ? ref8 : {
    color: "#CDCDCD",
    width: 5 // color and width of vertical lines

  };
  horizontal = (ref9 = chartOpts != null ? chartOpts.horizontal : void 0) != null ? ref9 : false; // whether to interchange x and y-axes

  v_over_h = (ref10 = chartOpts != null ? chartOpts.v_over_h : void 0) != null ? ref10 : horizontal; // whether vertical lines should be on top of horizontal lines

  tipclass = (ref11 = chartOpts != null ? chartOpts.tipclass : void 0) != null ? ref11 : "tooltip"; // class name for tool tips
  // chartOpts end
  // further chartOpts: panelframe
  // accessors start

  xscale = null; // x-axis scale

  yscale = null; // y-axis scale

  segments = null; // segments selection

  tip = null; // tool tip selection

  svg = null; // SVG selection
  // accessors end
  //# the main function

  chart = function chart(selection, data) {
    // {mean, low, high} each vectors
    var direction, high, i, low, mean, myframe, ncat, segmentGroup, tipfunc, xlim, xticks, xval, yval; // args that are lists: check that they have all the pieces

    xlineOpts = d3panels.check_listarg_v_default(xlineOpts, {
      color: "#CDCDCD",
      width: 5
    });

    if (data.mean == null) {
      d3panels.displayError("cichart: data.mean is missing");
    }

    if (data.low == null) {
      d3panels.displayError("cichart: data.low is missing");
    }

    if (data.high == null) {
      d3panels.displayError("cichart: data.high is missing");
    } // input:


    mean = data.mean;
    low = data.low;
    high = data.high;
    ncat = mean.length;

    if (ncat !== low.length) {
      d3panels.displayError("cichart: low.length [" + low.length + "] != mean.length [" + ncat + "]");
    }

    if (ncat !== high.length) {
      d3panels.displayError("cichart: high.length [" + high.length + "] != mean.length [" + ncat + "]");
    }

    xticks = function () {
      var results;
      results = [];

      for (i in mean) {
        results.push(+i + 1);
      }

      return results;
    }();

    xcatlabels = xcatlabels != null ? xcatlabels : xticks;

    if (xcatlabels.length !== mean.length) {
      d3panels.displayError("cichart: xcatlabels.length [" + xcatlabels.length + "] != mean.length [" + ncat + "]");
    } // x- and y-axis limits + category locations


    ylim = ylim != null ? ylim : d3panels.pad_ylim(d3.extent(low.concat(high)));
    xlim = [0.5, mean.length + 0.5]; // expand segcolor and vertsegcolor to length of mean

    segcolor = d3panels.expand2vector(d3panels.forceAsArray(segcolor), mean.length);
    vertsegcolor = d3panels.expand2vector(d3panels.forceAsArray(vertsegcolor), mean.length);

    if (horizontal) {
      chartOpts.ylim = xlim.reverse();
      chartOpts.xlim = ylim;
      chartOpts.xlab = ylab;
      chartOpts.ylab = xlab;
      chartOpts.xlineOpts = chartOpts.ylineOpts;
      chartOpts.ylineOpts = xlineOpts;
      chartOpts.yNA = chartOpts.xNA;
      chartOpts.xNA = chartOpts.yNA;
      chartOpts.yticks = xticks;
      chartOpts.yticklab = xcatlabels;
      chartOpts.v_over_h = v_over_h;
    } else {
      chartOpts.ylim = ylim;
      chartOpts.xlim = xlim;
      chartOpts.xlab = xlab;
      chartOpts.ylab = ylab;
      chartOpts.ylineOpts = chartOpts.ylineOpts;
      chartOpts.xlineOpts = xlineOpts;
      chartOpts.xticks = xticks;
      chartOpts.xticklab = xcatlabels;
      chartOpts.v_over_h = v_over_h;
    } // set up frame


    myframe = d3panels.panelframe(chartOpts); // Create SVG

    myframe(selection);
    svg = myframe.svg(); // grab scale functions

    xscale = myframe.xscale();
    yscale = myframe.yscale();
    segmentGroup = svg.append("g").attr("id", "segments"); // lines from low to high

    segments = segmentGroup.selectAll("empty").data(low).enter().append("line").attr("x1", function (d, i) {
      if (!horizontal) {
        return xscale(i + 1);
      }

      return xscale(d);
    }).attr("x2", function (d, i) {
      if (!horizontal) {
        return xscale(i + 1);
      }

      return xscale(high[i]);
    }).attr("y1", function (d, i) {
      if (!horizontal) {
        return yscale(d);
      }

      return yscale(i + 1);
    }).attr("y2", function (d, i) {
      if (!horizontal) {
        return yscale(high[i]);
      }

      return yscale(i + 1);
    }).attr("fill", "none").attr("stroke", function (d, i) {
      return vertsegcolor[i];
    }).attr("stroke-width", segstrokewidth).attr("shape-rendering", "crispEdges"); // lines at low, mean, and high

    yval = mean.concat(low, high);

    xval = function () {
      var results;
      results = [];

      for (i in yval) {
        results.push(+(i % ncat) + 1);
      }

      return results;
    }();

    segments = segmentGroup.selectAll("empty").data(yval).enter().append("line").attr("x1", function (d, i) {
      if (horizontal) {
        return xscale(d);
      } else {
        if (i < ncat) {
          return xscale(xval[i] - segwidth / 2);
        }

        return xscale(xval[i] - segwidth / 3);
      }
    }).attr("x2", function (d, i) {
      if (horizontal) {
        return xscale(d);
      } else {
        if (i < ncat) {
          return xscale(xval[i] + segwidth / 2);
        }

        return xscale(xval[i] + segwidth / 3);
      }
    }).attr("y1", function (d, i) {
      if (horizontal) {
        if (i < ncat) {
          return yscale(xval[i] - segwidth / 2);
        }

        return yscale(xval[i] - segwidth / 3);
      } else {
        return yscale(d);
      }
    }).attr("y2", function (d, i) {
      if (horizontal) {
        if (i < ncat) {
          return yscale(xval[i] + segwidth / 2);
        }

        return yscale(xval[i] + segwidth / 3);
      } else {
        return yscale(d);
      }
    }).attr("fill", "none").attr("stroke", function (d, i) {
      return segcolor[i % mean.length];
    }).attr("stroke-width", segstrokewidth).attr("shape-rendering", "crispEdges");
    direction = horizontal ? "north" : "east";

    tipfunc = function tipfunc(d, i) {
      var f, index;
      index = i % mean.length;
      f = d3panels.formatAxis([low[index], mean[index]], 1);
      return f(mean[index]) + " (" + f(low[index]) + " - " + f(high[index]) + ")";
    };

    tip = d3panels.tooltip_create(d3.select("body"), segments, {
      direction: direction,
      tipclass: tipclass
    }, tipfunc); // move box to front

    return myframe.box().raise();
  }; // functions to grab stuff


  chart.yscale = function () {
    return yscale;
  };

  chart.xscale = function () {
    return xscale;
  };

  chart.segments = function () {
    return segments;
  };

  chart.tip = function () {
    return tip;
  };

  chart.svg = function () {
    return svg;
  }; // function to remove chart


  chart.remove = function () {
    svg.remove();
    d3panels.tooltip_destroy(tip);
    return null;
  }; // return the chart function


  return chart;
};"use strict";

// Generated by CoffeeScript 2.6.1
// crosstab: Display of a cross-tabulation (a two-way table)
d3panels.crosstab = function (chartOpts) {
  var bordercolor, cellPad, chart, colrect, fontsize, height, hilitcolor, margin, rectcolor, ref, ref1, ref2, ref3, ref4, ref5, ref6, ref7, ref8, ref9, rowrect, svg, title, titlepos, width;

  if (chartOpts == null) {
    chartOpts = {}; // make sure it's defined
  } // chartOpts start


  width = (ref = chartOpts != null ? chartOpts.width : void 0) != null ? ref : 600; // overall width of chart in pixels

  height = (ref1 = chartOpts != null ? chartOpts.height : void 0) != null ? ref1 : 300; // overall height of chart in pixels

  margin = (ref2 = chartOpts != null ? chartOpts.margin : void 0) != null ? ref2 : {
    left: 60,
    top: 80,
    right: 40,
    bottom: 20 // margins in pixels

  };
  cellPad = (ref3 = chartOpts != null ? chartOpts.cellPad : void 0) != null ? ref3 : null; // padding of cells (if null, we take cell width * 0.1)

  titlepos = (ref4 = chartOpts != null ? chartOpts.titlepos : void 0) != null ? ref4 : 50; // position of title in pixels

  title = (ref5 = chartOpts != null ? chartOpts.title : void 0) != null ? ref5 : ""; // chart title

  fontsize = (ref6 = chartOpts != null ? chartOpts.fontsize : void 0) != null ? ref6 : null; // font size (if null, we take cell height * 0.5)

  rectcolor = (ref7 = chartOpts != null ? chartOpts.rectcolor : void 0) != null ? ref7 : "#e6e6e6"; // color of rectangle

  hilitcolor = (ref8 = chartOpts != null ? chartOpts.hilitcolor : void 0) != null ? ref8 : "#e9cfec"; // color of rectangle when highlighted

  bordercolor = (ref9 = chartOpts != null ? chartOpts.bordercolor : void 0) != null ? ref9 : "black"; // color of borders
  // chartOpts end
  // accessors start

  rowrect = null; // row header rectangle selection

  colrect = null; // col header rectangle selection

  svg = null; // SVG selection
  // accessors end
  //# the main function

  chart = function chart(selection, data) {
    // {x, y, xcat, ycat, xlabel, ylabel} (xcat, ycat, xlabel, ylabel are optional; x and y in {0,1,2,...})
    var borders, cell, cellHeight, cellWidth, cells, collab, cols, denom, i, j, k, l, n, ncol, nrow, plot_height, plot_width, rect, ref10, ref11, ref12, ref13, ref14, ref15, ref16, ref17, rowlab, rows, tab, titles, values, xscale, xv, yscale, yv; // args that are lists: check that they have all the pieces

    margin = d3panels.check_listarg_v_default(margin, {
      left: 60,
      top: 40,
      right: 40,
      bottom: 60
    });

    if (data.x == null) {
      d3panels.displayError("crosstab: data.x is missing");
    }

    if (data.y == null) {
      d3panels.displayError("crosstab: data.y is missing");
    }

    n = data.x.length;

    if (data.y.length !== n) {
      d3panels.displayError("crosstab: data.x.length [" + data.x.length + "] != data.y.length [" + data.y.length + "]");
    }

    data.xcat = (ref10 = data != null ? data.xcat : void 0) != null ? ref10 : function () {
      var k, len, ref11, results;
      ref11 = d3.range(d3.max(data.x));
      results = [];

      for (k = 0, len = ref11.length; k < len; k++) {
        xv = ref11[k];
        results.push(xv + 1);
      }

      return results;
    }();
    data.ycat = (ref11 = data != null ? data.ycat : void 0) != null ? ref11 : function () {
      var k, len, ref12, results;
      ref12 = d3.range(d3.max(data.y));
      results = [];

      for (k = 0, len = ref12.length; k < len; k++) {
        yv = ref12[k];
        results.push(yv + 1);
      }

      return results;
    }();
    ncol = data.xcat.length;

    if (d3.max(data.x) > ncol || d3.min(data.x) <= 0) {
      d3panels.displayError("crosstab: data.x should be in range 1-" + ncol + " [was " + d3.min(data.x) + " - " + d3.max(data.x) + "]");
    }

    nrow = data.ycat.length;

    if (d3.max(data.y) > nrow || d3.min(data.y) <= 0) {
      d3panels.displayError("crosstab: data.y should be in range 1-" + nrow + " [was " + d3.min(data.y) + " - " + d3.max(data.y) + "]");
    } // convert x and y to 0,1,2,...


    data.x = function () {
      var k, len, ref12, results;
      ref12 = data.x;
      results = [];

      for (k = 0, len = ref12.length; k < len; k++) {
        xv = ref12[k];
        results.push(xv - 1);
      }

      return results;
    }();

    data.y = function () {
      var k, len, ref12, results;
      ref12 = data.y;
      results = [];

      for (k = 0, len = ref12.length; k < len; k++) {
        yv = ref12[k];
        results.push(yv - 1);
      }

      return results;
    }();

    tab = d3panels.calc_crosstab(data); // in case labels weren't provided

    data.xlabel = (ref12 = data != null ? data.xlabel : void 0) != null ? ref12 : "";
    data.ylabel = (ref13 = data != null ? data.ylabel : void 0) != null ? ref13 : ""; // turn it into a vector of cells

    cells = [];

    for (i = k = 0, ref14 = nrow; 0 <= ref14 ? k <= ref14 : k >= ref14; i = 0 <= ref14 ? ++k : --k) {
      for (j = l = 0, ref15 = ncol; 0 <= ref15 ? l <= ref15 : l >= ref15; j = 0 <= ref15 ? ++l : --l) {
        cell = {
          value: tab[i][j],
          row: i,
          col: j,
          shaded: false,
          rowpercent: "",
          colpercent: ""
        };

        if (i < nrow - 1 && (j < ncol - 1 || j === ncol)) {
          cell.shaded = true;
        }

        if (j < ncol - 1 && (i < nrow - 1 || i === nrow)) {
          cell.shaded = true;
        }

        if (i < nrow - 1) {
          denom = tab[nrow][j] - tab[nrow - 1][j];
          cell.colpercent = denom > 0 ? Math.round(100 * tab[i][j] / denom) + "%" : "\u2014";
        } else if (i === nrow - 1) {
          denom = tab[nrow][j];
          cell.colpercent = denom > 0 ? "(" + Math.round(100 * tab[i][j] / denom) + "%)" : "\u2014";
        } else {
          cell.colpercent = cell.value;
        }

        if (j < ncol - 1) {
          denom = tab[i][ncol] - tab[i][ncol - 1];
          cell.rowpercent = denom > 0 ? Math.round(100 * tab[i][j] / denom) + "%" : "\u2014";
        } else if (j === ncol - 1) {
          denom = tab[i][ncol];
          cell.rowpercent = denom > 0 ? "(" + Math.round(100 * tab[i][j] / denom) + "%)" : "\u2014";
        } else {
          cell.rowpercent = cell.value;
        }

        cells.push(cell);
      }
    } // widths and heights


    plot_width = width - margin.left - margin.right;
    plot_height = height - margin.top - margin.bottom;
    cellWidth = plot_width / (ncol + 2);
    cellHeight = plot_height / (nrow + 2);
    fontsize = fontsize != null ? fontsize : cellHeight * 0.5;
    cellPad = cellPad != null ? cellPad : cellWidth * 0.1;
    xscale = d3.scaleBand().domain(function () {
      var results = [];

      for (var m = 0, ref16 = ncol + 1; 0 <= ref16 ? m <= ref16 : m >= ref16; 0 <= ref16 ? m++ : m--) {
        results.push(m);
      }

      return results;
    }.apply(this)).range([margin.left, width - margin.right]);
    yscale = d3.scaleBand().domain(function () {
      var results = [];

      for (var m = 0, ref17 = nrow + 1; 0 <= ref17 ? m <= ref17 : m >= ref17; 0 <= ref17 ? m++ : m--) {
        results.push(m);
      }

      return results;
    }.apply(this)).range([margin.top, height - margin.bottom]); // Select the svg element, if it exists.

    svg = selection.append("svg").attr("width", width).attr("height", height).attr("class", "d3panels"); // rectangles for body of table

    rect = svg.append("g").attr("id", "value_rect");
    rect.selectAll("empty").data(cells).enter().append("rect").attr("x", function (d) {
      return xscale(d.col + 1);
    }).attr("y", function (d) {
      return yscale(d.row + 1);
    }).attr("width", cellWidth).attr("height", cellHeight).attr("fill", function (d) {
      if (d.shaded) {
        return rectcolor;
      } else {
        return "none";
      }
    }).attr("stroke", function (d) {
      if (d.shaded) {
        return rectcolor;
      } else {
        return "none";
      }
    }).attr("stroke-width", 0).style("pointer-events", "none").attr("shape-rendering", "crispEdges"); // text for the body of the table

    values = svg.append("g").attr("id", "values");
    values.selectAll("empty").data(cells).enter().append("text").attr("x", function (d) {
      return xscale(d.col + 1) + cellWidth - cellPad;
    }).attr("y", function (d) {
      return yscale(d.row + 1) + cellHeight / 2;
    }).text(function (d) {
      return d.value;
    }).attr("class", function (d) {
      return "crosstab row" + d.row + " col" + d.col;
    }).style("font-size", fontsize).style("pointer-events", "none"); // rectangles for the column headings

    colrect = svg.append("g").attr("id", "colrect");
    cols = colrect.selectAll("empty").data(data.xcat.concat("Total")).enter().append("rect").attr("x", function (d, i) {
      return xscale(i + 1);
    }).attr("y", yscale(0)).attr("width", cellWidth).attr("height", cellHeight).attr("fill", "white").attr("stroke", "white").attr("shape-rendering", "crispEdges").on("mouseover", function (event, d) {
      i = cols.nodes().indexOf(this);
      d3.select(this).attr("fill", hilitcolor).attr("stroke", hilitcolor);
      return values.selectAll(".col" + i).text(function (d) {
        return d.colpercent;
      });
    }).on("mouseout", function (event, d) {
      i = cols.nodes().indexOf(this);
      d3.select(this).attr("fill", "white").attr("stroke", "white");
      return values.selectAll("text.col" + i).text(function (d) {
        return d.value;
      });
    }); // labels in the column headings

    collab = svg.append("g").attr("id", "collab");
    collab.selectAll("empty").data(data.xcat.concat("Total")).enter().append("text").attr("x", function (d, i) {
      return xscale(i + 1) + cellWidth - cellPad;
    }).attr("y", yscale(0) + cellHeight / 2).text(function (d) {
      return d;
    }).attr("class", "crosstab").style("font-size", fontsize).style("pointer-events", "none"); // rectangles for the row headings

    rowrect = svg.append("g").attr("id", "rowrect");
    rows = rowrect.selectAll("empty").data(data.ycat.concat("Total")).enter().append("rect").attr("x", xscale(0)).attr("y", function (d, i) {
      return yscale(i + 1);
    }).attr("width", cellWidth).attr("height", cellHeight).attr("fill", "white").attr("stroke", "white").attr("shape-rendering", "crispEdges").on("mouseover", function (event, d) {
      i = rows.nodes().indexOf(this);
      d3.select(this).attr("fill", hilitcolor).attr("stroke", hilitcolor);
      return values.selectAll(".row" + i).text(function (d) {
        return d.rowpercent;
      });
    }).on("mouseout", function (event, d) {
      i = rows.nodes().indexOf(this);
      d3.select(this).attr("fill", "white").attr("stroke", "white");
      return values.selectAll(".row" + i).text(function (d) {
        return d.value;
      });
    }); // labels in the column headings

    rowlab = svg.append("g").attr("id", "rowlab");
    rowlab.selectAll("empty").data(data.ycat.concat("Total")).enter().append("text").attr("x", xscale(0) + cellWidth - cellPad).attr("y", function (d, i) {
      return yscale(i + 1) + cellHeight / 2;
    }).text(function (d) {
      return d;
    }).attr("class", "crosstab").style("font-size", fontsize).style("pointer-events", "none"); // border around central part

    borders = svg.append("g").attr("id", "borders");
    borders.append("rect").attr("x", xscale(1)).attr("y", yscale(1)).attr("width", cellWidth * ncol).attr("height", cellHeight * nrow).attr("fill", "none").attr("stroke", bordercolor).attr("stroke-width", 2).style("pointer-events", "none").attr("shape-rendering", "crispEdges"); // border around overall total

    borders.append("rect").attr("x", xscale(ncol + 1)).attr("y", yscale(nrow + 1)).attr("width", cellWidth).attr("height", cellHeight).attr("fill", "none").attr("stroke", bordercolor).attr("stroke-width", 2).style("pointer-events", "none").attr("shape-rendering", "crispEdges"); // row and column headings and optional overall title

    titles = svg.append("g").attr("id", "titles");
    titles.append("text").attr("class", "crosstabtitle").attr("x", margin.left + (ncol + 1) * cellWidth / 2).attr("y", margin.top - cellHeight / 2).text(data.xlabel).style("font-size", fontsize).style("font-weight", "bold");
    titles.append("text").attr("class", "crosstab").attr("x", xscale(0) + cellWidth - cellPad).attr("y", yscale(0) + cellHeight / 2).text(data.ylabel).style("font-size", fontsize).style("font-weight", "bold");
    return titles.append("text").attr("class", "crosstabtitle").attr("x", margin.left + (width - margin.left - margin.right) / 2).attr("y", margin.top - titlepos).text(title).style("font-size", fontsize);
  }; // functions to grab stuff


  chart.rowrect = function () {
    return rowrect;
  };

  chart.colrect = function () {
    return colrect;
  };

  chart.svg = function () {
    return svg;
  }; // function to remove chart


  chart.remove = function () {
    svg.remove();
    return null;
  }; // return the chart function


  return chart;
};"use strict";

// Generated by CoffeeScript 2.5.1
// curvechart: chart with multiple curves
d3panels.curvechart = function (chartOpts) {
  var chart, curves, indtip, linecolor, linecolorhilit, linewidth, linewidthhilit, ref, ref1, ref2, ref3, ref4, ref5, ref6, svg, tipclass, xlim, xscale, ylim, yscale;

  if (chartOpts == null) {
    chartOpts = {}; // make sure it's defined
  } // chartOpts start


  xlim = (ref = chartOpts != null ? chartOpts.xlim : void 0) != null ? ref : null; // x-axis limits (if null, taken from data)

  ylim = (ref1 = chartOpts != null ? chartOpts.ylim : void 0) != null ? ref1 : null; // y-axis limits (if null, taken from data)

  linecolor = (ref2 = chartOpts != null ? chartOpts.linecolor : void 0) != null ? ref2 : null; // color of curves (if null, use pastel colors by group)

  linecolorhilit = (ref3 = chartOpts != null ? chartOpts.linecolorhilit : void 0) != null ? ref3 : null; // color of highlighted curve (if null, use dark colors by group)

  linewidth = (ref4 = chartOpts != null ? chartOpts.linewidth : void 0) != null ? ref4 : 2; // width of curve

  linewidthhilit = (ref5 = chartOpts != null ? chartOpts.linewidthhilit : void 0) != null ? ref5 : 2; // width of highlighted curve

  tipclass = (ref6 = chartOpts != null ? chartOpts.tipclass : void 0) != null ? ref6 : "tooltip"; // class name for tool tips
  // chartOpts end
  // further chartOpts: panelframe (omit xNA yNA xNA_size yNA_size)
  // accessors start

  xscale = null; // x-axis scale

  yscale = null; // y-axis scale

  curves = null; // curves selection

  indtip = null; // tooltip selection

  svg = null; // SVG selection
  // accessors end
  //# the main function

  chart = function chart(selection, data) {
    // {x, y, indID, group}
    var add_curves, i, j, myframe, n_ind, ref7, x, y;

    if (data.x == null) {
      // x and y both ragged arrays indexed as y[subject][response_index]
      // if x has one subject, y's should all have same length, and x is then expanded to match
      d3panels.displayError("curvechart: data.x is missing");
    }

    if (data.y == null) {
      d3panels.displayError("curvechart: data.y is missing");
    }

    x = data.x;
    y = data.y;
    n_ind = y.length;

    if (x.length === 1 && y.length > 1) {
      // expand to same length
      for (j = i = 2, ref7 = n_ind; 2 <= ref7 ? i <= ref7 : i >= ref7; j = 2 <= ref7 ? ++i : --i) {
        x.push(x[0]);
      }
    }

    if (x.length !== n_ind) {
      d3panels.displayError("curvechart: data.x.length (" + x.length + ") != data.y.length (" + n_ind + ")");
    } // x- and y-axis limits


    xlim = xlim != null ? xlim : d3panels.matrixExtent(x);
    ylim = ylim != null ? ylim : d3panels.matrixExtent(y);
    chartOpts.xlim = xlim;
    chartOpts.ylim = ylim; // don't allow NA boxes

    chartOpts.xNA = false;
    chartOpts.yNA = false; // set up frame

    myframe = d3panels.panelframe(chartOpts); // create SVG

    myframe(selection);
    svg = myframe.svg(); // scales

    xscale = myframe.xscale();
    yscale = myframe.yscale();
    add_curves = d3panels.add_curves({
      linecolor: linecolor,
      linecolorhilit: linecolorhilit,
      linewidth: linewidth,
      linewidthhilit: linewidthhilit,
      tipclass: tipclass
    });
    add_curves(myframe, data);
    curves = add_curves.curves();
    indtip = add_curves.indtip(); // move box to front

    return myframe.box().raise();
  }; // functions to grab stuff


  chart.xscale = function () {
    return xscale;
  };

  chart.yscale = function () {
    return yscale;
  };

  chart.curves = function () {
    return curves;
  };

  chart.indtip = function () {
    return indtip;
  };

  chart.svg = function () {
    return svg;
  }; // function to remove chart


  chart.remove = function () {
    svg.remove();
    d3panels.tooltip_destroy(indtip);
    return null;
  }; // return the chart function


  return chart;
};"use strict";

// Generated by CoffeeScript 2.5.1
// dotchart: scatter plot where one dimension is categorical (sometimes called a strip chart)
var indexOf = [].indexOf;

d3panels.dotchart = function (chartOpts) {
  var chart, horizontal, indtip, jitter, pointcolor, points, pointsize, pointstroke, ref, ref1, ref10, ref11, ref12, ref13, ref14, ref15, ref16, ref2, ref3, ref4, ref5, ref6, ref7, ref8, ref9, svg, tipclass, v_over_h, xNA, xNA_size, xcategories, xcatlabels, xlab, xlineOpts, xscale, yNA, yNA_size, ylab, ylim, yscale;

  if (chartOpts == null) {
    chartOpts = {}; // make sure it's defined
  } // chartOpts start


  xcategories = (ref = chartOpts != null ? chartOpts.xcategories : void 0) != null ? ref : null; // group categories

  xcatlabels = (ref1 = chartOpts != null ? chartOpts.xcatlabels : void 0) != null ? ref1 : null; // labels for group categories

  xNA = (ref2 = chartOpts != null ? chartOpts.xNA : void 0) != null ? ref2 : {
    handle: true,
    force: false // handle: include separate boxes for NAs; force: include whether or not NAs in data

  };
  yNA = (ref3 = chartOpts != null ? chartOpts.yNA : void 0) != null ? ref3 : {
    handle: true,
    force: false // handle: include separate boxes for NAs; force: include whether or not NAs in data

  };
  xNA_size = (ref4 = chartOpts != null ? chartOpts.xNA_size : void 0) != null ? ref4 : {
    width: 20,
    gap: 10 // width and gap for x=NA box

  };
  yNA_size = (ref5 = chartOpts != null ? chartOpts.yNA_size : void 0) != null ? ref5 : {
    width: 20,
    gap: 10 // width and gap for y=NA box

  };
  ylim = (ref6 = chartOpts != null ? chartOpts.ylim : void 0) != null ? ref6 : null; // y-axis limits

  xlab = (ref7 = chartOpts != null ? chartOpts.xlab : void 0) != null ? ref7 : "Group"; // x-axis title

  ylab = (ref8 = chartOpts != null ? chartOpts.ylab : void 0) != null ? ref8 : "Response"; // y-axis title

  xlineOpts = (ref9 = chartOpts != null ? chartOpts.xlineOpts : void 0) != null ? ref9 : {
    color: "#cdcdcd",
    width: 5 // color and width of vertical lines

  };
  pointcolor = (ref10 = chartOpts != null ? chartOpts.pointcolor : void 0) != null ? ref10 : null; // fill color of points

  pointstroke = (ref11 = chartOpts != null ? chartOpts.pointstroke : void 0) != null ? ref11 : "black"; // color of points' outer circle

  pointsize = (ref12 = chartOpts != null ? chartOpts.pointsize : void 0) != null ? ref12 : 3; // color of points

  jitter = (ref13 = chartOpts != null ? chartOpts.jitter : void 0) != null ? ref13 : "beeswarm"; // method for jittering points (beeswarm|random|none)

  tipclass = (ref14 = chartOpts != null ? chartOpts.tipclass : void 0) != null ? ref14 : "tooltip"; // class name for tool tips

  horizontal = (ref15 = chartOpts != null ? chartOpts.horizontal : void 0) != null ? ref15 : false; // whether to interchange x and y-axes

  v_over_h = (ref16 = chartOpts != null ? chartOpts.v_over_h : void 0) != null ? ref16 : horizontal; // whether vertical lines should be on top of horizontal lines
  // chartOpts end
  // further chartOpts: panelframe
  // accessors start

  xscale = null; // x-axis scale

  yscale = null; // y-axis scale

  xNA = xNA; // true if x-axis NAs are handled in a separate box

  yNA = yNA; // true if y-axis NAs are handled in a separate box

  points = null; // point selection

  indtip = null; // tooltip selection

  svg = null; // SVG selection
  // accessors end
  //# the main function

  chart = function chart(selection, data) {
    // data = {x, y, indID, group} # x should be a set of positive integers; xcategories has the possible values
    var force, g, group, i, indID, jitter_width, myframe, ngroup, pointGroup, ref17, ref18, ref19, ref20, scaledPoints, u, x, xlim, xv, y; // args that are lists: check that they have all the pieces

    xNA = d3panels.check_listarg_v_default(xNA, {
      handle: true,
      force: false
    });
    yNA = d3panels.check_listarg_v_default(yNA, {
      handle: true,
      force: false
    });
    xNA_size = d3panels.check_listarg_v_default(xNA, {
      width: 20,
      gap: 10
    });
    yNA_size = d3panels.check_listarg_v_default(yNA, {
      width: 20,
      gap: 10
    });

    if (data.x == null) {
      d3panels.displayError("dotchart: data.x is missing");
    }

    if (data.y == null) {
      d3panels.displayError("dotchart: data.y is missing");
    }

    x = d3panels.missing2null(data.x);
    y = d3panels.missing2null(data.y); // grab indID if it's there
    // if no indID, create a vector of them

    indID = (ref17 = data != null ? data.indID : void 0) != null ? ref17 : function () {
      var results = [];

      for (var j = 1, ref18 = x.length; 1 <= ref18 ? j <= ref18 : j >= ref18; 1 <= ref18 ? j++ : j--) {
        results.push(j);
      }

      return results;
    }.apply(this); // a few checks

    if (x.length !== y.length) {
      d3panels.displayError("dotchart: length(x) [" + x.length + "] != length(y) [" + y.length + "]");
    }

    if (indID.length !== x.length) {
      d3panels.displayError("dotchart: length(indID) [" + indID.length + "] != length(x) [" + x.length + "]");
    } // groups of colors


    group = (ref19 = data != null ? data.group : void 0) != null ? ref19 : function () {
      var j, len, results;
      results = [];

      for (j = 0, len = x.length; j < len; j++) {
        i = x[j];
        results.push(1);
      }

      return results;
    }();
    group = d3panels.expand2vector(group, x.length); // force it to be a vector not scalar

    ngroup = d3.max(group);

    group = function () {
      var j, len, results; // changed from (1,2,3,...) to (0,1,2,...)

      results = [];

      for (j = 0, len = group.length; j < len; j++) {
        g = group[j];
        results.push(g != null ? g - 1 : g);
      }

      return results;
    }();

    if (d3panels.sumArray(function () {
      var j, len, results;
      results = [];

      for (j = 0, len = group.length; j < len; j++) {
        g = group[j];
        results.push(g < 0 || g > ngroup - 1);
      }

      return results;
    }()) > 0) {
      d3panels.displayError("dotchart: group values out of range");
      console.log("ngroup: " + ngroup);
      console.log("distinct groups: " + d3panels.unique(group));
    }

    if (group.length !== x.length) {
      d3panels.displayError("dotchart: group.length (" + group.length + ") != x.length (" + x.length + ")");
    } // colors of the points in the different groups


    pointcolor = pointcolor != null ? pointcolor : d3panels.selectGroupColors(ngroup, "dark");
    pointcolor = d3panels.expand2vector(pointcolor, ngroup);

    if (pointcolor.length < ngroup) {
      d3panels.displayError("add_points: pointcolor.length (" + pointcolor.length + ") < ngroup (" + ngroup + ")");
    }

    xcategories = xcategories != null ? xcategories : d3panels.unique(x);
    xcategories = d3panels.forceAsArray(xcategories); // force it to be an array rather than a scalar

    xcatlabels = xcatlabels != null ? xcatlabels : xcategories;
    xcatlabels = d3panels.forceAsArray(xcatlabels);

    if (xcatlabels.length !== xcategories.length) {
      d3panels.displayError("dotchart: xcatlabels.length [" + xcatlabels.length + "] != xcategories.length [" + xcategories.length + "]");
    } // check all x in xcategories


    if (d3panels.sumArray(function () {
      var j, len, results;
      results = [];

      for (j = 0, len = x.length; j < len; j++) {
        xv = x[j];
        results.push(xv != null && !(indexOf.call(xcategories, xv) >= 0));
      }

      return results;
    }()) > 0) {
      d3panels.displayError("dotchart: Some x values not in xcategories");
      console.log("xcategories:");
      console.log(xcategories);
      console.log("x:");
      console.log(x);

      for (i in x) {
        if (x[i] != null && !(ref20 = x[i], indexOf.call(xcategories, ref20) >= 0)) {
          x[i] = null;
        }
      }
    } // x- and y-axis limits


    ylim = ylim != null ? ylim : d3panels.pad_ylim(d3.extent(y));
    xlim = [d3.min(xcategories) - 0.5, d3.max(xcategories) + 0.5]; // whether to include separate boxes for NAs

    xNA.handle = xNA.force || xNA.handle && !x.every(function (v) {
      return v != null;
    });
    yNA.handle = yNA.force || yNA.handle && !y.every(function (v) {
      return v != null;
    });

    if (horizontal) {
      chartOpts.ylim = xlim.reverse();
      chartOpts.xlim = ylim;
      chartOpts.xlab = ylab;
      chartOpts.ylab = xlab;
      chartOpts.xlineOpts = chartOpts.ylineOpts;
      chartOpts.ylineOpts = xlineOpts;
      chartOpts.yNA = xNA.handle;
      chartOpts.xNA = yNA.handle;
      chartOpts.xNA_size = yNA_size;
      chartOpts.yNA_size = xNA_size;
      chartOpts.yticks = xcategories;
      chartOpts.yticklab = xcatlabels;
      chartOpts.v_over_h = v_over_h;
    } else {
      chartOpts.ylim = ylim;
      chartOpts.xlim = xlim;
      chartOpts.xlab = xlab;
      chartOpts.ylab = ylab;
      chartOpts.ylineOpts = chartOpts.ylineOpts;
      chartOpts.xlineOpts = xlineOpts;
      chartOpts.xNA = xNA.handle;
      chartOpts.yNA = yNA.handle;
      chartOpts.xNA_size = xNA_size;
      chartOpts.yNA_size = yNA_size;
      chartOpts.xticks = xcategories;
      chartOpts.xticklab = xcatlabels;
      chartOpts.v_over_h = v_over_h;
    } // set up frame


    myframe = d3panels.panelframe(chartOpts); // Create SVG

    myframe(selection);
    svg = myframe.svg(); // grab scale functions

    xscale = myframe.xscale();
    yscale = myframe.yscale(); // scaled versions of points

    if (horizontal) {
      scaledPoints = function () {
        var results;
        results = [];

        for (i in x) {
          results.push({
            x: xscale(y[i]),
            y: yscale(x[i])
          });
        }

        return results;
      }();
    } else {
      scaledPoints = function () {
        var results;
        results = [];

        for (i in x) {
          results.push({
            x: xscale(x[i]),
            y: yscale(y[i])
          });
        }

        return results;
      }();
    }

    pointGroup = svg.append("g").attr("id", "points");
    points = pointGroup.selectAll("empty").data(scaledPoints).enter().append("circle").attr("class", function (d, i) {
      return "pt" + i;
    }).attr("r", pointsize).attr("fill", function (d, i) {
      return pointcolor[group[i]];
    }).attr("stroke", pointstroke).attr("stroke-width", "1").attr("cx", function (d) {
      return d.x;
    }).attr("cy", function (d) {
      return d.y;
    });
    indtip = d3panels.tooltip_create(d3.select("body"), points, {
      tipclass: tipclass
    }, function (d, i) {
      return indID[i];
    });

    if (jitter === "random") {
      jitter_width = 0.2;

      u = function () {
        var results;
        results = [];

        for (i in scaledPoints) {
          results.push((Math.random() - 0.5) * jitter_width);
        }

        return results;
      }();

      if (horizontal) {
        points.attr("cy", function (d, i) {
          if (x[i] != null) {
            return yscale(x[i] + u[i]);
          }

          return yscale(x[i]) + u[i] / jitter_width * xNA_size.width / 2;
        });
      } else {
        points.attr("cx", function (d, i) {
          if (x[i] != null) {
            return xscale(x[i] + u[i]);
          }

          return xscale(x[i]) + u[i] / jitter_width * xNA_size.width / 2;
        });
      }
    } else if (jitter === "beeswarm") {
      if (horizontal) {
        d3.range(scaledPoints.length).map(function (i) {
          return scaledPoints[i].fx = scaledPoints[i].x;
        });
        force = d3.forceSimulation(scaledPoints).force("y", d3.forceY(function (d) {
          return d.y;
        })).force("collide", d3.forceCollide(pointsize * 1.1)).stop();
      } else {
        d3.range(scaledPoints.length).map(function (i) {
          return scaledPoints[i].fy = scaledPoints[i].y;
        });
        force = d3.forceSimulation(scaledPoints).force("x", d3.forceX(function (d) {
          return d.x;
        })).force("collide", d3.forceCollide(pointsize * 1.1)).stop();
      }

      (function () {
        var results = [];

        for (var j = 0; j <= 30; j++) {
          results.push(j);
        }

        return results;
      }).apply(this).map(function (d) {
        force.tick();
        return points.attr("cx", function (d) {
          return d.x;
        }).attr("cy", function (d) {
          return d.y;
        });
      });
    } else if (jitter !== "none") {
      d3panels.displayError('dotchart: jitter should be "beeswarm", "random", or "none"');
    } // move box to front


    return myframe.box().raise();
  }; // functions to grab stuff


  chart.xscale = function () {
    return xscale;
  };

  chart.yscale = function () {
    return yscale;
  };

  chart.xNA = function () {
    return xNA.handle;
  };

  chart.yNA = function () {
    return yNA.handle;
  };

  chart.points = function () {
    return points;
  };

  chart.indtip = function () {
    return indtip;
  };

  chart.svg = function () {
    return svg;
  }; // function to remove chart


  chart.remove = function () {
    svg.remove();
    d3panels.tooltip_destroy(indtip);
    return null;
  }; // return the chart function


  return chart;
};"use strict";

// Generated by CoffeeScript 2.6.1
// heatmap: heat map panel
d3panels.heatmap = function (chartOpts) {
  var cellSelect, cells, celltip, chart, colors, hilitcolor, margin, nullcolor, ref, ref1, ref2, ref3, ref4, ref5, ref6, ref7, ref8, svg, tipclass, xlim, xscale, ylim, yscale, zlim, zscale, zthresh;

  if (chartOpts == null) {
    chartOpts = {}; // make sure it's defined
  } // chartOpts start


  margin = (ref = chartOpts != null ? chartOpts.margin : void 0) != null ? ref : {
    left: 60,
    top: 40,
    right: 40,
    bottom: 40,
    inner: 0 // margins in pixels (left, top, right, bottom, inner)

  };
  xlim = (ref1 = chartOpts != null ? chartOpts.xlim : void 0) != null ? ref1 : null; // x-axis limits (if null take from data)

  ylim = (ref2 = chartOpts != null ? chartOpts.ylim : void 0) != null ? ref2 : null; // y-axis limits (if null take from data)

  nullcolor = (ref3 = chartOpts != null ? chartOpts.nullcolor : void 0) != null ? ref3 : "#e6e6e6"; // color for empty cells

  colors = (ref4 = chartOpts != null ? chartOpts.colors : void 0) != null ? ref4 : ["slateblue", "white", "crimson" // vector of three colors for the color scale (negative - zero - positive)
  ];
  zlim = (ref5 = chartOpts != null ? chartOpts.zlim : void 0) != null ? ref5 : null; // z-axis limits (if null take from data, symmetric about 0)

  zthresh = (ref6 = chartOpts != null ? chartOpts.zthresh : void 0) != null ? ref6 : null; // z threshold; if |z| < zthresh, not shown

  hilitcolor = (ref7 = chartOpts != null ? chartOpts.hilitcolor : void 0) != null ? ref7 : "black"; // color of box around highlighted cell

  tipclass = (ref8 = chartOpts != null ? chartOpts.tipclass : void 0) != null ? ref8 : "tooltip"; // class name for tool tips
  // chartOpts end
  // further chartOpts: panelframe (omit xNA yNA xNA_size yNA_size)
  // accessors start

  xscale = null; // x-axis scale

  yscale = null; // y-axis scale

  zscale = null; // z-axis scale

  cells = null; // cell selection

  celltip = null; // cell tooltip selection

  svg = null; // SVG selection
  // accessors end

  cellSelect = null; // actual name for the cell selection
  //# the main function

  chart = function chart(selection, data) {
    // {x, y, z}  # z should be a double-indexed square matrix, z[xval][yval]
    var cell, cellrect, i, j, myframe, nx, ny, ref10, ref9, tooltipfunc, xlabels, xmid, xmid_scaled, xv, ylabels, ymid, ymid_scaled, yv, zmax, zmin; //   optionally, include xcat and ycat in place of x and y
    //       then: categorial scales on x and y axis
    // args that are lists: check that they have all the pieces

    margin = d3panels.check_listarg_v_default(margin, {
      left: 60,
      top: 40,
      right: 40,
      bottom: 40,
      inner: 0
    });

    if (!(data.x != null || data.xcat != null)) {
      d3panels.displayError("heatmap: data.x is missing");
    }

    if (!(data.y != null || data.ycat != null)) {
      d3panels.displayError("heatmap: data.y is missing");
    }

    if (data.z == null) {
      d3panels.displayError("heatmap: data.z is missing");
    } // xcat and ycat included?


    if (data.xcat != null) {
      data.x = function () {
        var results;
        results = [];

        for (i in data.xcat) {
          results.push(+i);
        }

        return results;
      }();

      xlim = xlim != null ? xlim : [-0.5, data.x.length - 0.5];
      chartOpts.xticks = data.x;
      chartOpts.xlineOpts = {
        color: "none",
        width: 0
      };
      chartOpts.xlab = (ref9 = chartOpts != null ? chartOpts.xlab : void 0) != null ? ref9 : "";
    }

    if (data.ycat != null) {
      data.y = function () {
        var results;
        results = [];

        for (i in data.ycat) {
          results.push(+i);
        }

        return results;
      }();

      ylim = ylim != null ? ylim : [-0.5, data.x.length - 0.5];
      chartOpts.yticks = data.y;
      chartOpts.ylineOpts = {
        color: "none",
        width: 0
      };
      chartOpts.ylab = (ref10 = chartOpts != null ? chartOpts.ylab : void 0) != null ? ref10 : "";
    } // check input sizes


    nx = data.x.length;
    ny = data.y.length;

    if (data.z.length !== nx) {
      d3panels.displayError("heatmap: data.x.length (" + nx + ") != data.z.length (" + data.z.length + ")");
    }

    for (i in data.z) {
      if (data.z[i].length !== ny) {
        d3panels.displayError("heatmap: data.y.length (" + ny + ") != data.z[" + i + "].length (" + data.z[i].length + ")");
      }
    } // organize by cell


    cells = [];

    for (i in data.z) {
      for (j in data.z[i]) {
        cells.push({
          x: data.x[i],
          y: data.y[j],
          z: data.z[i][j],
          xindex: +i,
          yindex: +j
        });
      }
    } // calc x and y midpoints


    xmid = d3panels.calc_midpoints(d3panels.pad_vector(data.x));
    ymid = d3panels.calc_midpoints(d3panels.pad_vector(data.y)); // x and y axis limits

    xlim = xlim != null ? xlim : d3.extent(xmid);
    ylim = ylim != null ? ylim : d3.extent(ymid); // z-axis (color) limits; if not provided, make symmetric about 0

    zmin = d3panels.matrixMin(data.z);
    zmax = d3panels.matrixMaxAbs(data.z);
    zlim = zlim != null ? zlim : [-zmax, 0, zmax];

    if (zlim.length !== colors.length) {
      d3panels.displayError("heatmap: zlim.length (" + zlim.length + ") != colors.length (" + colors.length + ")");
    }

    zscale = d3.scaleLinear().domain(zlim).range(colors); // discard cells with |z| < zthresh

    zthresh = zthresh != null ? zthresh : zmin - 1;

    cells = function () {
      var k, len, results;
      results = [];

      for (k = 0, len = cells.length; k < len; k++) {
        cell = cells[k];

        if (Math.abs(cell.z) >= zthresh) {
          results.push(cell);
        }
      }

      return results;
    }(); // set up frame


    chartOpts.margin = margin;
    chartOpts.xlim = xlim;
    chartOpts.ylim = ylim;
    chartOpts.xNA = false; // don't allow NA boxes

    chartOpts.yNA = false;
    myframe = d3panels.panelframe(chartOpts); // create SVG

    myframe(selection);
    svg = myframe.svg(); // scales

    xscale = myframe.xscale();
    yscale = myframe.yscale(); // x- and y-axis labels

    xlabels = myframe.xlabels();
    ylabels = myframe.ylabels(); // scaled x and y midpoints

    xmid_scaled = function () {
      var k, len, results;
      results = [];

      for (k = 0, len = xmid.length; k < len; k++) {
        xv = xmid[k];
        results.push(xscale(xv));
      }

      return results;
    }();

    ymid_scaled = function () {
      var k, len, results;
      results = [];

      for (k = 0, len = ymid.length; k < len; k++) {
        yv = ymid[k];
        results.push(yscale(yv));
      }

      return results;
    }(); // calculate x,y,width,height of rectangles


    d3panels.calc_cell_rect(cells, xmid_scaled, ymid_scaled);
    cellrect = svg.append("g").attr("id", "cells");
    cellSelect = cellrect.selectAll("empty").data(cells).enter().append("rect").attr("x", function (d) {
      return d.left;
    }).attr("y", function (d) {
      return d.top;
    }).attr("width", function (d) {
      return d.width;
    }).attr("height", function (d) {
      return d.height;
    }).attr("class", function (d, i) {
      return "cell" + i;
    }).attr("fill", function (d) {
      if (d.z != null) {
        return zscale(d.z);
      } else {
        return nullcolor;
      }
    }).attr("stroke", "none").attr("stroke-width", "1").attr("shape-rendering", "crispEdges").on("mouseover", function (event, d) {
      d3.select(this).attr("stroke", hilitcolor).raise();

      if (data.xcat != null) {
        svg.select("text#xlab" + d.x).attr("opacity", 1); // show categorical scales
      }

      if (data.ycat != null) {
        return svg.select("text#ylab" + d.y).attr("opacity", 1);
      }
    }).on("mouseout", function (event, d) {
      d3.select(this).attr("stroke", "none");

      if (data.xcat != null) {
        svg.select("text#xlab" + d.x).attr("opacity", 0); // hide categorical scales
      }

      if (data.ycat != null) {
        return svg.select("text#ylab" + d.y).attr("opacity", 0);
      }
    });

    tooltipfunc = function tooltipfunc(d, i) {
      var x, y, z;
      x = d3panels.formatAxis(data.x)(d.x);
      y = d3panels.formatAxis(data.y)(d.y);
      z = d3panels.formatAxis([0, zmax / 100])(d.z);

      if (data.xcat != null && data.ycat != null) {
        return "" + z;
      }

      if (data.xcat != null) {
        return "(" + y + ") &rarr; " + z;
      }

      if (data.ycat != null) {
        return "(" + x + ") &rarr; " + z;
      }

      return "(" + x + ", " + y + ") &rarr; " + z;
    };

    celltip = d3panels.tooltip_create(d3.select("body"), cellrect.selectAll("rect"), {
      tipclass: tipclass
    }, tooltipfunc); // handle categorical scales:
    //    replace text with category labels, add IDs, and hide them initially

    if (data.xcat != null) {
      xlabels.text(function (d, i) {
        return data.xcat[i];
      }).attr("opacity", 0).attr("id", function (d, i) {
        return "xlab" + data.x[i];
      });
    }

    if (data.ycat != null) {
      ylabels.text(function (d, i) {
        return data.ycat[i];
      }).attr("opacity", 0).attr("id", function (d, i) {
        return "ylab" + data.y[i];
      });
    } // move box to front


    return myframe.box().raise();
  }; // functions to grab stuff


  chart.xscale = function () {
    return xscale;
  };

  chart.yscale = function () {
    return yscale;
  };

  chart.zscale = function () {
    return zscale;
  };

  chart.cells = function () {
    return cellSelect;
  };

  chart.celltip = function () {
    return celltip;
  };

  chart.svg = function () {
    return svg;
  }; // function to remove chart


  chart.remove = function () {
    svg.remove();
    d3panels.tooltip_destroy(celltip);
    return null;
  }; // return the chart function


  return chart;
};"use strict";

// Generated by CoffeeScript 2.5.1
// lodchart: plot of LOD curves
d3panels.lodchart = function (chartOpts) {
  var chart, chrSelect, linecolor, linewidth, markerSelect, markertip, pointcolor, pointsize, pointstroke, ref, ref1, ref2, ref3, ref4, ref5, ref6, _svg, tipclass, _xscale, ylim, _yscale;

  if (chartOpts == null) {
    chartOpts = {}; // make sure it's defined
  } // chartOpts start


  linecolor = (ref = chartOpts != null ? chartOpts.linecolor : void 0) != null ? ref : "darkslateblue"; // color for LOD curves

  linewidth = (ref1 = chartOpts != null ? chartOpts.linewidth : void 0) != null ? ref1 : 2; // width (pixels) for LOD curves

  pointcolor = (ref2 = chartOpts != null ? chartOpts.pointcolor : void 0) != null ? ref2 : "#e9cfec"; // color of points at markers

  pointsize = (ref3 = chartOpts != null ? chartOpts.pointsize : void 0) != null ? ref3 : 0; // pointsize at markers (if 0, no points plotted)

  pointstroke = (ref4 = chartOpts != null ? chartOpts.pointstroke : void 0) != null ? ref4 : "black"; // color of circle around points at markers

  ylim = (ref5 = chartOpts != null ? chartOpts.ylim : void 0) != null ? ref5 : null; // y-axis limits; if null, use range of data

  tipclass = (ref6 = chartOpts != null ? chartOpts.tipclass : void 0) != null ? ref6 : "tooltip"; // class name for tool tips
  // chartOpts end
  // further chartOpts: chrpanelframe
  // accessors start

  _xscale = null; // x-axis scale (vector by chromosome)

  _yscale = null; // y-axis scale

  chrSelect = null; // chromosome rectangle selection

  markerSelect = null; // points at markers selection

  markertip = null; // tooltips selection

  _svg = null; // SVG selection
  // accessors end
  //# the main function

  chart = function chart(selection, data) {
    // data = {chr, pos, lod, marker} each an ordered vector
    var add2chart, i, myframe, self_chart;

    if (data.chr == null) {
      //    optionally also chrname, chrstart, chrend with chr IDs, start and end positions
      d3panels.displayError("lodchart: data.chr is missing");
    }

    if (data.pos == null) {
      d3panels.displayError("lodchart: data.pos is missing");
    }

    if (data.lod == null) {
      d3panels.displayError("lodchart: data.lod is missing");
    }

    if (data.marker == null) {
      d3panels.displayError("lodchart: data.marker is missing");
    } // check lengths


    if (data.pos.length !== data.chr.length) {
      d3panels.displayError("lodchart: data.pos.length (" + data.pos.length + ") != data.chr.length (" + data.chr.length + ")");
    }

    if (data.lod.length !== data.chr.length) {
      d3panels.displayError("lodchart: data.lod.length (" + data.lod.length + ") != data.chr.length (" + data.chr.length + ")");
    }

    if (data.marker == null) {
      data.marker = [function () {
        var results;
        results = [];

        for (i in data.chr) {
          results.push('');
        }

        return results;
      }()]; // if data.marker not included, create it with a bunch of blanks
    }

    if (data.marker.length !== data.chr.length) {
      d3panels.displayError("lodchart: data.marker.length (" + data.marker.length + ") != data.chr.length (" + data.chr.length + ")");
    } // create chrname, chrstart, chrend if missing


    data = d3panels.add_chrname_start_end(data); // organize positions and LOD scores by chromosomes

    data = d3panels.reorgLodData(data); // y-axis limits

    chartOpts.ylim = ylim != null ? ylim : [0, d3.max(data.lod) * 1.05]; // set up frame

    myframe = d3panels.chrpanelframe(chartOpts); // Create SVG

    myframe(selection, {
      chr: data.chrname,
      start: data.chrstart,
      end: data.chrend
    });
    _svg = myframe.svg(); // grab scale functions

    _xscale = myframe.xscale();
    _yscale = myframe.yscale(); // chromosome rectangles

    chrSelect = myframe.chrSelect(); // dummy chart for calling add_lodcurve()

    self_chart = {
      svg: function svg() {
        return _svg;
      },
      xscale: function xscale() {
        return _xscale;
      },
      yscale: function yscale() {
        return _yscale;
      }
    }; // plot curves and points

    add2chart = d3panels.add_lodcurve(chartOpts);
    add2chart(self_chart, data); // grab selections

    markerSelect = add2chart.markerSelect();
    markertip = add2chart.markertip(); // move box to front

    return myframe.box().raise();
  }; // functions to grab stuff


  chart.xscale = function () {
    return _xscale;
  };

  chart.yscale = function () {
    return _yscale;
  };

  chart.chrSelect = function () {
    return chrSelect;
  };

  chart.markerSelect = function () {
    return markerSelect;
  };

  chart.markertip = function () {
    return markertip;
  };

  chart.svg = function () {
    return _svg;
  }; // function to remove chart


  chart.remove = function () {
    _svg.remove();

    d3panels.tooltip_destroy(markertip);
    return null;
  }; // return the chart function


  return chart;
};"use strict";

// Generated by CoffeeScript 2.6.1
// add_lodcurve: add lod curve to a lodchart() chart
d3panels.add_lodcurve = function (chartOpts) {
  var chart, g, horizontal, linecolor, linedash, linewidth, markerSelect, markertip, pointcolor, pointsize, pointstroke, ref, ref1, ref2, ref3, ref4, ref5, ref6, ref7, tipclass;

  if (chartOpts == null) {
    chartOpts = {}; // make sure it's defined
  } // chartOpts start


  linecolor = (ref = chartOpts != null ? chartOpts.linecolor : void 0) != null ? ref : "darkslateblue"; // color for LOD curves

  linewidth = (ref1 = chartOpts != null ? chartOpts.linewidth : void 0) != null ? ref1 : 2; // width (pixels) for LOD curves (if 0, no curves plotted)

  linedash = (ref2 = chartOpts != null ? chartOpts.linedash : void 0) != null ? ref2 : ""; // 'dash array' to make dotted lines

  pointcolor = (ref3 = chartOpts != null ? chartOpts.pointcolor : void 0) != null ? ref3 : "#e9cfec"; // color of points at markers

  pointsize = (ref4 = chartOpts != null ? chartOpts.pointsize : void 0) != null ? ref4 : 0; // pointsize at markers (if 0, no points plotted)

  pointstroke = (ref5 = chartOpts != null ? chartOpts.pointstroke : void 0) != null ? ref5 : "black"; // color of circle around points at markers

  tipclass = (ref6 = chartOpts != null ? chartOpts.tipclass : void 0) != null ? ref6 : "tooltip"; // class name for tool tips

  horizontal = (ref7 = chartOpts != null ? chartOpts.horizontal : void 0) != null ? ref7 : false; // if true, chromosomes on vertical axis (xlab, ylab, etc stay the same)
  // chartOpts end
  // accessors start

  markerSelect = null; // points at markers selection

  markertip = null; // tooltips selection
  // accessors end

  g = null; // group for lod curve

  chart = function chart(prevchart, data) {
    // prevchart = chart function used to create lodchart to which we're adding
    var bigpointsize, chr, curves, hiddenpoints, i, j, len, lodcurve, markerpoints, ref8, svg, xscale, yscale;

    if (data.chr == null) {
      // data = {chr, pos, lod, marker} each an ordered vector
      //    optionally also chrname, chrstart, chrend with chr IDs, start and end positions
      d3panels.displayError("add_lodcurve: data.chr is missing");
    }

    if (data.pos == null) {
      d3panels.displayError("add_lodcurve: data.pos is missing");
    }

    if (data.lod == null) {
      d3panels.displayError("add_lodcurve: data.lod is missing");
    }

    if (data.marker == null) {
      d3panels.displayError("add_lodcurve: data.marker is missing");
    } // check lengths


    if (data.pos.length !== data.chr.length) {
      d3panels.displayError("add_lodcurve: data.pos.length (" + data.pos.length + ") != data.chr.length (" + data.chr.length + ")");
    }

    if (data.lod.length !== data.chr.length) {
      d3panels.displayError("add_lodcurve: data.lod.length (" + data.lod.length + ") != data.chr.length (" + data.chr.length + ")");
    }

    if (data.marker == null) {
      data.marker = [function () {
        var results;
        results = [];

        for (i in data.chr) {
          results.push('');
        }

        return results;
      }()]; // if data.marker not included, create it with a bunch of blanks
    }

    if (data.marker.length !== data.chr.length) {
      d3panels.displayError("add_lodcurve: data.marker.length (" + data.lod.length + ") != data.chr.length (" + data.chr.length + ")");
    } // create chrname, chrstart, chrend if missing


    data = d3panels.add_chrname_start_end(data);

    if (!(data.posByChr != null && data.lodByChr != null && data.markerinfo != null)) {
      // organize positions and LOD scores by chromosomes
      data = d3panels.reorgLodData(data);
    }

    svg = prevchart.svg();
    g = svg.append("g").attr("id", "lod_curve"); // grab scale functions

    xscale = prevchart.xscale();
    yscale = prevchart.yscale(); // lod curves by chr

    lodcurve = function lodcurve(chr) {
      return d3.line().x(function (d, i) {
        if (horizontal) {
          return yscale(data.lodByChr[chr][i]);
        }

        return xscale[chr](d);
      }).y(function (d, i) {
        if (horizontal) {
          return xscale[chr](d);
        }

        return yscale(data.lodByChr[chr][i]);
      });
    }; // add curves


    if (linewidth > 0) {
      curves = g.append("g").attr("id", "curves");
      ref8 = data.chrname;

      for (j = 0, len = ref8.length; j < len; j++) {
        chr = ref8[j];
        curves.append("path").datum(data.posByChr[chr]).attr("d", lodcurve(chr)).attr("stroke", linecolor).attr("fill", "none").attr("stroke-width", linewidth).attr("stroke-dasharray", linedash).style("pointer-events", "none");
      }
    } // points at markers


    if (pointsize > 0) {
      markerpoints = g.append("g").attr("id", "markerpoints_visible");
      markerpoints.selectAll("empty").data(data.markerinfo).enter().append("circle").attr("cx", function (d) {
        if (horizontal) {
          return yscale(d.lod);
        }

        return xscale[d.chr](d.pos);
      }).attr("cy", function (d) {
        if (horizontal) {
          return xscale[d.chr](d.pos);
        }

        return yscale(d.lod);
      }).attr("r", function (d) {
        if (d.lod != null) {
          return pointsize;
        } else {
          return null;
        }
      }).attr("fill", pointcolor).attr("stroke", pointstroke).attr("pointer-events", "hidden");
    } // these hidden points are what get selected...a bit larger


    hiddenpoints = g.append("g").attr("id", "markerpoints_hidden");
    bigpointsize = d3.max([2 * pointsize, 3]);
    markerSelect = hiddenpoints.selectAll("empty").data(data.markerinfo).enter().append("circle").attr("cx", function (d) {
      if (horizontal) {
        return yscale(d.lod);
      }

      return xscale[d.chr](d.pos);
    }).attr("cy", function (d) {
      if (horizontal) {
        return xscale[d.chr](d.pos);
      }

      return yscale(d.lod);
    }).attr("id", function (d) {
      return d.name;
    }).attr("r", function (d) {
      if (d.lod != null) {
        return bigpointsize;
      } else {
        return null;
      }
    }).attr("opacity", 0).attr("fill", pointcolor).attr("stroke", pointstroke).attr("stroke-width", "1").on("mouseover", function () {
      return d3.select(this).attr("opacity", 1);
    }).on("mouseout", function () {
      return d3.select(this).attr("opacity", 0);
    });
    return markertip = d3panels.tooltip_create(d3.select("body"), markerSelect, {
      tipclass: tipclass
    }, function (d, i) {
      return [d.name, " LOD = " + d3.format('.2f')(d.lod)];
    });
  }; // functions to grab stuff


  chart.markerSelect = function () {
    return markerSelect;
  };

  chart.markertip = function () {
    return markertip;
  }; // function to remove chart


  chart.remove = function () {
    g.remove();
    d3panels.tooltip_destroy(markertip);
    return null;
  }; // return the chart function


  return chart;
};"use strict";

// Generated by CoffeeScript 2.6.1
// add_curves: add curves to a plain panelframe() chart
d3panels.add_curves = function (chartOpts) {
  var chart, curveGroup, curves, indtip, linecolor, linecolorhilit, linewidth, linewidthhilit, ref, ref1, ref2, ref3, ref4, tipclass;

  if (chartOpts == null) {
    chartOpts = {}; // make sure it's defined
  } // chartOpts start


  linecolor = (ref = chartOpts != null ? chartOpts.linecolor : void 0) != null ? ref : null; // color for curves (if null, use pastel colors by group)

  linecolorhilit = (ref1 = chartOpts != null ? chartOpts.linecolorhilit : void 0) != null ? ref1 : null; // color for curves when hightlighted (if null, use dark colors by group)

  linewidth = (ref2 = chartOpts != null ? chartOpts.linewidth : void 0) != null ? ref2 : 2; // width (pixels) for curves

  linewidthhilit = (ref3 = chartOpts != null ? chartOpts.linewidthhilit : void 0) != null ? ref3 : 2; // width (pixels) for curves

  tipclass = (ref4 = chartOpts != null ? chartOpts.tipclass : void 0) != null ? ref4 : "tooltip"; // class name for tool tips
  // chartOpts end
  // accessors start

  curves = null; // select the curve

  indtip = null; // tool tip selection
  // accessors end

  curveGroup = null; // group containing the curves

  chart = function chart(prevchart, data) {
    // prevchart = chart function used to create lodchart to which we're adding
    var curvefunc, dataByPoint, g, group, i, indID, j, k, n_ind, ngroup, ref5, ref6, ref7, svg, x, xscale, y, yscale;

    if (data.x == null) {
      // data = {x, y, indID, group}
      //    x and y both ragged arrays indexed as y[subject][response_index]
      // if x has one subject, y's should all have same length, and x is then expanded to match
      d3panels.displayError("add_curves: data.x is missing");
    }

    if (data.y == null) {
      d3panels.displayError("add_curves: data.y is missing");
    }

    x = function () {
      var k, len, ref5, results;
      ref5 = data.x;
      results = [];

      for (k = 0, len = ref5.length; k < len; k++) {
        x = ref5[k];
        results.push(d3panels.missing2null(x));
      }

      return results;
    }();

    y = function () {
      var k, len, ref5, results;
      ref5 = data.y;
      results = [];

      for (k = 0, len = ref5.length; k < len; k++) {
        y = ref5[k];
        results.push(d3panels.missing2null(y));
      }

      return results;
    }();

    n_ind = y.length;

    if (x.length === 1 && y.length > 1) {
      // expand to same length
      for (j = k = 2, ref5 = n_ind; 2 <= ref5 ? k <= ref5 : k >= ref5; j = 2 <= ref5 ? ++k : --k) {
        x.push(x[0]);
      }
    }

    if (x.length !== n_ind) {
      d3panels.displayError("add_curves: data.x.length (" + x.length + ") != data.y.length (" + n_ind + ")");
    }

    indID = (ref6 = data != null ? data.indID : void 0) != null ? ref6 : function () {
      var results = [];

      for (var l = 1; 1 <= n_ind ? l <= n_ind : l >= n_ind; 1 <= n_ind ? l++ : l--) {
        results.push(l);
      }

      return results;
    }.apply(this);

    if (indID.length !== n_ind) {
      d3panels.displayError("add_curves: data.indID.length (" + indID.length + ") != data.y.length (" + n_ind + ")");
    }

    group = (ref7 = data != null ? data.group : void 0) != null ? ref7 : function () {
      var results;
      results = [];

      for (i in y) {
        results.push(1);
      }

      return results;
    }();
    group = d3panels.expand2vector(group, n_ind); // force it to be a vector not scalar

    ngroup = d3.max(group);

    group = function () {
      var l, len, results; // changed from (1,2,3,...) to (0,1,2,...)

      results = [];

      for (l = 0, len = group.length; l < len; l++) {
        g = group[l];
        results.push(g != null ? g - 1 : g);
      }

      return results;
    }();

    if (d3panels.sumArray(function () {
      var l, len, results;
      results = [];

      for (l = 0, len = group.length; l < len; l++) {
        g = group[l];
        results.push(g < 0 || g > ngroup - 1);
      }

      return results;
    }()) > 0) {
      d3panels.displayError("add_curves: group values out of range");
      console.log("distinct groups: " + d3panels.unique(group));
    }

    if (group.length !== n_ind) {
      d3panels.displayError("add_curves: data.group.length (" + group.length + ") != data.y.length (" + n_ind + ")");
    } // check that x's and y's are all of the same length


    for (i in y) {
      if (x[i].length !== y[i].length) {
        d3panels.displayError("add_curves: length(x) (" + x[i].length + ") != length(y) (" + y[i].length + ") for individual " + indID[i] + " (index " + (i + 1) + ")");
      }
    } // default light line colors


    linecolor = linecolor != null ? linecolor : d3panels.selectGroupColors(ngroup, "pastel");
    linecolor = d3panels.expand2vector(linecolor, ngroup); // default dark line colors

    linecolorhilit = linecolorhilit != null ? linecolorhilit : d3panels.selectGroupColors(ngroup, "dark");
    linecolorhilit = d3panels.expand2vector(linecolorhilit, ngroup);
    svg = prevchart.svg(); // grab scale functions

    xscale = prevchart.xscale();
    yscale = prevchart.yscale(); // reorganize data

    dataByPoint = [];

    for (i in y) {
      dataByPoint.push(function () {
        var results;
        results = [];

        for (j in y[i]) {
          if (x[i][j] != null && y[i][j] != null) {
            results.push({
              x: x[i][j],
              y: y[i][j]
            });
          }
        }

        return results;
      }());
    }

    curvefunc = d3.line().x(function (d) {
      return xscale(d.x);
    }).y(function (d) {
      return yscale(d.y);
    });
    curveGroup = svg.append("g").attr("id", "curves");
    curves = curveGroup.selectAll("empty").data(d3.range(n_ind)).enter().append("path").datum(function (d) {
      return dataByPoint[d];
    }).attr("d", curvefunc).attr("class", function (d, i) {
      return "path" + i;
    }).attr("fill", "none").attr("stroke", function (d, i) {
      return linecolor[group[i]];
    }).attr("stroke-width", linewidth).on("mouseover.panel", function (event, d) {
      i = curves.nodes().indexOf(this);
      return d3.select(this).attr("stroke", linecolorhilit[group[i]]).attr("stroke-width", linewidthhilit).raise();
    }).on("mouseout.panel", function (event, d) {
      var e;
      e = curves.nodes();
      i = e.indexOf(this);
      return d3.select(this).attr("stroke", linecolor[group[i]]).attr("stroke-width", linewidth);
    });
    indtip = d3panels.tooltip_create(d3.select("body"), curves, {
      tipclass: tipclass
    }, function (d, i) {
      return indID[i];
    }); // move box to front

    return prevchart.box().raise();
  }; // functions to grab stuff


  chart.curves = function () {
    return curves;
  };

  chart.indtip = function () {
    return indtip;
  }; // function to remove chart


  chart.remove = function () {
    curveGroup.remove();
    d3panels.tooltip_destroy(indtip);
    return null;
  }; // return the chart function


  return chart;
};"use strict";

// Generated by CoffeeScript 2.5.1
// add_points: add points to a plain panelframe() chart
d3panels.add_points = function (chartOpts) {
  var chart, indtip, jitter, pointGroup, pointcolor, points, pointsize, pointstroke, ref, ref1, ref2, ref3, ref4, tipclass;

  if (chartOpts == null) {
    chartOpts = {}; // make sure it's defined
  } // chartOpts start


  pointcolor = (ref = chartOpts != null ? chartOpts.pointcolor : void 0) != null ? ref : null; // fill color of points

  pointsize = (ref1 = chartOpts != null ? chartOpts.pointsize : void 0) != null ? ref1 : 3; // size of points

  pointstroke = (ref2 = chartOpts != null ? chartOpts.pointstroke : void 0) != null ? ref2 : "black"; // color of points' outer circle

  jitter = (ref3 = chartOpts != null ? chartOpts.jitter : void 0) != null ? ref3 : "beeswarm"; // method for jittering NA points (beeswarm|random|none)

  tipclass = (ref4 = chartOpts != null ? chartOpts.tipclass : void 0) != null ? ref4 : "tooltip"; // class name for tool tips
  // chartOpts end
  // accessors start

  points = null; // points selection

  indtip = null; // tooltip selection
  // accessors end

  pointGroup = null; // group containing the curves

  chart = function chart(prevchart, data) {
    // prevchart = chart function used to create lodchart to which we're adding
    var force, g, group, i, indID, ngroup, ref5, ref6, ref7, scaledPoints, svg, ux, uy, x, xscale, xwid, y, yscale, ywid;

    if (data.x == null) {
      // data = {x, y, indID, group}
      d3panels.displayError("add_points: data.x is missing");
    }

    if (data.y == null) {
      d3panels.displayError("add_points: data.y is missing");
    }

    x = d3panels.missing2null(data.x);
    y = d3panels.missing2null(data.y);

    if (x.length !== y.length) {
      d3panels.displayError("add_points: x.length (" + x.length + ") != y.length (" + y.length + ")");
    } // grab indID if it's there
    // if no indID, create a vector of them


    indID = (ref5 = data != null ? data.indID : void 0) != null ? ref5 : null;
    indID = indID != null ? indID : function () {
      var results = [];

      for (var j = 1, ref6 = x.length; 1 <= ref6 ? j <= ref6 : j >= ref6; 1 <= ref6 ? j++ : j--) {
        results.push(j);
      }

      return results;
    }.apply(this);

    if (indID.length !== x.length) {
      d3panels.displayError("add_points: indID.length (" + indID.length + ") != x.length (" + x.length + ")");
    } // groups of colors


    group = (ref7 = data != null ? data.group : void 0) != null ? ref7 : function () {
      var j, len, results;
      results = [];

      for (j = 0, len = x.length; j < len; j++) {
        i = x[j];
        results.push(1);
      }

      return results;
    }();
    group = d3panels.expand2vector(group, x.length); // force it to be a vector not scalar

    ngroup = d3.max(group);

    group = function () {
      var j, len, results; // changed from (1,2,3,...) to (0,1,2,...)

      results = [];

      for (j = 0, len = group.length; j < len; j++) {
        g = group[j];
        results.push(g != null ? g - 1 : g);
      }

      return results;
    }();

    if (d3panels.sumArray(function () {
      var j, len, results;
      results = [];

      for (j = 0, len = group.length; j < len; j++) {
        g = group[j];
        results.push(g < 0 || g > ngroup - 1);
      }

      return results;
    }()) > 0) {
      d3panels.displayError("add_points: group values out of range");
      console.log("ngroup: " + ngroup);
      console.log("distinct groups: " + d3panels.unique(group));
    }

    if (group.length !== x.length) {
      d3panels.displayError("add_points: group.length (" + group.length + ") != x.length (" + x.length + ")");
    } // colors of the points in the different groups


    pointcolor = pointcolor != null ? pointcolor : d3panels.selectGroupColors(ngroup, "dark");
    pointcolor = d3panels.expand2vector(pointcolor, ngroup);

    if (pointcolor.length < ngroup) {
      d3panels.displayError("add_points: pointcolor.length (" + pointcolor.length + ") < ngroup (" + ngroup + ")");
    }

    svg = prevchart.svg(); // grab scale functions

    xscale = prevchart.xscale();
    yscale = prevchart.yscale();
    pointGroup = svg.append("g").attr("id", "points");
    points = pointGroup.selectAll("empty").data(d3.range(x.length)).enter().append("circle").attr("cx", function (d, i) {
      return xscale(x[i]);
    }).attr("cy", function (d, i) {
      return yscale(y[i]);
    }).attr("class", function (d, i) {
      return "pt" + i;
    }).attr("r", pointsize).attr("fill", function (d, i) {
      return pointcolor[group[i]];
    }).attr("stroke", pointstroke).attr("stroke-width", "1");
    indtip = d3panels.tooltip_create(d3.select("body"), points, {
      tipclass: tipclass
    }, function (d, i) {
      return indID[i];
    }); // jitter missing values?

    if (prevchart.xNA() || prevchart.yNA()) {
      if (jitter === "random") {
        xwid = 20 - pointsize - 2;
        xwid = xwid <= 2 ? 2 : xwid;
        ywid = 20 - pointsize - 2;
        ywid = ywid <= 2 ? 2 : ywid;

        ux = function () {
          var results;
          results = [];

          for (i in x) {
            results.push((Math.random() - 0.5) * xwid);
          }

          return results;
        }();

        uy = function () {
          var results;
          results = [];

          for (i in x) {
            results.push((Math.random() - 0.5) * ywid);
          }

          return results;
        }();

        points.attr("cx", function (d, i) {
          if (x[i] != null) {
            return xscale(x[i]);
          }

          return xscale(x[i]) + ux[i];
        }).attr("cy", function (d, i) {
          if (y[i] != null) {
            return yscale(y[i]);
          }

          return yscale(y[i]) + uy[i];
        });
      } else if (jitter === "beeswarm") {
        scaledPoints = function () {
          var results;
          results = [];

          for (i in x) {
            results.push({
              x: xscale(x[i]),
              y: yscale(y[i]),
              xnull: x[i] == null,
              ynull: y[i] == null
            });
          }

          return results;
        }(); // assign .fx and .fy when you don't want .x or .y to change


        d3.range(scaledPoints.length).map(function (i) {
          if (!scaledPoints[i].xnull) {
            scaledPoints[i].fx = scaledPoints[i].x;
          }

          if (!scaledPoints[i].ynull) {
            return scaledPoints[i].fy = scaledPoints[i].y;
          }
        });
        force = d3.forceSimulation(scaledPoints).force("x", d3.forceX(function (d) {
          return d.x;
        })).force("y", d3.forceY(function (d) {
          return d.y;
        })).force("collide", d3.forceCollide(pointsize * 1.1)).stop();
        (function () {
          var results = [];

          for (var j = 0; j <= 30; j++) {
            results.push(j);
          }

          return results;
        }).apply(this).map(function (d) {
          force.tick();
          return points.attr("cx", function (d, i) {
            return scaledPoints[i].x;
          }).attr("cy", function (d, i) {
            return scaledPoints[i].y;
          });
        });
      } else if (jitter !== "none") {
        d3panels.displayError('add_points: jitter should be "beeswarm", "random", or "none"');
      }
    } // move box to front


    return prevchart.box().raise();
  }; // functions to grab stuff


  chart.points = function () {
    return points;
  };

  chart.indtip = function () {
    return indtip;
  }; // function to remove chart


  chart.remove = function () {
    pointGroup.remove();
    d3panels.tooltip_destroy(indtip);
    return null;
  }; // return the chart function


  return chart;
};"use strict";

// Generated by CoffeeScript 2.6.1
// lodheatmap: heat map for multiple LOD curves (with one dimension broken by chromosomes)
d3panels.lodheatmap = function (chartOpts) {
  var cellSelect, cells, celltip, chart, chrGap, colors, equalCells, height, hilitcolor, horizontal, margin, nullcolor, ref, ref1, ref10, ref11, ref12, ref13, ref14, ref2, ref3, ref4, ref5, ref6, ref7, ref8, ref9, svg, tipclass, width, xlab, xscale, ylab, ylim, yscale, zlim, zscale, zthresh;

  if (chartOpts == null) {
    chartOpts = {}; // make sure it's defined
  } // chartOpts start


  width = (ref = chartOpts != null ? chartOpts.width : void 0) != null ? ref : 800; // overall height of chart in pixels

  height = (ref1 = chartOpts != null ? chartOpts.height : void 0) != null ? ref1 : 500; // overall width of chart in pixels

  margin = (ref2 = chartOpts != null ? chartOpts.margin : void 0) != null ? ref2 : {
    left: 60,
    top: 40,
    right: 40,
    bottom: 40 // margins in pixels (left, top, right, bottom)

  };
  colors = (ref3 = chartOpts != null ? chartOpts.colors : void 0) != null ? ref3 : ["slateblue", "white", "crimson" // vector of three colors for the color scale (negative - zero - positive)
  ];
  nullcolor = (ref4 = chartOpts != null ? chartOpts.nullcolor : void 0) != null ? ref4 : "#e6e6e6"; // color for empty cells

  xlab = (ref5 = chartOpts != null ? chartOpts.xlab : void 0) != null ? ref5 : null; // x-axis label

  ylab = (ref6 = chartOpts != null ? chartOpts.ylab : void 0) != null ? ref6 : ""; // y-axis label

  ylim = (ref7 = chartOpts != null ? chartOpts.ylim : void 0) != null ? ref7 : null; // y-axis limits (if null take from data)

  zlim = (ref8 = chartOpts != null ? chartOpts.zlim : void 0) != null ? ref8 : null; // z-axis limits (if null take from data, symmetric about 0)

  zthresh = (ref9 = chartOpts != null ? chartOpts.zthresh : void 0) != null ? ref9 : null; // z threshold; if |z| < zthresh, not shown

  horizontal = (ref10 = chartOpts != null ? chartOpts.horizontal : void 0) != null ? ref10 : false; // if true, have chromosomes arranged vertically

  hilitcolor = (ref11 = chartOpts != null ? chartOpts.hilitcolor : void 0) != null ? ref11 : "black"; // color of box around highlighted cell

  chrGap = (ref12 = chartOpts != null ? chartOpts.chrGap : void 0) != null ? ref12 : 6; // gap between chromosomes (in pixels)

  equalCells = (ref13 = chartOpts != null ? chartOpts.equalCells : void 0) != null ? ref13 : false; // if true, make all cells equal-sized; in this case, chartOpts.chrGap is ignored

  tipclass = (ref14 = chartOpts != null ? chartOpts.tipclass : void 0) != null ? ref14 : "tooltip"; // class name for tool tips
  // chartOpts end
  // further chartOpts: chrpanelframe
  // accessors start

  xscale = null; // x-axis scale (vector by chromosome)

  yscale = null; // y-axis scale

  zscale = null; // z-axis scale

  cells = null; // cell selection

  celltip = null; // cell tooltip selection

  svg = null; // SVG selection
  // accessors end

  cellSelect = null; // actual name for the cell selection
  //# the main function

  chart = function chart(selection, data) {
    // (chr, pos, lod) optionally: y or ycat giving scale for y-axis
    var cellg, celltipfunc, chr, direction, i, j, k, l, len, len1, len2, len3, len4, lod, m, myframe, n, n_lod, n_pos, o, pos, ref15, ref16, ref17, ref18, ref19, x, xmid_scaled, y, ylabels, ymid, ymid_scaled, yv, zmax, zmin; // also, optionally poslabel (e.g. marker name)
    // also, optionally chrname, chrstart, chrend
    // args that are lists: check that they have all the pieces

    margin = d3panels.check_listarg_v_default(margin, {
      left: 60,
      top: 40,
      right: 40,
      bottom: 40
    });

    if (data.chr == null) {
      d3panels.displayError("lodheatmap: data.chr is missing");
    }

    if (data.pos == null) {
      d3panels.displayError("lodheatmap: data.pos is missing");
    }

    if (data.lod == null) {
      d3panels.displayError("lodheatmap: data.lod is missing");
    } // for categorical scale


    if (data.ycat != null) {
      data.y = function () {
        var results;
        results = [];

        for (i in data.ycat) {
          results.push(i + 1);
        }

        return results;
      }(); // if data.ycat provided (categorical labels), data.y ignored

    }

    if (data.y == null) {
      data.ycat = function () {
        var results;
        results = [];

        for (i in data.lod[0]) {
          results.push(i + 1);
        }

        return results;
      }();

      data.y = function () {
        var results;
        results = [];

        for (i in data.lod[0]) {
          results.push(i + 1);
        }

        return results;
      }(); // if neither data.ycat nor data.y provided, create labels

    }

    data.y = function () {
      var k, len, ref15, results;
      ref15 = data.y; // make sure it's numeric

      results = [];

      for (k = 0, len = ref15.length; k < len; k++) {
        yv = ref15[k];
        results.push(+yv);
      }

      return results;
    }();

    n_pos = data.chr.length;
    n_lod = data.y.length; // check inputs

    if (n_pos !== data.pos.length) {
      d3panels.displayError("lodheatmap: data.pos.length (" + data.pos.length + ") != data.chr.length (" + n_pos + ")");
    }

    if (n_pos !== data.lod.length) {
      d3panels.displayError("lodheatmap: data.lod.length (" + data.lod.length + ") != data.chr.length (" + n_pos + ")");
    }

    for (i in data.lod) {
      if (data.lod[i].length !== data.y.length) {
        d3panels.displayError("lodheatmap: data.lod[" + i + "].length (" + data.lod[i].length + ") != data.y.length (" + n_lod + ")");
      }
    }

    if (data.poslabel != null) {
      if (data.poslabel.length !== n_pos) {
        d3panels.displayError("lodheatmap: data.poslabel.length (" + data.poslabel.length + ") != data.chr.length (" + n_pos + ")");
      }
    } else {
      // create position labels
      data.poslabel = function () {
        var results;
        results = [];

        for (i in data.chr) {
          results.push(data.chr[i] + "@" + d3panels.formatAxis(data.pos)(data.pos[i]));
        }

        return results;
      }();
    }

    if (data.chrname == null) {
      // create chrname if missing
      data.chrname = d3panels.unique(data.chr);
    }

    data.chrname = d3panels.forceAsArray(data.chrname); // if equalCells, change positions to dummy values

    if (equalCells) {
      data.pos = [];
      ref15 = data.chrname;

      for (k = 0, len = ref15.length; k < len; k++) {
        chr = ref15[k];
        data.pos = data.pos.concat(function () {
          var results;
          results = [];

          for (i in data.chr) {
            if (data.chr[i] === chr) {
              results.push(+i);
            }
          }

          return results;
        }());
      }
    } // create chrstart, chrend if missing


    data = d3panels.add_chrname_start_end(data); // if equalCells, adjust chrGap to make chromosome ends equal

    if (equalCells) {
      chrGap = (width - margin.left - margin.right - 2 * data.chrname.length) / data.chr.length + 2;
    } // organize positions and LOD scores by chromosomes


    data = d3panels.reorgLodData(data); // y-axis midpoints

    ymid = d3panels.calc_midpoints(d3panels.pad_vector(data.y)); // set up frame

    chartOpts.ylim = ylim != null ? ylim : d3.extent(ymid);
    chartOpts.horizontal = horizontal;
    chartOpts.xlab = xlab;
    chartOpts.ylab = ylab;
    chartOpts.chrGap = chrGap;
    chartOpts.width = width;
    chartOpts.height = height;
    chartOpts.margin = margin;

    if (data.ycat != null) {
      chartOpts.yticks = data.y;
      chartOpts.yticklab = data.ycat; // categorical labels
    }

    myframe = d3panels.chrpanelframe(chartOpts); // Create SVG

    myframe(selection, {
      chr: data.chrname,
      start: data.chrstart,
      end: data.chrend
    });
    svg = myframe.svg(); // grab scale functions

    xscale = myframe.xscale();
    yscale = myframe.yscale(); // y-axis labels

    ylabels = myframe.ylabels(); // scaled y-axis midpoints

    ymid_scaled = function () {
      var l, len1, results;
      results = [];

      for (l = 0, len1 = ymid.length; l < len1; l++) {
        y = ymid[l];
        results.push(yscale(y));
      }

      return results;
    }(); // x-axis midpoints


    xmid_scaled = {};
    ref16 = data.chrname;

    for (l = 0, len1 = ref16.length; l < len1; l++) {
      chr = ref16[l];
      xmid_scaled[chr] = d3panels.calc_midpoints(d3panels.pad_vector(function () {
        var len2, m, ref17, results;
        ref17 = data.posByChr[chr];
        results = [];

        for (m = 0, len2 = ref17.length; m < len2; m++) {
          x = ref17[m];
          results.push(xscale[chr](x));
        }

        return results;
      }(), (chrGap - 2) / 2));
    } // z-axis (color) limits; if not provided, make symmetric about 0


    zmin = d3panels.matrixMin(data.lod);
    zmax = d3panels.matrixMaxAbs(data.lod);
    zlim = zlim != null ? zlim : [-zmax, 0, zmax];

    if (zlim.length !== colors.length) {
      d3panels.displayError("lodheatmap: zlim.length (" + zlim.length + ") != colors.length (" + colors.length + ")");
    }

    zscale = d3.scaleLinear().domain(zlim).range(colors);
    zthresh = zthresh != null ? zthresh : zmin - 1; // create cells for plotting

    cells = [];
    ref17 = data.chrname;

    for (m = 0, len2 = ref17.length; m < len2; m++) {
      chr = ref17[m];
      ref18 = data.posByChr[chr];

      for (i = n = 0, len3 = ref18.length; n < len3; i = ++n) {
        pos = ref18[i];
        ref19 = data.lodByChr[chr][i];

        for (j = o = 0, len4 = ref19.length; o < len4; j = ++o) {
          lod = ref19[j];

          if (Math.abs(lod) >= zthresh) {
            cells.push({
              lod: lod,
              chr: chr,
              pos: pos,
              poslabel: data.poslabelByChr[chr][i],
              posindex: +i,
              lodindex: +j
            });
          }
        }
      }
    }

    d3panels.calc_chrcell_rect(cells, xmid_scaled, ymid_scaled);
    cellg = svg.append("g").attr("id", "cells");
    cellSelect = cellg.selectAll("empty").data(cells).enter().append("rect").attr("x", function (d) {
      if (horizontal) {
        return d.top;
      }

      return d.left;
    }).attr("y", function (d) {
      if (horizontal) {
        return d.left;
      }

      return d.top;
    }).attr("width", function (d) {
      if (horizontal) {
        return d.height;
      }

      return d.width;
    }).attr("height", function (d) {
      if (horizontal) {
        return d.width;
      }

      return d.height;
    }).attr("class", function (d, i) {
      return "cell" + i;
    }).attr("fill", function (d) {
      if (d.lod != null) {
        return zscale(d.lod);
      } else {
        return nullcolor;
      }
    }).attr("stroke", "none").attr("stroke-width", "1").attr("shape-rendering", "crispEdges").on("mouseover", function (event, d) {
      d3.select(this).attr("stroke", hilitcolor).raise();

      if (data.ycat != null) {
        return svg.select("text#ylab" + d.lodindex).attr("opacity", 1);
      }
    }).on("mouseout", function (event, d) {
      d3.select(this).attr("stroke", "none");

      if (data.ycat != null) {
        return svg.select("text#ylab" + d.lodindex).attr("opacity", 0);
      }
    }); // if horizontal, remove y-axis labels and lines

    if (data.ycat != null) {
      svg.selectAll("g#ylines").remove();
      ylabels.attr("opacity", 0).attr("id", function (d, i) {
        return "ylab" + i;
      });
    } // tool tips


    celltipfunc = function celltipfunc(d) {
      var lodlabel, z;
      z = d3.format(".2f")(Math.abs(d.lod));
      lodlabel = data.ycat != null ? data.ycat[d.lodindex] : d3panels.formatAxis(data.y)(data.y[d.lodindex]);

      if (horizontal) {
        return lodlabel + ", " + d.poslabel + " &rarr; " + z;
      }

      return d.poslabel + ", " + lodlabel + " &rarr; " + z;
    };

    direction = horizontal ? "north" : "east";
    celltip = d3panels.tooltip_create(d3.select("body"), cellg.selectAll("rect"), {
      direction: direction,
      tipclass: tipclass
    }, celltipfunc);
    return myframe.box().raise();
  }; // functions to grab stuff


  chart.xscale = function () {
    return xscale;
  };

  chart.yscale = function () {
    return yscale;
  };

  chart.zscale = function () {
    return yscale;
  };

  chart.cells = function () {
    return cellSelect;
  };

  chart.celltip = function () {
    return celltip;
  };

  chart.svg = function () {
    return svg;
  }; // function to remove chart


  chart.remove = function () {
    svg.remove();
    d3panels.tooltip_destroy(celltip);
    return null;
  }; // return the chart function


  return chart;
};"use strict";

// Generated by CoffeeScript 2.6.1
// mapchart: plot of a genetic marker map
d3panels.mapchart = function (chartOpts) {
  var chart, horizontal, linecolor, linecolorhilit, linewidth, markerSelect, martip, ref, ref1, ref10, ref2, ref3, ref4, ref5, ref6, ref7, ref8, ref9, shiftStart, svg, tickwidth, tipclass, v_over_h, xlab, xlineOpts, xscale, ylab, yscale;

  if (chartOpts == null) {
    chartOpts = {}; // make sure it's defined
  } // chartOpts start


  tickwidth = (ref = chartOpts != null ? chartOpts.tickwidth : void 0) != null ? ref : 10; // width of ticks at markers

  linecolor = (ref1 = chartOpts != null ? chartOpts.linecolor : void 0) != null ? ref1 : "slateblue"; // line color

  linecolorhilit = (ref2 = chartOpts != null ? chartOpts.linecolorhilit : void 0) != null ? ref2 : "Orchid"; // line color when highlighted

  linewidth = (ref3 = chartOpts != null ? chartOpts.linewidth : void 0) != null ? ref3 : 3; // line width (pixels)

  xlab = (ref4 = chartOpts != null ? chartOpts.xlab : void 0) != null ? ref4 : "Chromosome"; // x-axis label

  ylab = (ref5 = chartOpts != null ? chartOpts.ylab : void 0) != null ? ref5 : "Position (cM)"; // y-axis label

  xlineOpts = (ref6 = chartOpts != null ? chartOpts.xlineOpts : void 0) != null ? ref6 : {
    color: "#cdcdcd",
    width: 5 // color and width of vertical lines

  };
  horizontal = (ref7 = chartOpts != null ? chartOpts.horizontal : void 0) != null ? ref7 : false; // whether chromosomes should be laid at horizontally

  v_over_h = (ref8 = chartOpts != null ? chartOpts.v_over_h : void 0) != null ? ref8 : horizontal; // whether vertical lines should be on top of horizontal lines

  shiftStart = (ref9 = chartOpts != null ? chartOpts.shiftStart : void 0) != null ? ref9 : false; // if true, shift start of chromosomes to 0

  tipclass = (ref10 = chartOpts != null ? chartOpts.tipclass : void 0) != null ? ref10 : "tooltip"; // class name for tool tips
  // chartOpts end
  // further chartOpts: panelframe (omit xNA yNA xNA_size yNA_size)
  // accessors start

  xscale = null; // x-axis scale

  yscale = null; // y-axis scale

  markerSelect = null; // marker segment selection

  martip = null; // marker tool tip selection

  svg = null; // SVG selection
  // accessors end
  //# the main function

  chart = function chart(selection, data) {
    // {chr, pos, marker, (optionally) chrname}
    var chr, chrscale, direction, extentByChr, i, j, k, l, len, len1, markerpos, markers, minpos, myframe, n_chr, n_pos, pos, ref11, ref12, these_index, these_pos, tipfunc, x, xlim, xticklab, xticks, ylim; // args that are lists: check that they have all the pieces

    xlineOpts = d3panels.check_listarg_v_default(xlineOpts, {
      color: "#cdcdcd",
      width: 5
    });

    if (data.chr == null) {
      d3panels.displayError("mapchart: data.chr is missing");
    }

    if (data.pos == null) {
      d3panels.displayError("mapchart: data.pos is missing");
    }

    if (data.marker == null) {
      d3panels.displayError("mapchart: data.marker is missing");
    }

    n_pos = data.pos.length;

    if (data.chr.length !== n_pos) {
      d3panels.displayError("mapchart: data.chr.length (" + data.chr.length + ") != data.pos.length (" + n_pos + ")");
    }

    if (data.marker.length !== n_pos) {
      d3panels.displayError("mapchart: data.marker.length (" + data.marker.length + ") != data.pos.length (" + n_pos + ")");
    }

    if (data.chrname == null) {
      data.chrname = d3panels.unique(data.chr);
    }

    data.chrname = d3panels.forceAsArray(data.chrname);
    data.adjpos = data.pos.slice(0); // shift positions so that each chromosome starts at 0

    if (shiftStart) {
      ref11 = data.chrname;

      for (k = 0, len = ref11.length; k < len; k++) {
        chr = ref11[k];

        these_pos = function () {
          var results;
          results = [];

          for (i in data.pos) {
            if (data.chr[i] === chr) {
              results.push(data.pos[i]);
            }
          }

          return results;
        }();

        these_index = function () {
          var results;
          results = [];

          for (i in data.pos) {
            if (data.chr[i] === chr) {
              results.push(i);
            }
          }

          return results;
        }();

        minpos = d3.min(these_pos);

        these_pos = function () {
          var l, len1, results;
          results = [];

          for (l = 0, len1 = these_pos.length; l < len1; l++) {
            x = these_pos[l];
            results.push(x - minpos);
          }

          return results;
        }();

        for (j in these_pos) {
          data.adjpos[these_index[j]] = these_pos[j];
        }
      }
    } // hereafter: data.adjpos is location to be plotted
    //            data.pos remains the real position
    // find min and max position on each chromosome


    extentByChr = {};
    ref12 = data.chrname;

    for (l = 0, len1 = ref12.length; l < len1; l++) {
      chr = ref12[l];

      pos = function () {
        var results;
        results = [];

        for (i in data.adjpos) {
          if (data.chr[i] === chr) {
            results.push(data.adjpos[i]);
          }
        }

        return results;
      }();

      extentByChr[chr] = d3.extent(pos);
    }

    ylim = ylim != null ? ylim : d3.extent(data.adjpos);
    n_chr = data.chrname.length;
    xlim = [0.5, n_chr + 0.5];

    xticks = function () {
      var len2, m, ref13, results;
      ref13 = d3.range(n_chr);
      results = [];

      for (m = 0, len2 = ref13.length; m < len2; m++) {
        i = ref13[m];
        results.push(i + 1);
      }

      return results;
    }();

    xticklab = data.chrname;
    chartOpts.xNA = false; // don't allow NA boxes

    chartOpts.yNA = false;

    if (horizontal) {
      chartOpts.xlim = ylim;
      chartOpts.ylim = xlim.reverse();
      chartOpts.xlineOpts = chartOpts.ylineOpts;
      chartOpts.ylineOpts = xlineOpts;
      chartOpts.xlab = ylab;
      chartOpts.ylab = xlab;
      chartOpts.xticks = chartOpts.yticks;
      chartOpts.yticks = xticks;
      chartOpts.nxticks = chartOpts.nyticks;
      chartOpts.xticklab = chartOpts.yticklab;
      chartOpts.yticklab = xticklab;
      chartOpts.v_over_h = v_over_h;
    } else {
      chartOpts.xlim = xlim;
      chartOpts.ylim = ylim.reverse();
      chartOpts.xlineOpts = xlineOpts;
      chartOpts.xlab = xlab;
      chartOpts.ylab = ylab;
      chartOpts.xticks = xticks;
      chartOpts.xticklab = xticklab;
      chartOpts.v_over_h = v_over_h;
    } // set up frame


    myframe = d3panels.panelframe(chartOpts); // Create SVG

    myframe(selection);
    svg = myframe.svg(); // grab scale functions

    xscale = myframe.xscale();
    yscale = myframe.yscale();

    chrscale = function chrscale(chr) {
      var chrpos;
      chrpos = data.chrname.indexOf(chr) + 1;

      if (!horizontal) {
        return xscale(chrpos);
      }

      return yscale(chrpos);
    }; // vertical lines for each chromosome


    svg.append("g").attr("id", "chromosomes").selectAll("empty").data(data.chrname).enter().append("line").attr("x1", function (d) {
      if (horizontal) {
        return xscale(extentByChr[d][0]);
      }

      return chrscale(d);
    }).attr("x2", function (d) {
      if (horizontal) {
        return xscale(extentByChr[d][1]);
      }

      return chrscale(d);
    }).attr("y1", function (d) {
      if (horizontal) {
        return chrscale(d);
      }

      return yscale(extentByChr[d][0]);
    }).attr("y2", function (d) {
      if (horizontal) {
        return chrscale(d);
      }

      return yscale(extentByChr[d][1]);
    }).attr("fill", "none").attr("stroke", linecolor).attr("stroke-width", linewidth).attr("shape-rendering", "crispEdges").style("pointer-events", "none"); // hash with rounded marker positions

    markerpos = {};

    for (i in data.marker) {
      markerpos[data.marker[i]] = d3.format(".1f")(data.pos[i]);
    }

    markers = svg.append("g").attr("id", "points");
    markerSelect = markers.selectAll("empty").data(data.marker).enter().append("line").attr("x1", function (d, i) {
      if (horizontal) {
        return xscale(data.adjpos[i]);
      }

      return chrscale(data.chr[i]) - tickwidth;
    }).attr("x2", function (d, i) {
      if (horizontal) {
        return xscale(data.adjpos[i]);
      }

      return chrscale(data.chr[i]) + tickwidth;
    }).attr("y1", function (d, i) {
      if (horizontal) {
        return chrscale(data.chr[i]) - tickwidth;
      }

      return yscale(data.adjpos[i]);
    }).attr("y2", function (d, i) {
      if (horizontal) {
        return chrscale(data.chr[i]) + tickwidth;
      }

      return yscale(data.adjpos[i]);
    }).attr("id", function (d) {
      return d;
    }).attr("fill", "none").attr("stroke", linecolor).attr("stroke-width", linewidth).attr("shape-rendering", "crispEdges").on("mouseover.paneltip", function () {
      return d3.select(this).attr("stroke", linecolorhilit);
    }).on("mouseout.paneltip", function () {
      return d3.select(this).attr("stroke", linecolor);
    });

    tipfunc = function tipfunc(d, i) {
      return d + " (" + markerpos[d] + ")";
    };

    direction = horizontal ? "north" : "east";
    martip = d3panels.tooltip_create(d3.select("body"), markers.selectAll("line"), {
      direction: direction,
      tipclass: tipclass
    }, tipfunc); // move box to front

    return myframe.box().raise();
  }; // functions to grab stuff


  chart.xscale = function () {
    return xscale;
  };

  chart.yscale = function () {
    return yscale;
  };

  chart.markerSelect = function () {
    return markerSelect;
  };

  chart.martip = function () {
    return martip;
  };

  chart.svg = function () {
    return svg;
  }; // function to remove chart


  chart.remove = function () {
    svg.remove();
    d3panels.tooltip_destroy(martip);
    return null;
  }; // return the chart function


  return chart;
};"use strict";

// Generated by CoffeeScript 2.5.1
// scatterplot: plot scatter of points, y versus x
d3panels.scatterplot = function (chartOpts) {
  var chart, indtip, jitter, pointcolor, points, pointsize, pointstroke, ref, ref1, ref10, ref2, ref3, ref4, ref5, ref6, ref7, ref8, ref9, svg, tipclass, xNA, xNA_size, xlim, xscale, yNA, yNA_size, ylim, yscale;

  if (chartOpts == null) {
    chartOpts = {}; // make sure it's defined
  } // chartOpts start


  xNA = (ref = chartOpts != null ? chartOpts.xNA : void 0) != null ? ref : {
    handle: true,
    force: false // handle: include separate boxes for NAs; force: include whether or not NAs in data

  };
  yNA = (ref1 = chartOpts != null ? chartOpts.yNA : void 0) != null ? ref1 : {
    handle: true,
    force: false // handle: include separate boxes for NAs; force: include whether or not NAs in data

  };
  xNA_size = (ref2 = chartOpts != null ? chartOpts.xNA_size : void 0) != null ? ref2 : {
    width: 20,
    gap: 10 // width and gap for x=NA box

  };
  yNA_size = (ref3 = chartOpts != null ? chartOpts.yNA_size : void 0) != null ? ref3 : {
    width: 20,
    gap: 10 // width and gap for y=NA box

  };
  xlim = (ref4 = chartOpts != null ? chartOpts.xlim : void 0) != null ? ref4 : null; // x-axis limits

  ylim = (ref5 = chartOpts != null ? chartOpts.ylim : void 0) != null ? ref5 : null; // y-axis limits

  pointcolor = (ref6 = chartOpts != null ? chartOpts.pointcolor : void 0) != null ? ref6 : null; // fill color of points

  pointstroke = (ref7 = chartOpts != null ? chartOpts.pointstroke : void 0) != null ? ref7 : "black"; // color of points' outer circle

  pointsize = (ref8 = chartOpts != null ? chartOpts.pointsize : void 0) != null ? ref8 : 3; // color of points

  jitter = (ref9 = chartOpts != null ? chartOpts.jitter : void 0) != null ? ref9 : "beeswarm"; // method for jittering NA points (beeswarm|random|none)

  tipclass = (ref10 = chartOpts != null ? chartOpts.tipclass : void 0) != null ? ref10 : "tooltip"; // class name for tool tips
  // chartOpts end
  // further chartOpts: panelframe
  // accessors start

  xscale = null; // x-axis scale

  yscale = null; // y-axis scale

  xNA = xNA; // true if x-axis NAs are handled in a separate box

  yNA = yNA; // true if y-axis NAs are handled in a separate box

  points = null; // points selection

  indtip = null; // tooltip selection

  svg = null; // SVG selection
  // accessors end
  //# the main function

  chart = function chart(selection, data) {
    // data = {x, y, indID, group}
    var addpts, myframe, x, y; // args that are lists: check that they have all the pieces

    xNA = d3panels.check_listarg_v_default(xNA, {
      handle: true,
      force: false
    });
    yNA = d3panels.check_listarg_v_default(yNA, {
      handle: true,
      force: false
    });
    xNA_size = d3panels.check_listarg_v_default(xNA, {
      width: 20,
      gap: 10
    });
    yNA_size = d3panels.check_listarg_v_default(yNA, {
      width: 20,
      gap: 10
    });

    if (data.x == null) {
      d3panels.displayError("scatterplot: data.x is missing");
    }

    if (data.y == null) {
      d3panels.displayError("scatterplot: data.y is missing");
    } // missing values can be any of null, "NA", or ""; replacing with nulls


    x = d3panels.missing2null(data.x);
    y = d3panels.missing2null(data.y);

    if (x.length !== y.length) {
      d3panels.displayError("scatterplot: x.length (" + x.length + ") != y.length (" + y.length + ")");
    } // whether to include separate boxes for NAs


    xNA.handle = xNA.force || xNA.handle && !x.every(function (v) {
      return v != null;
    });
    yNA.handle = yNA.force || yNA.handle && !y.every(function (v) {
      return v != null;
    });
    xlim = xlim != null ? xlim : d3panels.pad_ylim(d3.extent(x));
    ylim = ylim != null ? ylim : d3panels.pad_ylim(d3.extent(y)); // set up frame

    chartOpts.xlim = xlim;
    chartOpts.ylim = ylim;
    chartOpts.xNA = xNA.handle;
    chartOpts.yNA = yNA.handle;
    chartOpts.xNA_size = xNA_size;
    chartOpts.yNA_size = yNA_size;
    myframe = d3panels.panelframe(chartOpts); // Create SVG

    myframe(selection);
    svg = myframe.svg(); // grab scale functions

    xscale = myframe.xscale();
    yscale = myframe.yscale(); // add points

    addpts = d3panels.add_points({
      pointcolor: pointcolor,
      pointstroke: pointstroke,
      pointsize: pointsize,
      jitter: jitter,
      tipclass: tipclass
    });
    addpts(myframe, {
      x: x,
      y: y,
      indID: data.indID,
      group: data.group
    });
    points = addpts.points();
    return indtip = addpts.indtip();
  }; // functions to grab stuff


  chart.xscale = function () {
    return xscale;
  };

  chart.yscale = function () {
    return yscale;
  };

  chart.xNA = function () {
    return xNA.handle;
  };

  chart.yNA = function () {
    return yNA.handle;
  };

  chart.points = function () {
    return points;
  };

  chart.indtip = function () {
    return indtip;
  };

  chart.svg = function () {
    return svg;
  }; // function to remove chart


  chart.remove = function () {
    svg.remove();
    d3panels.tooltip_destroy(indtip);
    return null;
  }; // return the chart function


  return chart;
};"use strict";

// Generated by CoffeeScript 2.5.1
// trichart: plot scatter of points, y versus x
// (x,y,z) -> ((x*2+y)/sqrt(3), y)
// xlim: [0, 2/sqrt(3)]
// ylim: [0, 1]
d3panels.trichart = function (chartOpts) {
  var boxcolor, boxwidth, chart, gridcolor, gridlines, gridwidth, height, indtip, labelpos, labels, margin, pointcolor, points, pointsize, pointstroke, pscale, rectcolor, ref, ref1, ref10, ref11, ref12, ref13, ref14, ref15, ref16, ref2, ref3, ref4, ref5, ref6, ref7, ref8, ref9, svg, tipclass, title, titlepos, width, xscale, yscale;

  if (chartOpts == null) {
    chartOpts = {}; // make sure it's defined
  } // chartOpts start


  width = (ref = chartOpts != null ? chartOpts.width : void 0) != null ? ref : 600; // overall width of chart in pixels

  height = (ref1 = chartOpts != null ? chartOpts.height : void 0) != null ? ref1 : 520; // overall height of chart in pixels

  margin = (ref2 = chartOpts != null ? chartOpts.margin : void 0) != null ? ref2 : {
    left: 60,
    top: 40,
    right: 60,
    bottom: 10 // margins in pixels (left, top, right, bottom)

  };
  labelpos = (ref3 = chartOpts != null ? chartOpts.labelpos : void 0) != null ? ref3 : 10; // pixels between vertex and vertex label (horizontally)

  titlepos = (ref4 = chartOpts != null ? chartOpts.titlepos : void 0) != null ? ref4 : 20; // position of chart title in pixels

  title = (ref5 = chartOpts != null ? chartOpts.title : void 0) != null ? ref5 : ""; // chart title

  labels = (ref6 = chartOpts != null ? chartOpts.labels : void 0) != null ? ref6 : ["(1,0,0)", "(0,1,0)", "(0,0,1)" // labels on the corners
  ];
  rectcolor = (ref7 = chartOpts != null ? chartOpts.rectcolor : void 0) != null ? ref7 : "#e6e6e6"; // color of background rectangle

  boxcolor = (ref8 = chartOpts != null ? chartOpts.boxcolor : void 0) != null ? ref8 : "black"; // color of outer rectangle box

  boxwidth = (ref9 = chartOpts != null ? chartOpts.boxwidth : void 0) != null ? ref9 : 2; // width of outer box in pixels

  pointcolor = (ref10 = chartOpts != null ? chartOpts.pointcolor : void 0) != null ? ref10 : null; // fill color of points

  pointstroke = (ref11 = chartOpts != null ? chartOpts.pointstroke : void 0) != null ? ref11 : "black"; // color of points' outer circle

  pointsize = (ref12 = chartOpts != null ? chartOpts.pointsize : void 0) != null ? ref12 : 3; // color of points

  gridlines = (ref13 = chartOpts != null ? chartOpts.gridlines : void 0) != null ? ref13 : 0; // number of grid lines

  gridcolor = (ref14 = chartOpts != null ? chartOpts.gridcolor : void 0) != null ? ref14 : "white"; // color of grid lines

  gridwidth = (ref15 = chartOpts != null ? chartOpts.gridwidth : void 0) != null ? ref15 : 1; // width of grid lines in pixels

  tipclass = (ref16 = chartOpts != null ? chartOpts.tipclass : void 0) != null ? ref16 : "tooltip"; // class name for tool tips
  // chartOpts end
  // accessors start

  xscale = null; // x-axis scale

  yscale = null; // y-axis scale

  pscale = null; // pt -> (x,y) in pixels

  points = null; // points selection

  indtip = null; // tooltip selection

  svg = null; // SVG selection
  // accessors end
  //# the main function

  chart = function chart(selection, data) {
    // data = {p, indID, group}
    var d, first, flag_length_not_3, flag_out_of_range, flag_sum_not_1, frame, framefunc, g, gr, group, i, indID, indices, j, len, n, ngroup, p, p1, p2, p3, p4, plot_height, plot_width, ref17, ref18, second, sum, v, vertices, vv, xlim, xy, ylim; // p = [[p00, p01, p02], [p10, p11, p12], ...]
    // args that are lists: check that they have all the pieces

    margin = d3panels.check_listarg_v_default(margin, {
      left: 60,
      top: 40,
      right: 60,
      bottom: 10
    });

    if (data.p == null) {
      d3panels.displayError("trichart: data.p is missing");
    } // missing values can be any of null, "NA", or ""; replacing with nulls


    p = function () {
      var j, len, ref17, results;
      ref17 = data.p;
      results = [];

      for (j = 0, len = ref17.length; j < len; j++) {
        v = ref17[j];
        results.push(d3panels.missing2null(v));
      }

      return results;
    }(); // check points


    flag_length_not_3 = false;
    flag_sum_not_1 = false;
    flag_out_of_range = false;

    for (j = 0, len = p.length; j < len; j++) {
      v = p[j];

      if (v.length !== 3) {
        flag_length_not_3 = true;
      }

      sum = d3panels.sumArray(v);

      if (d3panels.abs(sum - 1) > 1e-6) {
        flag_sum_not_1;
      }

      if (d3panels.sumArray(function () {
        var k, len1, results;
        results = [];

        for (k = 0, len1 = v.length; k < len1; k++) {
          vv = v[k];
          results.push(vv < 0 || vv > 1);
        }

        return results;
      }()) > 0) {
        flag_out_of_range = true;
      }
    }

    if (flag_length_not_3) {
      d3panels.displayError("trichart: points not all of length 3");
    }

    if (flag_sum_not_1) {
      d3panels.displayError("trichart: points not all summing to 1");
    }

    if (flag_out_of_range) {
      d3panels.displayError("trichart: points not all in [0,1]");
    }

    n = p.length;
    indID = (ref17 = data != null ? data.indID : void 0) != null ? ref17 : function () {
      var results;
      results = [];

      for (i in p) {
        results.push(+i + 1);
      }

      return results;
    }();

    if (indID.length !== n) {
      d3panels.displayError("trichart: data.indID.length (" + indID.length + ") != data.p.length (" + n + ")");
    } // groups of colors


    group = (ref18 = data != null ? data.group : void 0) != null ? ref18 : function () {
      var results;
      results = [];

      for (i in p) {
        results.push(1);
      }

      return results;
    }();
    group = d3panels.expand2vector(group, n); // force it to be a vector not scalar

    ngroup = d3.max(group);

    group = function () {
      var k, len1, results; // changed from (1,2,3,...) to (0,1,2,...)

      results = [];

      for (k = 0, len1 = group.length; k < len1; k++) {
        g = group[k];
        results.push(g != null ? g - 1 : g);
      }

      return results;
    }();

    if (d3panels.sumArray(function () {
      var k, len1, results;
      results = [];

      for (k = 0, len1 = group.length; k < len1; k++) {
        g = group[k];
        results.push(g < 0 || g > ngroup - 1);
      }

      return results;
    }()) > 0) {
      d3panels.displayError("add_points: group values out of range");
      console.log("ngroup: " + ngroup);
      console.log("distinct groups: " + d3panels.unique(group));
    }

    if (group.length !== n) {
      d3panels.displayError("trichart: data.group.length (" + group.length + ") != data.p.length (" + n + ")");
    } // colors of the points in the different groups


    pointcolor = pointcolor != null ? pointcolor : d3panels.selectGroupColors(ngroup, "dark");
    pointcolor = d3panels.expand2vector(pointcolor, ngroup);

    if (pointcolor.length < ngroup) {
      d3panels.displayError("add_points: pointcolor.length (" + pointcolor.length + ") < ngroup (" + ngroup + ")");
    }

    xlim = [0, 2 / Math.sqrt(3)];
    ylim = [0, 1]; // calculate height and width to use

    plot_height = height - margin.top - margin.bottom;
    plot_width = width - margin.left - margin.right;

    if (plot_height > plot_width / xlim[1]) {
      d = plot_height - plot_width / xlim[1];
      margin.top += d / 2;
      margin.bottom += d / 2;
      plot_height -= d;
    } else {
      d = plot_width - plot_height * xlim[1];
      margin.left += d / 2;
      margin.right += d / 2;
      plot_width -= d;
    } // calculate scales


    xscale = d3.scaleLinear().domain(xlim).range([margin.left, margin.left + plot_width]);
    yscale = d3.scaleLinear().domain(ylim).range([plot_height + margin.top, margin.top]);

    pscale = function pscale(p) {
      sum = d3panels.sumArray(p);
      return {
        x: xscale((p[0] * 2.0 + p[1]) / Math.sqrt(3.0) / sum),
        y: yscale(p[1] / sum)
      };
    }; // convert points to (x,y)


    xy = function () {
      var k, len1, results;
      results = [];

      for (k = 0, len1 = p.length; k < len1; k++) {
        v = p[k];
        results.push({
          x: (v[0] * 2.0 + v[1]) / Math.sqrt(3.0),
          y: v[1]
        });
      }

      return results;
    }(); // Create SVG


    svg = selection.append("svg"); // Update the dimensions

    svg.attr("width", width).attr("height", height).attr("class", "d3panels"); // draw triangle

    frame = svg.append("g").attr("id", "frame");
    vertices = [{
      x: xlim[0],
      y: ylim[0]
    }, {
      x: xlim[1] / 2,
      y: ylim[1]
    }, {
      x: xlim[1],
      y: ylim[0]
    }];
    framefunc = d3.line().x(function (d) {
      return xscale(vertices[d].x);
    }).y(function (d) {
      return yscale(vertices[d].y);
    });

    indices = function () {
      var results;
      results = [];

      for (i in vertices) {
        results.push(+i);
      }

      return results;
    }().concat(0);

    frame.append("path").datum(indices).attr("d", framefunc).attr("fill", rectcolor).attr("stroke", boxcolor).attr("stroke-width", boxwidth); // add gridlines

    if (gridlines > 0) {
      gr = function () {
        var results = [];

        for (var k = 1; 1 <= gridlines ? k <= gridlines : k >= gridlines; 1 <= gridlines ? k++ : k--) {
          results.push(k);
        }

        return results;
      }.apply(this).map(function (i) {
        return i / (gridlines + 1);
      });

      p1 = gr.map(function (x) {
        return [x, 0, 1 - x];
      });
      p2 = gr.map(function (x) {
        return [x, 1 - x, 0];
      });
      p3 = gr.map(function (x) {
        return [0, 1 - x, x];
      });
      p4 = gr.map(function (x) {
        return [1 - x, 0, x];
      });
      first = p1.concat(p2).concat(p3);
      second = p2.concat(p3).concat(p4);
      g = frame.append("g").attr("class", "gridlines").selectAll("empty").data(first).enter().append("line").attr("x1", function (d) {
        return pscale(d).x;
      }).attr("y1", function (d) {
        return pscale(d).y;
      }).attr("x2", function (d, i) {
        return pscale(second[i]).x;
      }).attr("y2", function (d, i) {
        return pscale(second[i]).y;
      }).attr("stroke", gridcolor).attr("stroke-width", gridwidth).attr("shape-rendering", "crispEdges").style("pointer-events", "none").attr("fill", "none"); // draw outer box again

      frame.append("path").datum(indices).attr("d", framefunc).attr("fill", "none").attr("stroke", boxcolor).attr("stroke-width", boxwidth);
    } // add title


    frame.append("g").attr("class", "title").append("text").text(title).attr("x", plot_width / 2 + margin.left).attr("y", margin.top - titlepos); // add labels

    frame.append("g").attr("id", "labels").selectAll("empty").data(vertices).enter().append("text").attr("x", function (d, i) {
      return xscale(d.x) + [-1, +1, +1][i] * labelpos;
    }).attr("y", function (d) {
      return yscale(d.y);
    }).style("dominant-baseline", "middle").style("text-anchor", function (d, i) {
      return ["end", "start", "start"][i];
    }).text(function (d, i) {
      return labels[i];
    }); // add points

    points = svg.append("g").attr("id", "points").selectAll("empty").data(p).enter().append("circle").attr("r", pointsize).attr("cx", function (d) {
      return pscale(d).x;
    }).attr("cy", function (d) {
      return pscale(d).y;
    }).attr("fill", function (d, i) {
      return pointcolor[group[i]];
    }).attr("stroke", pointstroke).attr("stroke-width", 1); // individual tooltips

    return indtip = d3panels.tooltip_create(d3.select("body"), points, {
      tipclass: tipclass
    }, function (d, i) {
      return indID[i];
    });
  }; // functions to grab stuff


  chart.xscale = function () {
    return xscale;
  };

  chart.yscale = function () {
    return yscale;
  };

  chart.pscale = function () {
    return pscale;
  };

  chart.points = function () {
    return points;
  };

  chart.indtip = function () {
    return indtip;
  };

  chart.svg = function () {
    return svg;
  }; // function to remove chart


  chart.remove = function () {
    svg.remove();
    d3panels.tooltip_destroy(indtip);
    return null;
  }; // return the chart function


  return chart;
};"use strict";

// Generated by CoffeeScript 2.5.1
// histchart: chart with multiple curves
d3panels.histchart = function (chartOpts) {
  var chart, curves, density, indtip, linecolor, linecolorhilit, linewidth, linewidthhilit, ref, ref1, ref10, ref2, ref3, ref4, ref5, ref6, ref7, ref8, ref9, rotate_ylab, svg, tipclass, xlab, xlim, xscale, ylab, ylim, yscale;

  if (chartOpts == null) {
    chartOpts = {}; // make sure it's defined
  } // chartOpts start


  xlim = (ref = chartOpts != null ? chartOpts.xlim : void 0) != null ? ref : null; // x-axis limits (if null, taken from data)

  ylim = (ref1 = chartOpts != null ? chartOpts.ylim : void 0) != null ? ref1 : null; // y-axis limits (if null, taken from data)

  xlab = (ref2 = chartOpts != null ? chartOpts.xlab : void 0) != null ? ref2 : ""; // x-axis label

  ylab = (ref3 = chartOpts != null ? chartOpts.ylab : void 0) != null ? ref3 : ""; // y-axis label

  rotate_ylab = (ref4 = chartOpts != null ? chartOpts.rotate_ylab : void 0) != null ? ref4 : null; // whether to rotate the y-axis label

  linecolor = (ref5 = chartOpts != null ? chartOpts.linecolor : void 0) != null ? ref5 : null; // color of curves (if null, use pastel colors by group)

  linecolorhilit = (ref6 = chartOpts != null ? chartOpts.linecolorhilit : void 0) != null ? ref6 : null; // color of highlighted curve (if null, use dark colors by group)

  linewidth = (ref7 = chartOpts != null ? chartOpts.linewidth : void 0) != null ? ref7 : 2; // width of curve

  linewidthhilit = (ref8 = chartOpts != null ? chartOpts.linewidthhilit : void 0) != null ? ref8 : 2; // width of highlighted curve

  density = (ref9 = chartOpts != null ? chartOpts.density : void 0) != null ? ref9 : true; // density scale (vs counts)

  tipclass = (ref10 = chartOpts != null ? chartOpts.tipclass : void 0) != null ? ref10 : "tooltip"; // class name for tool tips
  // chartOpts end
  // further chartOpts: panelframe (omit xNA yNA xNA_size yNA_size)
  // accessors start

  xscale = null; // x-axis scale

  yscale = null; // y-axis scale

  curves = null; // curves selection

  indtip = null; // tooltip selection

  svg = null; // SVG selection
  // accessors end
  //# the main function

  chart = function chart(selection, data) {
    // {x, breaks, indID}
    var add_curves, breaks, brlim, d, f, freq, i, j, k, l, len, len1, maxn, maxpos, myframe, n_ind, p, path_data, path_x, path_y, pt, ref11, x, xv, xx;

    if (data.x == null) {
      // x is a 2-d ragged array indexed as x[subject][response_index]
      // breaks is either a number or its a vector of breakpoints
      //    if breaks is missing, we take 2*sqrt(maximum number of x values)
      // indID is optional; if provided, it should have length x.length
      d3panels.displayError("histchart: data.x is missing");
    }

    x = data.x;

    data.group = function () {
      var results;
      results = [];

      for (i in x) {
        results.push(+i + 1);
      }

      return results;
    }();

    n_ind = x.length;

    if (data.breaks == null) {
      maxn = d3.max(function () {
        var k, len, results;
        results = [];

        for (k = 0, len = x.length; k < len; k++) {
          xv = x[k];
          results.push(xv.length);
        }

        return results;
      }());
      data.breaks = [2 * Math.ceil(Math.sqrt(maxn) + 1)];
    }

    breaks = d3panels.forceAsArray(data.breaks);
    xlim = xlim != null ? xlim : d3panels.matrixExtent(x);

    if (breaks.length === 1) {
      // number
      breaks = d3panels.calc_breaks(breaks[0], xlim[0], xlim[1]);
    } // omit values that are not within the limit


    brlim = [d3.min(breaks) - 1e-6, d3.max(breaks) + 1e-6];

    x = function () {
      var k, len, results;
      results = [];

      for (k = 0, len = x.length; k < len; k++) {
        xx = x[k];
        results.push(function () {
          var l, len1, results1;
          results1 = [];

          for (l = 0, len1 = xx.length; l < len1; l++) {
            xv = xx[l];

            if (xv >= brlim[0] & xv <= brlim[1]) {
              results1.push(xv);
            }
          }

          return results1;
        }());
      }

      return results;
    }(); // calculate frequencies


    freq = function () {
      var k, len, results;
      results = [];

      for (k = 0, len = x.length; k < len; k++) {
        xv = x[k];
        results.push(d3panels.calc_freq(xv, breaks, !density));
      }

      return results;
    }(); // find maximum location for each curve (to use for tool tips)


    maxpos = [];

    for (k = 0, len = freq.length; k < len; k++) {
      f = freq[k];
      pt = {
        x: breaks[1],
        y: f[0]
      };
      ref11 = d3.range(f.length);

      for (l = 0, len1 = ref11.length; l < len1; l++) {
        j = ref11[l];

        if (f[j] > pt.y) {
          pt.y = f[j];
          pt.x = breaks[j + 1];
        }
      }

      maxpos.push(pt);
    } // y-axis limit


    ylim = ylim != null ? ylim : [0, d3panels.matrixMax(freq) * 1.05]; // set up frame

    chartOpts.xlim = xlim;
    chartOpts.ylim = ylim;
    chartOpts.xNA = false; // don't allow NA boxes

    chartOpts.yNA = false;
    chartOpts.xlab = xlab;
    chartOpts.ylab = ylab;
    chartOpts.rotate_ylab = rotate_ylab;
    myframe = d3panels.panelframe(chartOpts); // create SVG

    myframe(selection);
    svg = myframe.svg(); // scales

    xscale = myframe.xscale();
    yscale = myframe.yscale(); // curve data

    path_data = function () {
      var len2, m, results;
      results = [];

      for (m = 0, len2 = freq.length; m < len2; m++) {
        f = freq[m];
        results.push(d3panels.calc_hist_path(f, breaks));
      }

      return results;
    }(); // pull apart the path data


    path_x = function () {
      var len2, m, results;
      results = [];

      for (m = 0, len2 = path_data.length; m < len2; m++) {
        p = path_data[m];
        results.push(function () {
          var len3, n, results1;
          results1 = [];

          for (n = 0, len3 = p.length; n < len3; n++) {
            d = p[n];
            results1.push(d.x);
          }

          return results1;
        }());
      }

      return results;
    }();

    path_y = function () {
      var len2, m, results;
      results = [];

      for (m = 0, len2 = path_data.length; m < len2; m++) {
        p = path_data[m];
        results.push(function () {
          var len3, n, results1;
          results1 = [];

          for (n = 0, len3 = p.length; n < len3; n++) {
            d = p[n];
            results1.push(d.y);
          }

          return results1;
        }());
      }

      return results;
    }();

    add_curves = d3panels.add_curves({
      linecolor: linecolor,
      linecolorhilit: linecolorhilit,
      linewidth: linewidth,
      linewidthhilit: linewidthhilit,
      tipclass: tipclass
    });
    add_curves(myframe, {
      x: path_x,
      y: path_y,
      indID: data.indID,
      group: data.group
    });
    curves = add_curves.curves();
    indtip = add_curves.indtip(); // move box to front

    return myframe.box().raise();
  }; // functions to grab stuff


  chart.xscale = function () {
    return xscale;
  };

  chart.yscale = function () {
    return yscale;
  };

  chart.curves = function () {
    return curves;
  };

  chart.indtip = function () {
    return indtip;
  };

  chart.svg = function () {
    return svg;
  }; // function to remove chart


  chart.remove = function () {
    svg.remove();
    d3panels.tooltip_dstroy(indtip);
    return null;
  }; // return the chart function


  return chart;
};"use strict";

// Generated by CoffeeScript 2.6.1
// d3-based slider
d3panels.slider = function (chartOpts) {
  var buttoncolor, buttondotcolor, buttondotsize, buttonround, buttonsize, buttonstroke, _chart, height, margin, nticks, rectcolor, rectheight, ref, ref1, ref10, ref11, ref12, ref13, ref14, ref15, ref16, ref2, ref3, ref4, ref5, ref6, ref7, ref8, ref9, slider_svg, stopindex, textsize, tickgap, tickheight, ticks, ticks_at_stops, value, width;

  if (chartOpts == null) {
    chartOpts = {}; // make sure it's defined
  } // chartOpts start


  width = (ref = chartOpts != null ? chartOpts.width : void 0) != null ? ref : 800; // total width of svg for slider

  height = (ref1 = chartOpts != null ? chartOpts.height : void 0) != null ? ref1 : 80; // total height of svg for slider

  margin = (ref2 = chartOpts != null ? chartOpts.margin : void 0) != null ? ref2 : {
    left: 25,
    right: 25,
    inner: 0,
    top: 40,
    bottom: 40 // margins

  };
  rectheight = (ref3 = chartOpts != null ? chartOpts.rectheight : void 0) != null ? ref3 : 10; // height of slider scale

  rectcolor = (ref4 = chartOpts != null ? chartOpts.rectcolor : void 0) != null ? ref4 : "#ccc"; // color of slider scale

  buttonsize = (ref5 = chartOpts != null ? chartOpts.buttonsize : void 0) != null ? ref5 : rectheight * 2; // size of button

  buttoncolor = (ref6 = chartOpts != null ? chartOpts.buttoncolor : void 0) != null ? ref6 : "#eee"; // color of button

  buttonstroke = (ref7 = chartOpts != null ? chartOpts.buttonstroke : void 0) != null ? ref7 : "black"; // color of button border

  buttonround = (ref8 = chartOpts != null ? chartOpts.buttonround : void 0) != null ? ref8 : buttonsize * 0.2; // how much to round the button corners

  buttondotcolor = (ref9 = chartOpts != null ? chartOpts.buttondotcolor : void 0) != null ? ref9 : "slateblue"; // color of dot on button

  buttondotsize = (ref10 = chartOpts != null ? chartOpts.buttondotsize : void 0) != null ? ref10 : buttonsize / 4; // radius of dot on button

  tickheight = (ref11 = chartOpts != null ? chartOpts.tickheight : void 0) != null ? ref11 : 10; // height of ticks

  tickgap = (ref12 = chartOpts != null ? chartOpts.tickgap : void 0) != null ? ref12 : tickheight / 2; // gap below ticks

  textsize = (ref13 = chartOpts != null ? chartOpts.textsize : void 0) != null ? ref13 : 14; // font size for axis labels

  nticks = (ref14 = chartOpts != null ? chartOpts.nticks : void 0) != null ? ref14 : 5; // number of ticks

  ticks = (ref15 = chartOpts != null ? chartOpts.ticks : void 0) != null ? ref15 : null; // vector of ticks

  ticks_at_stops = (ref16 = chartOpts != null ? chartOpts.ticks_at_stops : void 0) != null ? ref16 : true; // if true, include scale (above slider) showing stops
  // chartOpts end
  // accessors start

  value = 0; // current value of slider

  stopindex = 0; // index of currently selected stop value
  // accessors end

  slider_svg = null;

  _chart = function chart(selection, callback, range, stops, initial_value) {
    var button, clamp_pixels, dragged, end_drag, xcscale, xscale; // args that are lists: check that they have all the pieces

    margin = d3panels.check_listarg_v_default(margin, {
      left: 25,
      right: 25,
      inner: 0,
      top: 40,
      bottom: 40
    });
    margin.left += margin.inner;
    margin.right += margin.inner;

    if (range == null) {
      range = [margin.left, width - margin.right];
    }

    if (margin.top != null && margin.top + margin.bottom > 0) {
      margin.top = height * margin.top / (margin.top + margin.bottom);
    } else {
      margin.top = height / 2;
    }

    if (initial_value != null) {
      value = initial_value;

      if (value < range[0]) {
        value = range[0];
      }

      if (value > range[1]) {
        value = range[1];
      }

      if (stops != null) {
        stopindex = d3panels.index_of_nearest(value, stops);
      }

      if (stops != null) {
        value = stops[stopindex]; // choose random values
      }
    } else {
      if (stops != null) {
        stopindex = Math.floor(Math.random() * stops.length);
        value = stops[stopindex];
      } else {
        value = (range[1] - range[0]) * Math.random() + range[0]; // stops included; pick random stop index
      } // initial value provided

    }

    slider_svg = selection.insert("svg").attr("height", height).attr("width", width); // fully continuous x scale

    xcscale = d3.scaleLinear().range([margin.left, width - margin.right]).domain(range).clamp(true); // xscale that handles stop positions

    xscale = function xscale(d) {
      if (stops != null) {
        return xcscale(stops[d3panels.index_of_nearest(d, stops)]);
      }

      return xcscale(d);
    }; // clamp pixels values to range of slider


    clamp_pixels = function clamp_pixels(pixels, interval) {
      if (pixels < interval[0]) {
        return interval[0];
      }

      if (pixels > interval[1]) {
        return interval[1];
      }

      return pixels;
    }; // insert bar


    slider_svg.insert("rect").attr("x", margin.left).attr("y", margin.top - rectheight / 2).attr("rx", rectheight * 0.3).attr("ry", rectheight * 0.3).attr("width", width - margin.left - margin.right).attr("height", rectheight).attr("fill", rectcolor);

    if (ticks == null) {
      // add scale
      ticks = xcscale.ticks(nticks);
    }

    slider_svg.selectAll("empty").data(ticks).enter().insert("line").attr("x1", function (d) {
      return xcscale(d);
    }).attr("x2", function (d) {
      return xcscale(d);
    }).attr("y1", margin.top + rectheight / 2 + tickgap).attr("y2", margin.top + rectheight / 2 + tickgap + tickheight).attr("stroke", "black").attr("shape-rendering", "crispEdges");
    slider_svg.selectAll("empty").data(ticks).enter().insert("text").attr("x", function (d) {
      return xcscale(d);
    }).attr("y", margin.top + rectheight / 2 + tickgap * 2 + tickheight).text(function (d) {
      return d;
    }).style("font-size", textsize).style("dominant-baseline", "hanging").style("text-anchor", "middle").style("pointer-events", "none").style("-webkit-user-select", "none").style("-moz-user-select", "none").style("-ms-user-select", "none"); // add scale for stops?

    if (stops != null && ticks_at_stops) {
      slider_svg.selectAll("empty").data(stops).enter().insert("line").attr("x1", function (d) {
        return xcscale(d);
      }).attr("x2", function (d) {
        return xcscale(d);
      }).attr("y1", margin.top - rectheight / 2 - tickgap).attr("y2", margin.top - rectheight / 2 - tickgap - tickheight).attr("stroke", "black").attr("shape-rendering", "crispEdges");
    } // add button


    button = slider_svg.insert("g").attr("id", "button").attr("transform", "translate(" + xscale(value) + ",0)");
    button.insert("rect").attr("x", -buttonsize / 2).attr("y", margin.top - buttonsize / 2).attr("height", buttonsize).attr("width", buttonsize).attr("rx", buttonround).attr("ry", buttonround).attr("stroke", buttonstroke).attr("stroke-width", 2).attr("fill", buttoncolor);
    button.insert("circle").attr("cx", 0).attr("cy", margin.top).attr("r", buttondotsize).attr("fill", buttondotcolor); // function to deal with dragging

    dragged = function dragged(event, d) {
      var clamped_pixels, pixel_value;
      pixel_value = event.x;
      clamped_pixels = clamp_pixels(pixel_value, [margin.left, width - margin.right]);
      value = xcscale.invert(clamped_pixels);
      d3.select(this).attr("transform", "translate(" + xcscale(value) + ",0)");

      if (stops != null) {
        stopindex = d3panels.index_of_nearest(value, stops);
        value = stops[stopindex];
      }

      if (callback != null) {
        return callback(_chart);
      }
    }; // function at end of dragging:


    end_drag = function end_drag(event, d) {
      var clamped_pixels, pixel_value;
      pixel_value = event.x;
      clamped_pixels = clamp_pixels(pixel_value, [margin.left, width - margin.right]);
      value = xcscale.invert(clamped_pixels);

      if (stops != null) {
        stopindex = d3panels.index_of_nearest(value, stops);
        value = stops[stopindex];
      }

      if (callback != null) {
        callback(_chart);
      }

      return d3.select(this).attr("transform", "translate(" + xcscale(value) + ",0)");
    }; // start the dragging


    button.call(d3.drag().on("drag", dragged).on("end", end_drag));

    if (callback != null) {
      // run the callback at the beginning
      return callback(_chart);
    }
  }; // functions to grab stuff


  _chart.value = function () {
    return value;
  };

  _chart.stopindex = function () {
    return stopindex;
  }; // function to remove the slider


  _chart.remove = function () {
    return slider_svg.remove();
  }; // return the chart function


  return _chart;
};"use strict";

// Generated by CoffeeScript 2.6.1
// a d3-based double-slider (or range slider)
d3panels.double_slider = function (chartOpts) {
  var buttoncolor, buttondotcolor, buttondotsize, buttonround, buttonsize, buttonstroke, _chart, height, margin, nticks, rectcolor, rectheight, ref, ref1, ref10, ref11, ref12, ref13, ref14, ref15, ref16, ref2, ref3, ref4, ref5, ref6, ref7, ref8, ref9, slider_svg, stopindex, textsize, tickgap, tickheight, ticks, ticks_at_stops, value, width;

  if (chartOpts == null) {
    chartOpts = {}; // make sure it's defined
  } // chartOpts start


  width = (ref = chartOpts != null ? chartOpts.width : void 0) != null ? ref : 800; // total width of svg for slider

  height = (ref1 = chartOpts != null ? chartOpts.height : void 0) != null ? ref1 : 80; // total height of svg for slider

  margin = (ref2 = chartOpts != null ? chartOpts.margin : void 0) != null ? ref2 : {
    left: 25,
    right: 25,
    inner: 0,
    top: 40,
    bottom: 40 // margins

  };
  rectheight = (ref3 = chartOpts != null ? chartOpts.rectheight : void 0) != null ? ref3 : 10; // height of slider scale

  rectcolor = (ref4 = chartOpts != null ? chartOpts.rectcolor : void 0) != null ? ref4 : "#ccc"; // color of slider scale

  buttonsize = (ref5 = chartOpts != null ? chartOpts.buttonsize : void 0) != null ? ref5 : rectheight * 2; // size of buttons

  buttoncolor = (ref6 = chartOpts != null ? chartOpts.buttoncolor : void 0) != null ? ref6 : "#eee"; // color of buttons (can be vector of length 2)

  buttonstroke = (ref7 = chartOpts != null ? chartOpts.buttonstroke : void 0) != null ? ref7 : "black"; // color of button borders (can be vector of length 2)

  buttonround = (ref8 = chartOpts != null ? chartOpts.buttonround : void 0) != null ? ref8 : buttonsize * 0.2; // how much to round the button corners

  buttondotcolor = (ref9 = chartOpts != null ? chartOpts.buttondotcolor : void 0) != null ? ref9 : ["slateblue", "orchid" // color of dot on buttons (can be vector of length 2)
  ];
  buttondotsize = (ref10 = chartOpts != null ? chartOpts.buttondotsize : void 0) != null ? ref10 : buttonsize / 4; // radius of dot on button

  tickheight = (ref11 = chartOpts != null ? chartOpts.tickheight : void 0) != null ? ref11 : 10; // height of ticks

  tickgap = (ref12 = chartOpts != null ? chartOpts.tickgap : void 0) != null ? ref12 : tickheight / 2; // gap below ticks

  textsize = (ref13 = chartOpts != null ? chartOpts.textsize : void 0) != null ? ref13 : 14; // font size for axis labels

  nticks = (ref14 = chartOpts != null ? chartOpts.nticks : void 0) != null ? ref14 : 5; // number of ticks

  ticks = (ref15 = chartOpts != null ? chartOpts.ticks : void 0) != null ? ref15 : null; // vector of ticks

  ticks_at_stops = (ref16 = chartOpts != null ? chartOpts.ticks_at_stops : void 0) != null ? ref16 : true; // if true, include scale (above slider) showing stops
  // chartOpts end
  // accessors start

  value = [0, 0 // current values of slider buttons
  ];
  stopindex = [0, 0 // indexes of currently selected stop values for buttons
  ]; // accessors end

  slider_svg = null;

  if (!Array.isArray(buttoncolor)) {
    buttoncolor = [buttoncolor, buttoncolor];
  }

  if (!Array.isArray(buttonstroke)) {
    buttonstroke = [buttonstroke, buttonstroke];
  }

  if (!Array.isArray(buttondotcolor)) {
    buttondotcolor = [buttondotcolor, buttondotcolor];
  }

  _chart = function chart(selection, callback1, callback2, range, stops, initial_value) {
    var buttons, callbacks, clamp_pixels, dragged, end_drag, start_drag, xcscale, xscale; // args that are lists: check that they have all the pieces

    margin = d3panels.check_listarg_v_default(margin, {
      left: 25,
      right: 25,
      inner: 0,
      top: 40,
      bottom: 40
    });
    callbacks = [callback1, callback2];
    margin.left += margin.inner;
    margin.right += margin.inner;

    if (range == null) {
      range = [margin.left, width - margin.right];
    }

    if (margin.top != null && margin.top + margin.bottom > 0) {
      margin.top = height * margin.top / (margin.top + margin.bottom);
    } else {
      margin.top = height / 2;
    }

    if (initial_value != null) {
      value = initial_value.map(function (d) {
        if (d < range[0]) {
          return range[0];
        }

        if (d > range[1]) {
          return range[1];
        }

        return d;
      });

      if (stops != null) {
        stopindex = value.map(function (d) {
          return d3panels.index_of_nearest(d, stops);
        });
      }

      if (stops != null) {
        value = stopindex.map(function (i) {
          return stops[i];
        }); // pick random values
      }
    } else {
      if (stops != null) {
        stopindex = [0, 1].map(function (i) {
          return Math.floor(Math.random() * stops.length);
        });
        value = stopindex.map(function (i) {
          return stops[i];
        });
      } else {
        value = [0, 1].map(function (i) {
          return (range[1] - range[0]) * Math.random() + range[0];
        }); // stops included; pick random stop index
      } // initial value provided

    }

    slider_svg = selection.insert("svg").attr("height", height).attr("width", width); // fully continuous x scale

    xcscale = d3.scaleLinear().range([margin.left, width - margin.right]).domain(range).clamp(true); // xscale that handles stop positions

    xscale = function xscale(d) {
      if (stops != null) {
        return xcscale(stops[d3panels.index_of_nearest(d, stops)]);
      }

      return xcscale(d);
    }; // clamp pixels values to range of slider


    clamp_pixels = function clamp_pixels(pixels, interval) {
      if (pixels < interval[0]) {
        return interval[0];
      }

      if (pixels > interval[1]) {
        return interval[1];
      }

      return pixels;
    }; // insert bar


    slider_svg.insert("rect").attr("x", margin.left).attr("y", margin.top - rectheight / 2).attr("rx", rectheight * 0.3).attr("ry", rectheight * 0.3).attr("width", width - margin.left - margin.right).attr("height", rectheight).attr("fill", rectcolor);

    if (ticks == null) {
      // add scale
      ticks = xcscale.ticks(nticks);
    }

    slider_svg.selectAll("empty").data(ticks).enter().insert("line").attr("x1", function (d) {
      return xcscale(d);
    }).attr("x2", function (d) {
      return xcscale(d);
    }).attr("y1", margin.top + rectheight / 2 + tickgap).attr("y2", margin.top + rectheight / 2 + tickgap + tickheight).attr("stroke", "black").attr("shape-rendering", "crispEdges");
    slider_svg.selectAll("empty").data(ticks).enter().insert("text").attr("x", function (d) {
      return xcscale(d);
    }).attr("y", margin.top + rectheight / 2 + tickgap * 2 + tickheight).text(function (d) {
      return d;
    }).style("font-size", textsize).style("dominant-baseline", "hanging").style("text-anchor", "middle").style("pointer-events", "none").style("-webkit-user-select", "none").style("-moz-user-select", "none").style("-ms-user-select", "none"); // add scale for stops?

    if (stops != null && ticks_at_stops) {
      slider_svg.selectAll("empty").data(stops).enter().insert("line").attr("x1", function (d) {
        return xcscale(d);
      }).attr("x2", function (d) {
        return xcscale(d);
      }).attr("y1", margin.top - rectheight / 2 - tickgap).attr("y2", margin.top - rectheight / 2 - tickgap - tickheight).attr("stroke", "black").attr("shape-rendering", "crispEdges");
    } // add buttons


    buttons = [0, 1].map(function (i) {
      return slider_svg.insert("g").attr("id", "button" + (i + 1)).attr("transform", function (d) {
        return "translate(" + xscale(value[i]) + ",0)";
      });
    });
    [0, 1].map(function (i) {
      buttons[i].insert("rect").attr("x", -buttonsize / 2).attr("y", margin.top - buttonsize / 2).attr("height", buttonsize).attr("width", buttonsize).attr("rx", buttonround).attr("ry", buttonround).attr("stroke", buttonstroke[i]).attr("stroke-width", 2).attr("fill", buttoncolor[i]);
      return buttons[i].insert("circle").attr("cx", 0).attr("cy", margin.top).attr("r", buttondotsize).attr("fill", buttondotcolor[i]);
    }); // at click, move to front

    start_drag = function start_drag(i) {
      return function (d) {
        return buttons[i].raise();
      };
    }; // function to deal with dragging


    dragged = function dragged(i) {
      return function (event, d) {
        var clamped_pixels, pixel_value;
        pixel_value = event.x;
        clamped_pixels = clamp_pixels(pixel_value, [margin.left, width - margin.right]);
        value[i] = xcscale.invert(clamped_pixels);
        d3.select(this).attr("transform", "translate(" + xcscale(value[i]) + ",0)");

        if (stops != null) {
          stopindex[i] = d3panels.index_of_nearest(value[i], stops);
          value[i] = stops[stopindex[i]];
        }

        if (callbacks[i] != null) {
          return callbacks[i](_chart);
        }
      };
    }; // function at end of dragging:


    end_drag = function end_drag(i) {
      return function (event, d) {
        var clamped_pixels, pixel_value;
        pixel_value = event.x;
        clamped_pixels = clamp_pixels(pixel_value, [margin.left, width - margin.right]);
        value[i] = xcscale.invert(clamped_pixels);

        if (stops != null) {
          stopindex[i] = d3panels.index_of_nearest(value[i], stops);
          value[i] = stops[stopindex[i]];
        }

        if (callbacks[i] != null) {
          callbacks[i](_chart);
        }

        return d3.select(this).attr("transform", "translate(" + xcscale(value[i]) + ",0)");
      };
    }; // start the dragging


    return [0, 1].map(function (i) {
      buttons[i].call(d3.drag().on("start", start_drag(i)).on("drag", dragged(i)).on("end", end_drag(i)));

      if (callbacks[i] != null) {
        // run the callback at the beginning
        return callbacks[i](_chart);
      }
    });
  }; // functions to grab stuff


  _chart.value = function () {
    return value;
  };

  _chart.stopindex = function () {
    return stopindex;
  }; // function to remove the slider


  _chart.remove = function () {
    return slider_svg.remove();
  }; // return the chart function


  return _chart;
};"use strict";

// Generated by CoffeeScript 2.6.1
// tool tips
d3panels.tooltip_create = function (selection, objects, options, tooltip_func) {
  var direction, fill, fontcolor, fontsize, in_duration, out_duration, pad, ref, ref1, ref2, ref3, ref4, tipclass, tipdiv, tipgroup, triChar, tridiv;
  tipclass = (ref = options != null ? options.tipclass : void 0) != null ? ref : "d3panels-tooltip";
  direction = (ref1 = options != null ? options.direction : void 0) != null ? ref1 : "east";
  out_duration = (ref2 = options != null ? options.out_duration : void 0) != null ? ref2 : 1000;
  in_duration = (ref3 = options != null ? options.in_duration : void 0) != null ? ref3 : 0;
  pad = (ref4 = options != null ? options.pad : void 0) != null ? ref4 : 8;
  fill = options != null ? options.fill : void 0;
  fontcolor = options != null ? options.fontcolor : void 0;
  fontsize = options != null ? options.fontsize : void 0;
  tipgroup = selection.append("g").attr("class", "d3panels-tooltip " + tipclass).style("opacity", 0).datum({
    direction: direction,
    pad: pad
  });
  tipdiv = tipgroup.append("div").attr("class", "d3panels-tooltip " + tipclass);

  if (direction === "east") {
    triChar = "\u25C0"; // triangle pointing left
  } else if (direction === "west") {
    triChar = "\u25B6"; // triangle pointing right
  } else if (direction === "north") {
    triChar = "\u25BC"; // triangle pointing down
  } else if (direction === "south") {
    triChar = "\u25B2"; // triangle pointing up
  } else {
    d3panels.displayError("tooltip_create: invalid direction (" + direction + ")");
  }

  tridiv = tipgroup.append("div").attr("class", "d3panels-tooltip-tri " + tipclass).html(triChar);

  if (fill != null) {
    tipdiv.style("background", fill);
  }

  if (fontcolor != null) {
    tipdiv.style("color", fontcolor);
  }

  if (fontsize != null) {
    tipdiv.style("font-size", fontsize + "px");
  }

  if (fill != null) {
    tridiv.style("color", fill);
  }

  if (fontsize != null) {
    tridiv.style("font-size", fontsize + "px");
  }

  objects.on("mouseover." + tipclass, function (event, d) {
    var i, mouseX, mouseY;
    i = objects.nodes().indexOf(this); // mouse position; make sure these are numbers

    mouseX = event.pageX * 1.0;
    mouseY = event.pageY * 1.0;
    tipdiv.html(tooltip_func(d, i));
    d3panels.tooltip_move(tipgroup, mouseX, mouseY);
    return d3panels.tooltip_show(tipgroup, in_duration);
  });
  objects.on("mouseout." + tipclass, function (d) {
    return d3panels.tooltip_hide(tipgroup, out_duration);
  });
  return tipgroup;
};

d3panels.tooltip_move = function (tipgroup, x, y) {
  var direction, divpad, fontsize, pad, posX, posY, shiftX, shiftY, tipbox_height, tipbox_width, tipdiv, triX, triY, tridiv;
  tipdiv = tipgroup.select("div.d3panels-tooltip");
  tridiv = tipgroup.select("div.d3panels-tooltip-tri");
  tipbox_height = tipdiv.node().getBoundingClientRect().height * 1.0;
  tipbox_width = tipdiv.node().getBoundingClientRect().width * 1.0; // make sure we have the font size

  fontsize = tridiv.style("font-size").replace("px", "") * 1.0;
  pad = tipgroup.datum().pad * 1.0 + fontsize;
  direction = tipgroup.datum().direction;
  shiftX = shiftY = 0; // <- for triangle, relative to tool tip box

  if (direction === "east") {
    posX = x + pad;
    posY = y - tipbox_height / 2.0;
    divpad = tipdiv.style("padding-left").replace("px", "") * 1.0;
    shiftX = -fontsize - divpad;
    shiftY = tipbox_height / 2.0 - fontsize / 2.0;
  } else if (direction === "west") {
    posX = x - tipbox_width * 1.0 - pad;
    posY = y - tipbox_height / 2.0;
    divpad = tipdiv.style("padding-right").replace("px", "") * 1.0;
    shiftX = tipbox_width - fontsize + divpad;
    shiftY = tipbox_height / 2.0 - fontsize / 2.0;
  } else if (direction === "north") {
    posX = x - tipbox_width / 2.0;
    posY = y - tipbox_height - pad;
    divpad = tipdiv.style("padding-bottom").replace("px", "") * 1.0;
    shiftX = tipbox_width / 2.0 - fontsize;
    shiftY = tipbox_height + divpad / 2.0 - fontsize / 2.0;
  } else if (direction === "south") {
    posX = x - tipbox_width / 2.0;
    posY = y + pad;
    divpad = tipdiv.style("padding-top").replace("px", "") * 1.0;
    shiftX = +tipbox_width / 2.0 - fontsize;
    shiftY = -fontsize;
  }

  tipdiv.style("left", posX + "px").style("top", posY + "px");
  triX = posX + shiftX;
  triY = posY + shiftY;
  return tridiv.style("left", triX + "px").style("top", triY + "px").style("width", tipbox_width).style("height", tipbox_height);
};

d3panels.tooltip_text = function (tipgroup, text) {
  return tipgroup.select("div.d3panels-tooltip").html(text);
};

d3panels.tooltip_show = function (tipgroup, duration) {
  return tipgroup.transition().duration(duration).style("opacity", 1);
};

d3panels.tooltip_hide = function (tipgroup, duration) {
  return tipgroup.transition().duration(duration).style("opacity", 0);
};

d3panels.tooltip_destroy = function (tipgroup) {
  return tipgroup.remove();
};    if (typeof define === "function" && define.amd) this.d3panels = d3panels, define(d3panels); else if (typeof module === "object" && module.exports) module.exports = d3panels; else this.d3panels = d3panels;

}(); // bottom of d3panels encapsulation