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plot_dadi_expansion.Rmd
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plot_dadi_expansion.Rmd
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---
title: "Expansion results"
author: "Abigail Shockey"
date: "September 12, 2016"
output: html_document
---
```{r, echo = FALSE, message = FALSE, warning = FALSE}
#log scale nu, separate plots for tau
library(ggplot2)
library(reshape2)
library(cowplot)
library(akima)
library(dplyr)
ll <- data.frame(a=rep(NA, times = 100))
```
### SFS
```{r, echo = FALSE, message = FALSE, warning = FALSE, fig.width = 18, fig.height = 18}
if (file.exists("observedSFS.txt") && file.exists("neutralModelSFS.txt")) {
observed_SFS <- read.table("observedSFS.txt")
neutral_SFS <- read.table("neutralModelSFS.txt")
expansion_SFS <- rbind(data.frame(Model="Observed",
Count=observed_SFS$V1,
Frequency=as.numeric(row.names(observed_SFS))),
data.frame(Model="Neutral",
Count= neutral_SFS$V1,
Frequency=as.numeric(row.names(observed_SFS))))
}
if (file.exists("expansionModelSFS.txt")) {
model <- read.table("expansionModelSFS.txt")
expansion_SFS <- rbind(data.frame(Model = expansion_SFS$Model,
Count=expansion_SFS$Count,
Frequency=expansion_SFS$Frequency),
data.frame(Model = "Expansion",
Count = model$V1,
Frequency=as.numeric(row.names(model))))
ggplot(expansion_SFS, aes(x=Frequency, y=Count, fill=Model)) +
geom_bar(stat="identity", position="dodge", show.legend = TRUE) +
scale_fill_brewer(palette="Paired") +
theme_bw() +
theme(text = element_text(size=22),
axis.text.x = element_text(angle=90, vjust=1),
axis.line = element_line(colour = "black"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
# panel.border = element_blank(),
panel.background = element_blank())
}
```
### Parameter Values
```{r, echo = FALSE, message = FALSE, warning = FALSE}
if (file.exists("dadi_expansionModel.txt")) {
expansion_params <- read.table("dadi_expansionModel.txt", header = TRUE)
expansion_params <- setNames(expansion_params, c("v","t","LL"))
params_df <- melt(expansion_params[,1:2], variable.name = "Parameter", value.name = "Value")
expansion.nu.plot <- ggplot(data = params_df[1:100,], aes(x=Parameter, y=Value)) + geom_boxplot() +
xlab("") +
theme(text = element_text(size=16),
axis.text.x = element_text(angle=90, vjust=1, size = 16))
expansion.tau.plot <- ggplot(data = params_df[101:200,], aes(x=Parameter, y=Value)) + geom_boxplot() +
xlab("") +
theme(text = element_text(size=16),
axis.text.x = element_text(angle=90, vjust=1, size = 16))
plot_grid(expansion.nu.plot, expansion.tau.plot, align = "h")
}
if (file.exists("dadi_expansionModel.txt")) {
expansion_params <- read.table("dadi_expansionModel.txt", header = TRUE)
summary(expansion_params)
max.nu <- max(expansion_params$nu)
max.tau <- max(expansion_params$tau)
}
```
### Parameter correlation
```{r, echo = FALSE, message = FALSE, warning = FALSE}
if (file.exists("dadi_expansionModel.txt")){
expansion_params <- read.table("dadi_expansionModel.txt", header = TRUE)
expansion_params <- setNames(expansion_params, c("v","t","LL"))
dat <- cor(as.matrix(expansion_params[,c("v","t", "LL")]), use = "pairwise.complete.obs", method = "pearson")
dat.m = melt(dat)
ggplot(dat.m, aes(x=Var2,y=Var1)) +
geom_tile(aes(fill= value)) +
geom_text(aes(fill = value, label = round(value, 2)), size=6) +
xlab(NULL) + ylab(NULL) +
scale_fill_gradient2(high="#b8b8b8", mid="white", low="#b8b8b8", midpoint=0, limits =c(-1,1)) +
theme_bw() +
theme(text = element_text(size=16),
axis.ticks=element_blank(),
panel.background=element_blank(),
panel.border=element_blank(),
panel.grid.major= element_blank(),
#axis.text.x = element_blank(),
#axis.text.y = element_blank(),
panel.grid.minor= element_blank())
}
```
### Likelihood surface
```{r, echo = FALSE, message = FALSE, warning = FALSE, fig.width = 18, fig.height = 18}
if (file.exists("likelihood_grid_expansion.txt")) {
param_grid_dadi <- read.table("likelihood_grid_expansion.txt", header=TRUE)
interpdf <-interp2xyz(interp(x=param_grid_dadi$nu, y=param_grid_dadi$T, z=param_grid_dadi$LL, duplicate="mean"), data.frame=TRUE)
interpdf %>%
filter(!is.na(z)) %>%
tbl_df() %>%
ggplot(aes(x = x, y = y, z = z, fill = z)) +
geom_tile() +
stat_contour(colour = "black", bins = 500) +
scale_fill_gradient(low="dark green", high="white") +
theme_bw()
}
```
### AIC
```{r, echo = FALSE, message = FALSE, warning = FALSE}
if (file.exists("dadi_expansionModel.txt")){
expansion_params <- read.table("dadi_expansionModel.txt", header = TRUE)
expansion_params <- setNames(expansion_params, c("v","t","LL"))
Expansion <- expansion_params$LL
ll <- cbind(ll, Expansion)
avg_expansion_ll <- median(expansion_params$LL)
cat("Average LL: ", avg_expansion_ll, "\n")
avg_expansion_AIC <- 2 * 2 - 2 * avg_expansion_ll
cat("Average AIC: ", avg_expansion_AIC, "\n")
max_expansion_ll <- max(expansion_params$LL)
cat("Max LL: ", max_expansion_ll, "\n")
max_expansion_AIC <- 2 * 2 - 2 * max_expansion_ll
cat("Max AIC: ", max_expansion_AIC, "\n")
max_expansion_ll_idx <- which(expansion_params$LL == max_expansion_ll)
max_expansion_nu <- expansion_params$v[max_expansion_ll_idx]
cat("v: ", max_expansion_nu, "\n")
max_expansion_tau <- expansion_params$t[max_expansion_ll_idx]
cat("t: ", max_expansion_tau, "\n")
}
```
## LL
```{r, echo = FALSE, message = FALSE, warning = FALSE}
ll$a <- NULL
ggplot(data = melt(ll, variable.name = "Model", value.name = "LL"), aes(x = Model, y = LL)) + geom_boxplot(aes(color = Model)) + theme(text = element_text(size=16))