#' Plots the results of a multi-tree Pagel correlation analysis.
#'
#' This function plots the results of a multi-tree Pagel correlation analysis created with pagel_multi. Depends on reshape2 and ggplot2.
#' @param pagel The results of pagel_multi.
#' @param what Select which parameter to plot. Options = "lik", "pvalue". Default = "pvalue"
#' @examples
#' plot(pagels, what="lik")
plot.pagel <- function(pagels, what="", ...) {
library(reshape2)
library(ggplot2)
if (class(pagels) != "pagel") {
cat("Object has to be of class \"pagel\" to plot.\n")
return
}
if (what == "lik") {
df <- data.frame(pagels$loglik_inds,pagels$loglik_deps)
df <- melt(df)
df$tree <- seq(1:length(pagels$loglik_inds))
names(df) <- c("model","loglik","tree")
p <- ggplot(df, aes(tree,loglik))
p + geom_point(aes(colour=factor(model)), size=3)
}
else {
l <- melt(pagels$p_values)
ggplot(l) + geom_histogram(aes(x=value),breaks=seq(0, 1, by=0.02), ...) + scale_y_continuous(name="count")+ scale_x_continuous(name="p-value")+ geom_vline(xintercept = 0.05, color="red")
}
}
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