plot.partitions: plot objects of class partitions

In sebastianduchene/ClockstaR: ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis

Description

This function plots the results from the gap statistic from package cluster, and a matrix with colours for the partition assignments.

Usage

plot.partitions(partitions.object, save.plot = F, file.name = "results_clockstar")

Arguments

partitions.object	An object of class 'partitions', obtained with partitions.bsd
save.plot	logical. Select T to save the plots to a pdf file, or F to print in two new graphics devices.
file.name	A character. If save.plot == T, the name of the file to print the results.

Author(s)

Sebastian Duchene

Examples

# Create a list of trees of class multiPhylo with four patterns of among-lineage rate variation 
tr.fix <- rtree(10)

set.seed(12345)
rates1 <- abs(rnorm(18, sd = 0.1))
set.seed(123456)
rates2 <- abs(rnorm(18, sd = 0.1))
set.seed(1234567)
rates3 <- abs(rnorm(18, sd = 0.1))
set.seed(12345678)
rates4 <- abs(rnorm(18, sd = 0.1))

trees.list <- list()

for(i in 1:20){
      trees.list[[i]] <- tr.fix
      if(i <= 5){
      	   trees.list[[i]]$edge.length <- abs(rates1 + rnorm(18, 0, 0.01)) 
      }else if(i > 5 && i <= 10){
      	    trees.list[[i]]$edge.length <- abs(rates2 + rnorm(18, 0, 0.01)) 
      }else if(i >= 10 && i < 15){
      	    trees.list[[i]]$edge.length <- abs(rates3 + rnorm(18, 0, 0.01))  
      }else{
	    trees.list[[i]]$edge.length <- abs(rates4 + rnorm(18, 0, 0.01)) 
      }
}

names(trees.list) <- paste0("tree", 1:20)
class(trees.list) <- "multiPhylo"

# Estimate sBSDmin distance for all pairs of trees:
trees.bsd <- bsd.matrix(trees.list)

# Find the optimal number of partitions:
partitions.object <- partitions(trees.bsd)

# plot partitions in two graphics devices
plot(partitions.object)






## The function is currently defined as
function (partitions.object, save.plot = F, file.name = "results_clockstar") 
{
    image(t(partitions.object$parts.mat), col = sample(rainbow(ncol(partitions.object$parts.mat))), 
        axes = F, ylab = "Data subset", main = "Partitioning scheme for values of k")
  mtext(text = gsub('([.]([a-z]|[A-Z])+)$', '', rownames(partitions.object$parts.mat)), side = 2, line = 0.3, at = seq(0, 1, 1/(nrow(partitions.object$parts.mat) - 1)), las = 1, cex = 0.6)
    mtext(text = colnames(partitions.object$parts.mat), side = 3, 
        line = 0.3, at = seq(0, 1, 1/(ncol(partitions.object$parts.mat) - 
            1)), las = 1, cex = 0.6)
    if (save.plot) {
        dev.copy2pdf(file = paste0(file.name, "_matrix.pdf"))
    }
    dev.new()
    plot(partitions.object$clusterdata)
    if (save.plot) {
        dev.copy2pdf(file = paste0(file.name, "_gapstats.pdf"))
        sapply(dev.list(), function(x) dev.off(x))
    }
  }

sebastianduchene/ClockstaR documentation built on May 29, 2019, 4:57 p.m.