October 2019
Intermediate to advanced
316 pages
9h 45m
English
Content preview from R Bioinformatics Cookbook
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How to do it...
Quantifying differences between trees with treespace can be executed using the following steps:
- Load the libraries:
library(ape)library(adegraphics)library(treespace)
- Load all the tree files into a multiPhylo object:
treefiles <- list.files(file.path(getwd(), "datasets", "ch4", "gene_trees"), full.names = TRUE) tree_list <- lapply(treefiles, read.tree) class(tree_list) <- "multiPhylo"
- Compute the Kendall-Colijn distances:
comparisons <- treespace(tree_list, nf = 3)
- Plot pairwise distances:
adegraphics::table.image(comparisons$D, nclass=25)
- Plot principal component analysis (PCA) and clusters:
plotGroves(comparisons$pco, lab.show=TRUE, lab.cex=1.5) groves <- findGroves(comparisons, nclust = 4) plotGroves(groves)
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