returnRersAsTree: Produce a gene tree with branch lengths representing RERs and...

In nclark-lab/RERconverge: Analysis of Convergence Between Organismal Traits and DNA/Protein Sequences

Produce a gene tree with branch lengths representing RERs and (optionally) display these RERs as branch labels

Description

Produce a gene tree with branch lengths representing RERs and (optionally) display these RERs as branch labels

Usage

returnRersAsTree(
  treesObj,
  rermat,
  index,
  phenv = NULL,
  rer.cex = 0.7,
  tip.cex = 0.7,
  nalab = "NA",
  plot = T
)

Arguments

treesObj.	A treesObj created by readTrees
rermat.	A residual matrix, output of the getAllResiduals() function
index.	A character denoting the name of gene, or a numeric value corresponding to the gene's row index in the residuals matrix
phenv.	A phenotype vector returned by tree2Paths or foreground2Paths
rer.cex.	Numeric expansion for RER labels
tip.cex.	Numeric expansion for tip labels
nalab.	Label given to any NA RERs
plot.	Whether to produce a plot displaying the RERs on the gene tree

Value

An object of class "phylo" with edge lengths representing RERs for the given gene

If plot = TRUE, also displays a plot of the gene tree with edges labeled with RERs

nclark-lab/RERconverge documentation built on March 2, 2024, 8:51 a.m.