plotRers: Plot the residuals reflecting the relative evolutionary rates...

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

Plot the residuals reflecting the relative evolutionary rates (RERs) of a gene across species present in the gene tree

Description

Plot the residuals reflecting the relative evolutionary rates (RERs) of a gene across species present in the gene tree

Usage

plotRers(
  rermat = NULL,
  index = NULL,
  phenv = NULL,
  rers = NULL,
  species_from = NULL,
  species_to = NULL,
  method = "k",
  xlims = NULL,
  plot = 1,
  xextend = 0.2,
  sortrers = F
)

Arguments

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
species_from/species_to.	Name translations: two vectors of equal length with corresponding elements. The function will translate any occurrence of species_from[n] to species_to[n] (if applicable).

Value

A plot of the RERs with foreground species labelled in red, and the rest in blue

nclark-lab/RERconverge documentation built on June 9, 2025, 6:02 a.m.