treePlotRers: Plot a cladogram with RERs shown as either labels...

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

Plot a cladogram with RERs shown as either labels (type="label") or a color heatmap along the branches (type="color") Wraps around returnRersAsTree or treePlotNew, respectively

Description

Plot a cladogram with RERs shown as either labels (type="label") or a color heatmap along the branches (type="color") Wraps around returnRersAsTree or treePlotNew, respectively

Usage

treePlotRers(
  treesObj,
  rermat = NULL,
  index = NULL,
  type = c("label", "color"),
  phenv = NULL,
  figwid = 10,
  ...
)

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
type.	Whether to display RERs as branch labels ('label') or a heatmap ('color')
phenv.	A phenotype vector returned by tree2Paths or foreground2Paths
....	Additional parameters to be passed to returnRersAsTree or treePlotNew #' @param figwid. Adjust x limits of plot.phylo by 1/figwid. May be related to figure width (requires some optimization)

Value

Plots a cladogram of the master tree with RERs displayed as branch labels or colors

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