plotContrasts: Function for plotting contrast values

In arborworkflows/aRbor: An R package with useful functions for Arbor workflows

Description

Function for plotting contrast values

Usage

plotContrasts(
  tree,
  dat,
  cex.tip.label = 0.5,
  label.offset = 0.02,
  legend = TRUE,
  cex.scale = c(1, 1),
  transparency.scale = c(255, 255),
  palette = rainbow,
  quantiles = c(0, 0.025, 0.25, 0.5, 0.75, 0.975, 1),
  colors.per.quantile = 100,
  pts = TRUE,
  ...
)

Arguments

tree	A tree of class 'phylo'
dat	A named vector of continuous phenotypic data
cex.tip.label	The character expansion factor for tip labels
label.offset	The relative amount the tip labels are offset from the tips of the tree
legend	Show legend or not?
cex.scale	Scale points
transparency.scale	Control transparency
palette	Set color pallette
quantiles	Quantiles for coloring
colors.per.quantile	Number of colors per quantile
pts	Add points on nodes?
...	Additional arguments passed to plot.phylo

Details

Phylogenetic independent contrasts are calculated at each node and plotted on the phylogeny, the value of of the absolute contrast is converted to a color scale. In addition, the relationship between node age and contrast value is plotted and a linear fit to the relationship between absolute contrast and the age of the node (The node-height test). Under BM the relationship should be 0.

arborworkflows/aRbor documentation built on June 11, 2020, 7:44 p.m.