plot.l1ou: Visualizes a shift configuration: tree and trait(s)

In khabbazian/l1ou: Tools for detecting past changes in the expected mean trait values and studying trait evolution from comparative data

Visualizes a shift configuration: tree and trait(s)

Description

Plots the tree annotated to show the edges with a shift, and the associated trait data side by side. Each trait is shown standardized, to visually highlight the species with low, average or high values. In other words, the axis scale shows the values of (trait - m)/sd where m is the observed trait mean and sd is the observed trait standard deviation. The values on the left and right side of the axis are the mininum and maximum of the standardized trait: (min-m)/sd and (max-m)/sd. The place where the bars start corresponds to the mean of the original trait values.

Usage

## S3 method for class 'l1ou'
plot(model, palette = NA, edge.shift.ann = TRUE,
  edge.shift.adj = c(0.5, -0.025), edge.label = c(), asterisk = TRUE,
  edge.label.ann = FALSE, edge.label.adj = c(0.5, 1), edge.label.pos = NA,
  edge.ann.cex = 1, plot.bar = TRUE, bar.axis = TRUE, ...)

Arguments

model	object of class l1ou returned by estimate_shift_configuration.
palette	vector of colors, of size the number of shifts plus one. The last element is the color for the background regime (regime at the root).
edge.shift.ann	logical. If TRUE, annotates edges by shift values.
edge.shift.adj	adjustment argument to give to edgelabel() for labeling edges by shift values.
edge.label	vector of size number of edges.
asterisk	logical. If TRUE, the shift positions will be annotated by "*". It is useful for gray scale plots.
edge.label.ann	logical. If TRUE, annotates edges by labels in tree$edge.label, if non-empty, or edge.label.
edge.label.adj	adjustment argument to give to edgelabel() for labeling edges.
edge.label.pos	relative position of the edge.label on the edge. 0 for the beginning of the edge and 1 for the end of the edge.
edge.ann.cex	amount by which the annotation text should be magnified relative to the default.
plot.bar	logical. If TRUE, the bars corresponding to the trait values will be plotted.
bar.axis	logical. If TRUE, the axis of of trait(s) range will be plotted.
...	further arguments to be passed on to plot.phylo.

Value

none.

Examples

data(lizard.traits, lizard.tree)
Y <- lizard.traits[,1]
eModel <- estimate_shift_configuration(lizard.tree, Y)
nEdges <- Nedge(lizard.tree)
ew <- rep(1,nEdges) 
ew[eModel$shift.configuration] <- 3
plot(eModel, cex=0.5, label.offset=0.02, edge.width=ew)

khabbazian/l1ou documentation built on Aug. 10, 2022, 7:41 p.m.