plotRates: Plot RRphylo rates at a specified node

In RRphylo: Phylogenetic Ridge Regression Methods for Comparative Studies

Plot RRphylo rates at a specified node

Description

This function generates customized functions to produce histograms and lollipop charts of the RRphylo rates computed for a given clade as compared to the rates computed for the rest of the tree.

Usage

plotRates(RR,node)

Arguments

RR	an object produced by RRphylo.
node	the node subtending the clade of interest.

Value

The function returns a list of functions:

$plotHist returns the histograms of rates (in ln absolute values) computed for the focal clade against rates computed the rest of the tree. The usage is: ...$plotHist(hist.args=list(col1,col2),legend.args=list()), where legend.args is a list of additional arguments passed to the function legend (if = NULL the legend is not plotted) and hist.args is a list of further arguments passed to the function plot.histogram. hist.args default arguments include histogram colors for background rates (col1) and rates of the clade under inspection (col2).

$plotLollipop returns the lollipop chart of the rates of individual branches of the focal clade collated in increasing rate value, and contrasted to the average rate computed over the rest of the tree branches (the vertical line). The usage is: ...$plotLollipop(lollipop.args=NULL,line.args=NULL), where lollipop.args is a list of further arguments passed to the function lollipoPlot and line.args is a list of additional arguments passed to the function line. This function additionally returns the vector of rates for the focal clade, collated in increasing order.

Author(s)

Silvia Castiglione, Pasquale Raia

See Also

RRphylo vignette

plotRates vignette

RRphylo vignette

plotRates vignette

Examples

data("DataApes")
DataApes$PCstage->PCstage
DataApes$Tstage->Tstage
cc<- 2/parallel::detectCores()

RRphylo(tree=Tstage,y=PCstage,clus=cc)->RRstage

plotRates(RRstage,node=72)->pR
pR$plotHist(hist.args=list(col1="cyan1",col2="blue"),legend.args=list(x="topright"))
pR$plotLollipop(lollipop.args=list(col="chartreuse",bg="chartreuse"),
                line.args=list(col="deeppink",lwd=2))

RRphylo documentation built on Aug. 8, 2025, 6:37 p.m.