RRphylo: plotRates – R documentation

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plotRates

Plot RRphylo rates at a specified node

Description

The function plotRates plots the RRphylo rates computed for a given clade as compared to the rates computed for the rest of the tree.

Usage

plotRates(RR,node,export.tiff =TRUE,foldername)

Arguments

`RR`	an object produced by `RRphylo`.
`node`	the node subtending the clade of interest.
`export.tiff`	if `TRUE` the function save a "rate_bars.tiff" file inside the working directory. It is `TRUE` by default.
`foldername`	the path of the folder where plots are to be found.

Value

The function produces two barplots. On the left side, the rates (in absolute values) computed for the focal clade (blue) are plotted against the rates of the rest of the tree (green). On the right side, the absolute rates of individual branches of the focal clade are collated in increasing rate value (blue bars), and contrasted to the average rate computed over the rest of the tree branches (the vertical red line). It also returns the rate values for both nodes and species descending from the focal node.

Examples

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

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

plotRates(RR,node=72,foldername=tempdir(),export.tiff = TRUE)

RRphylo

Phylogenetic Ridge Regression Methods for Comparative Studies

v2.5.0

GPL-2

Authors

Pasquale Raia, Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Mirko Di Febbraro, Antonio Profico, Francesco Carotenuto

Initial release

2020-12-03