plotRates: Plot RRphylo rates at a specified node
In pasraia/RRphylo: Phylogenetic Ridge Regression Methods for Comparative Studies

Description Usage Arguments Value See Also Examples

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

1	plotRates(RR,node,export.tiff =FALSE,foldername=NULL,filename=NULL)

`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`	has been deprecated; please see the argument `filename` instead.
`filename`	a character indicating the name of the tiff file and the path where it is to be saved. If no path is indicated the file is stored in the working directory.

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.

RRphylo vignette

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

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

plotRates(RR,node=72,export.tiff = FALSE)