plotRates function

Plot RRphylo rates at a specified node

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.

plotRates(RR,node)

Arguments

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

Returns

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.argsis a list of additional arguments passed to the functionlegend(if= NULLthe legend is not plotted) andhist.argsis a list of further arguments passed to the functionplot.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.argsis a list of further arguments passed to the functionlollipoPlotandline.argsis a list of additional arguments passed to the functionline`. This function additionally returns the vector of rates for the focal clade, collated in increasing order.

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))

See Also

c("list("RRphylo")", " vignette")

c("list("plotRates")", " vignette")

c("list("RRphylo")", " vignette")

c("list("plotRates")", " vignette")

Author(s)

Silvia Castiglione, Pasquale Raia