plotTrend: Graphical representation of search.trend results
In RRphylo: Phylogenetic Ridge Regression Methods for Comparative Studies

plotTrend

R Documentation

Graphical representation of search.trend results

Description

This function generates customized functions to produce plots of phenotype versus time and absolute evolutionary rates versus time regressions for the entire phylogeny and individual clades. Each custom function takes as first argument the index or name of the variable (as in the search.trend output in $trends.data$phenotypeVStime) to be plotted.

Usage

plotTrend(ST)

Arguments

`ST`	an object produced by `search.trend`.

Value

The function returns a list of functions:

$plotSTphen returns the plot of rescaled phenotype versus age regression. The 95% confidence intervals of slopes produced by regressing phenotypes simulated under the Brownian motion are plotted as a polygon. The usage is ...$plotSTphen(variable,plot.args=NULL,polygon.args=NULL,line.args=NULL), where variable is the index or name of the variable to be plotted, plot.args is a list of further arguments passed to the function plot, polygon.args is a list of further arguments passed to the function polygon, and line.args is a list of further arguments passed to the function lines. The functions automatically plots white points for internal nodes, red points for tips, a blue regression line, and a gray shaded polygon to represent the 95% confidence intervals of Brownian motion slopes.

$plotSTrates returns the plot of log rescaled rates versus age regression. The 95% confidence intervals of slopes produced by regressing rates simulated under the Brownian motion are plotted as a shaded area. The arguments are the same as described for $plotSTphen. In the case of multivariate y, the 2-norm vector of multiple rates (see RRphylo for details) can be plotted by setting variable = "rate" or variable = the number of actual variables + 1.

$plotSTphenNode returns plots of rescaled phenotype versus age regression for individual clades. The usage is ...$plotSTphenNode(variable,node,plot.args=NULL,lineTree.args=NULL, lineNode.args=NULL,node.palette=NULL), where variable is the same as plotSTphen and node is the vector of indices or numbers (as inputted to search.trend, to be indicated as character) of nodes to be plotted. The function allows up to nine nodes at the same time. plot.args is a list of further arguments passed to the function plot, including pch.node, a custom argument to set individual pch at nodes (its length can be one or as long as the number of nodes). lineTree.args is a list of further arguments passed to the function lines used to plot the regression line for the entire tree lineNode.args is a list of further arguments passed to the function lines used to plot the regression line for individual nodes. node.palette is the vector of colors specific to nodes points and lines. Its length can be one or as long as the number of nodes.

$plotSTratesNode returns plots of absolute rates versus age regression for individual clades. The arguments are the same as described for $plotSTphenNode. In the case of multivariate y, the 2-norm vector of multiple rates (see RRphylo for details) can be plotted by setting variable = "rate" or variable = the number of actual variables + 1.

Author(s)

Silvia Castiglione, Carmela Serio

References

Castiglione, S., Serio, C., Mondanaro, A., Di Febbraro, M., Profico, A., Girardi, G., & Raia, P. (2019) Simultaneous detection of macroevolutionary patterns in phenotypic means and rate of change with and within phylogenetic trees including extinct species. PLoS ONE, 14: e0210101. https://doi.org/10.1371/journal.pone.0210101

Examples

 ## Not run: 
data("DataOrnithodirans")
DataOrnithodirans$treedino->treedino
DataOrnithodirans$massdino->massdino
cc<- 2/parallel::detectCores()

# Extract Pterosaurs tree and data
library(ape)
extract.clade(treedino,746)->treeptero
massdino[match(treeptero$tip.label,names(massdino))]->massptero
massptero[match(treeptero$tip.label,names(massptero))]->massptero

RRphylo(tree=treeptero,y=log(massptero),clus=cc)->RRptero

search.trend(RR=RRptero, y=log(massptero), nsim=100, node=143, clus=cc,cov=NULL)->ST

plotTrend(ST)->plotST

plotST$plotSTphen(1) # to plot phenotypic trend through time for entire tree
plotST$plotSTphen("log(massptero)",plot.args=list(cex=1.2,col="blue")) # equivalent to above

plotST$plotSTrates(1) # to plot rates trend through time for entire tree

# to plot phenotypic trend through time for the clade
plotST$plotSTphenNode("log(massptero)",plot.args=list(xlab="Age",main="Phenotypic trend"),
                    lineTree.args=list(lty=1,col="pink"),lineNode.args=list(lwd=3),
                    node.palette=c("chartreuse"))

# to plot rates trend through time for the clade
plotST$plotSTratesNode("rate")

   
## End(Not run)

RRphylo documentation built on June 7, 2023, 5:49 p.m.