plot.nex: plot data matrix and phylogeny

In celiason/phenotools: Tools for the analysis and assembly of phenomic data in R

plot data matrix and phylogeny

Description

Plots a nexus dataset and optionally a tree

Usage

## S3 method for class 'nex'
plot(
  x,
  y = NULL,
  phy = NULL,
  legend.pos = c("none", "left", "right", "bottom", "top"),
  bw = FALSE,
  na.value = "lightgray",
  fsize = 8,
  fill = c("statelabels", "charpartition", "charset", "file"),
  ...
)

Arguments

x	a 'nex' object for plotting
y	unused
phy	a phylogeny in 'phylo' format
legend.pos	position of legend
bw	whether to plot in black (scoring present) and white (no scoring)
na.value	color for NA values in matrix
fsize	font size
fill	how to color cells in matrix
...	additional arguments (unused)

References

Brusatte, S. L., G. T. Lloyd, S. C. Wang, and M. A. Norell. 2014. Gradual Assembly of Avian Body Plan Culminated in Rapid Rates of Evolution across the Dinosaur-Bird Transition. Curr Biol 24:2386-2392. (PubMed)

Examples

## Not run: 
# load theropod dataset:
data(twig)
# plot data matrix
plot(twig[,1:10], fill="statelabels", legend.pos="top", na.value="black")
# plot matrix alongside phylogeny
library(ape)
s <- "(Tyrannosaurus_rex,(Archaeopteryx_lithographi,Anas_platyrhynchus));"
s <- "(trex,(al,ap));"
phy <- compute.brlen(read.tree(text=s))
plot(phy)
plot(x=twig[,1:20], phy=phy, fill="statelabels", legend.pos="top", na.value="white")

## End(Not run)

celiason/phenotools documentation built on Sept. 29, 2024, 5:43 p.m.