View source: R/phylo.heatmap.R
phylo.heatmap | R Documentation |
Multivariate phylogenetic heatmap
plot.
phylo.heatmap(tree, X, fsize=1, colors=NULL, standardize=FALSE, ...)
tree |
an object of class |
X |
a matrix containing data for multiple continuous characters in which |
fsize |
an integer or vector of length 3 containing the font size for the tip labels, the trait labels, and the legend text. (If a single integer is supplied, then the value will be recycled.) |
colors |
a vector of colors to be passed to |
standardize |
a logical value indicating whether or not to standardize each column of |
... |
optional arguments. So far these include: |
Function creates a plot.
Liam Revell liam.revell@umb.edu
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
## load data
data(anoletree)
data(anole.data)
## compute phylogenetic residuals
anole.data<-as.matrix(anole.data)
anole.resids<-cbind(anole.data[,1],
phyl.resid(anoletree,anole.data[,1,drop=FALSE],
anole.data[,2:ncol(anole.data)])$resid)
colnames(anole.resids)[1]<-"SVL"
## plot phylogenetic heatmap
phylo.heatmap(anoletree,anole.resids,
split=c(0.7,0.3),fsize=c(0.4,0.8,0.8),
standardize=TRUE,pts=FALSE)
par(mar=c(5.1,4.1,4.1,2.1)) ## reset margins to default
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.