on an old post asked of a
'Is there a way to use serif fonts for the color bar and cladelabels?'
The answer is 'yes' - and there are a few different ways to do it. Unfortunately, there is presently no way to
automatically use different font styles for different attributes of the
however, there are some work-arounds, as I'll illustrate below.
First, let's consider the simplest case of plotting to the R graphical user interface in an interactive
R session and in which we want to use a single font style (let's say
'serif') for all the
text on a plot.
We can do this most easily by setting the value of the graphical parameter
family to the
desired font. Note that readers should review the help page for
par to find out which
fonts are supported:
library(phytools) ## simulate some data for the purposes of illustration tree<-pbtree(n=26,tip.label=LETTERS, scale=100) x<-fastBM(tree) ## create our 'contMap' object obj<-contMap(tree,x,plot=FALSE) ## set our font family par(family="serif") ## plot plot(obj,fsize=1.2,lwd=6)
The same thing can be done if we want to export our plots as a PDF or PNG; except that we have to keep in mind that our fonts will differ depending on what type of file we choose. For instance:
png(file="contMap-tree.png",width=7,height=7, units="in",res=300,family="mono") plot(obj,fsize=0.9,lwd=6) dev.off()
## windows ## 2
Which will look like this:
If we want to use different fonts in (for instance) the tip labels & the legend, this gets a bit more complicated. The only way I can think to do this is to plot the object absent certain elements, and then add these in aferwards. Say, for instance:
plotTree(obj$tree,plot=FALSE) xlim<-get("last_plot.phylo",envir=.PlotPhyloEnv)$x.lim par(family="mono") plot(setMap(obj,c("white","black")),ftype="off",xlim=xlim) par(family="serif") tiplabels(obj$tree$tip.label,tip=1:Ntip(obj$tree),pos=4, font=3,frame="none")
(The first step is so that I can get the necessary x dimension to permit size for the tip labels even though I don't plan to plot the labels.)
Similarly, we could plot our
"contMap" object with the labels & then add our
gradient legend afterwards using
That's all there is to it.
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