I was just working through the problem of trying to get up (↑) and down (↓) arrows into figure axis labels in R.
Just copying and pasting unicode arrows into the R script works for axis labels that are to be rendered by the R graphical device within an interactive R session.
Unfortunately, this does not work for figures or R markdown to be rendered as HTML (e.g., using knitr) or as PDFs (e.g., using rmarkdown)!
After digging online for some hints (the most useful one I found
here, along with,
of course, R help),
the following is a better solution that uses the base function expression
:
library(phytools)
tips<-getStates(ecomorph.tree,"tips")
tip.cols<-cols[tips]
plotTree.barplot(ecomorph.tree,scores(pca)[,3],
args.plotTree=list(fsize=0.4),
args.barplot=list(col=tip.cols,
xlab=expression(paste("PC 3 (",""%up%"","limbs, ",
""%down%"","lamellae)",sep="")),
cex.lab=0.8))
legend("topright",levels(anole.ecomorph[,1]),
pch=22,pt.bg=cols,pt.cex=1.5,cex=0.9)
Here are the tree & data that I used:
ecomorph.tree
##
## Phylogenetic tree with 82 tips and 81 internal nodes.
##
## Tip labels:
## ahli, allogus, rubribarbus, imias, sagrei, bremeri, ...
##
## The tree includes a mapped, 6-state discrete character with states:
## CG, GB, TC, TG, Tr, Tw
##
## Rooted; includes branch lengths.
pca
## Phylogenetic pca
## Standard deviations:
## PC1 PC2 PC3 PC4
## 0.81378367 0.22553447 0.12277042 0.10577197
## PC5 PC6
## 0.04920179 0.03691686
## Loads:
## PC1 PC2 PC3
## SVL -0.9712234 0.16067288 0.01972570
## HL -0.9645111 0.16955087 -0.01203113
## HLL -0.9814164 -0.02674808 0.10315533
## FLL -0.9712265 0.17585694 0.10697935
## LAM -0.7810052 0.37429334 -0.47398703
## TL -0.9014509 -0.42528918 -0.07614571
## PC4 PC5 PC6
## SVL 0.14782215 -0.06211906 0.06935433
## HL 0.17994634 0.08064324 -0.04406887
## HLL -0.13790763 0.06887922 0.04126248
## FLL -0.09105747 -0.06075142 -0.04864769
## LAM -0.15871456 0.00217418 0.00875408
## TL 0.01709649 -0.01750404 -0.01088743
That's all for now.
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