Cannot change scale font size or control horizontal position in barplot

[theo-allnutt-bioinformatics]

Hi,

example of code: pdf(file="bartree.pdf",width=50,height=130)

plotTree.barplot(tree1,bardata,args.plotTree=list(fsize=3,ftype="reg",lwd=1),list(col="blue",space=1,xlab="genes@75%"))

dev.off()

How can the scale bar font size be altered? It is much smaller than tree labels. Also the figure has a very large gap between tree and bars. Is there a way to reduce it?

Thanks.

Data: https://drive.google.com/drive/folders/1kxyo8YIHRaXkukPNXRK-f298gQrOOx_D?usp=drive_link

[liamrevell]

I can't access your Google drive; however, all the options of plotTree.barplot in phytools are controlled either by par or using args.plotTree and args.barplot. Try this reproducible example to see what I mean:

## load packages
library(phytools)
## load data
data("sunfish.data")
data("sunfish.tree")
head(sunfish.data)
gape.width<-setNames(sunfish.data$gape.width,rownames(sunfish.data))
## create plot
par(cex.axis=0.8)
plotTree.barplot(sunfish.tree,gape.width,
  args.plotTree=list(fsize=0.8),
  args.barplot=list(xlab="trait axis"))

[liamrevell]

Please let me know if you still can't figure out how to make the most out of this function. -- Liam

[theo-allnutt-bioinformatics]

I have changed the sharing options - you should now be able to access the data. I have changed the axis font size, but the axis title font is unchanged. I still cannot change the large margin between the tree and the bars - see image attached.

pdf(file="bartree.pdf",width=50,height=130)

par(cex.axis=3)

plotTree.barplot(tree1,bardata,args.plotTree=list(fsize=3,ftype="reg",lwd=1),args.barplot=list(col="blue",space=1,xlab="genes@75%"))

dev.off()

Is there a manual / syntax for this function and it's options?

Thanks very much for your help.

[theo-allnutt-bioinformatics]

ok.. I found par() lists the options. par(cex.lab=3) changed the axis label size.

[theo-allnutt-bioinformatics]

From your reply on your blog: "Look at the help pages for phytools::plotTree and graphics::barplot for help identifying what the argument names for each object should be. -- Liam" I cannot find the help pages mentioned. Still can't work out how to reduce the gap. Do you have a link? Thanks.

[theo-allnutt-bioinformatics]

I found this.. is this the right page? https://www.rdocumentation.org/packages/phytools/versions/2.0-3

[liamrevell]

Dear Theo.

Maybe try working with the following code. It uses phytools but not plotTree.barplot.

library(phytools)
fam_tree<-read.tree(file="family_test.tre")
fam_genes<-read.table(file="famgenes75.txt",header=FALSE)
genes<-setNames(fam_genes[[2]],fam_genes[[1]])[fam_tree$tip.label]
png(file="example-plotTree.barplot.png",width=10,height=15,units="in",res=300)
par(mfrow=c(1,2))
plotTree(force.ultrametric(fam_tree,method="extend"),fsize=0.4,lwd=1,
  color="transparent",mar=c(5.1,1.1,1.1,0))
pp<-get("last_plot.phylo",envir=.PlotPhyloEnv)
plotTree(fam_tree,ftype="off",xlim=pp$x.lim,add=TRUE,lwd=1,mar=c(5.1,1.1,1.1,0))
qq<-get("last_plot.phylo",envir=.PlotPhyloEnv)
for(i in 1:Ntip(fam_tree))
  lines(c(pp$xx[i],qq$xx[i]),rep(pp$yy[i],2),lty="dotted",lwd=1,col="blue")
par(mar=c(5.1,0,1.1,1.1))
barplot(genes,horiz=TRUE,border=palette()[2],col=palette()[2],
  names.arg="")
dev.off()

Here is the figure I obtained.

[liamrevell]

I would love to use this example on my blog. Please let me know if it would be OK to post this solution there @theo-allnutt-bioinformatics.

[liamrevell]

PS. The reason there is such a large space between the tree & barplot in plotTree.barplot is because that function calculates the amount of horizontal space for the tree based on the total tree height & the maximum width of any tip label. Since your tree is non-ultrametric and the longest label is on a tip that is quite "shallow," the function leaves to much white space to the right of the tree. In this solution I line up the labels & then added linking lines from the tips on the plotted tree to each label, which I think is also more aesthetic. Saludos, Liam

[theo-allnutt-bioinformatics]

Hi, thanks, I will try your solution. Yes you can use the plot but please change / remove the tip names. Can you point to the help pages anyway? Theo

[liamrevell]

The arguments taken by arg.barplot and args.plotTree are the majority (but not all, due to the constraint of the plot type) of the arguments taken by graphics::barplot and phytools::plotTree, respectively. To see each of these two help pages, with phytools loaded, just run ?barplot or ?plotTree at the command prompt of your interactive R session. -- LIam