Monday, December 10, 2012

Plotting densityMap to PDF

A phytools user asks:
In the densityMap graphic you sent me it seemed like you had spread the branches apart some to make the tree more readable. Is that true? If so, could you tell me how?! I have attached a graphic I made and it looks terrible. . . .

Indeed it did look terrible.

In fact, there was really no mystery to how I used the same function to make a "nice" looking figure - I just used the 'grDevices' function pdf to plot directly to a PDF. This means I can set the dimensions of the plot to be anything I like, and squidged up branches and tip labels in an R plotting window will look nice!

Here's a quick example, using contMap (because densityMap is slow for large trees):
> tree<-pbtree(n=150)
> x<-fastBM(tree)
> pdf(file="contMap.pdf",height=14,width=5)
> # now the output of a plotting call will go to my PDF
> contMap(tree,x,outline=FALSE,fsize=c(0.6,1), lims=c(floor(range(x)[1]*10)/10,
> # you can probably ignoring the "lims" argument
> # I've just used it here to get a nicer legend
null device

And here's the result (pulled from the PDF - obviously reduced in quality as a result):

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