The function is available on my phytools page (direct link to the code here).
**A few preliminary steps are required before the function will work!**
1. Install the package 'extrafont' and its dependencies.
2. Download and install the xkcd font, xkcd.ttf. The procedure for adding new fonts will depend on your operating system. For Windows 7, go Start → Control Panel → Appearance and Personalization → Fonts and then just drag & drop the .ttf file into this window.
3. At least in Windows, you will have to download and install Ghostscript. This allows you to embed the xkcd font into the PDF in which the tree is outputted.
The input arguments for xkcdTree are as follows: tree, your R "phylo" object; file, your filename for output (xkcdTree saves your plotted tree as a PDF); gsPath, the complete path to the Ghostscript binary (for a gs9.06 in Windows 7, the default should work); fsize, lwd, and color should be relatively self-explanatory; finally jitter is a scalar for the uncertainty to add (more is more wiggly), and waver is a vector with the horizontal and vertical relative 'wavelength' of the uncertainty (smaller numbers result in a shorter wavelength). Note that my previous example (here) has much more jitter than the default.
Let's try it:
> library(phytools)
Loading required package: ape
...
> source("xkcdTree.R")
> tree<-pbtree(n=40)
> xkcdTree(tree,"testTree.pdf",color="black",fsize=1.5)
Loading required package: extrafont
...
Loading required package: ape
...
> source("xkcdTree.R")
> tree<-pbtree(n=40)
> xkcdTree(tree,"testTree.pdf",color="black",fsize=1.5)
Loading required package: extrafont
...
There is also a small bug in this were the argument 'lwd' doesn't do anything. Link to fixed version here.
ReplyDeleteHi Liam,
ReplyDeleteSorry to bother you again but after I tried this I encontered
xkcdTree(tree,"testTree.pdf", gsPath="C:/Program Files/gs/gs9.06/bin/gswin32c.exe", color="black",fsize=1.5)
**** NOTE: use in Windows requires the installation of Ghostscript to**** embed 'xkcd' font in PDF plot
**** NOTE: an 'embed_fonts' error most likely means that Ghostscript
**** is not installed or that the path is incorrect
Warning messages:
1: In pdf(file, family = "xkcd", width = dim[1], height = dim[2]) :
unknown AFM entity encountered
2: In pdf(file, family = "xkcd", width = dim[1], height = dim[2]) :
unknown AFM entity encountered
3: In pdf(file, family = "xkcd", width = dim[1], height = dim[2]) :
unknown AFM entity encountered
4: In pdf(file, family = "xkcd", width = dim[1], height = dim[2]) :
unknown AFM entity encountered
I added the extrafont, the xkcd font and installed Ghostscript. Is there a way I could check if something else isn't working?
Thanks.
Hi Andres.
ReplyDeleteIf it worked, it should have created your plot in a PDF. Did it? Those errors might not be an issue.
- Liam
Hi Liam,
ReplyDeleteOK. It just noticed it created a .pdf as expected. I thought something was wrong since the R Graphics device was just grey but that's a minor issue if the pdf was indeed created. Sorry for my confusion.
Great. As you know, Andres, 'phytools' is a work in progress - so there will be bugs. Nonetheless, I'm glad to hear that it works! Thanks for the report. - Liam
Delete