I want to make some figures illustrating a few pedigrees (adding some additional legends etc). I could of course draw them manually, or use some general graph-visualization tool, but it would be nice to have something where I can input a general pedigree structure and get e.g. proper symbols for sexes and maybe add some annotation.
Ideally, I would like a way to highlight different subsets to tillustrate e.g case/controls or other group overlays.
Any suggestions are welcome. The visualizations are only to be used to describe a method, and this is really not the core of my field.
I was aware of general graph-visualization tools like graphviz, but I was wondering if there was something more specific. OTOH, maybe I should go with graphviz and explore the possibilities.
Depending on how complex the pedigrees will be... you can consider also Microsoft's Visio. It's a very generic tool to draw all sorts of graphics, including graphs for pedigrees.
I seem to end up using the kinship2 CRAN package (and the plot function for pedigree objects), followed by some manual touchup on an eps export of the resulting figure. Thanks for all suggestions!
how about HaploPainter (http://haplopainter.sourceforge.net/index.html)? I'm using it for longer time and had realy good experience. It's free and the only drawback its works only on windows.
There is a 'kinship' package in R. As long as you have the following information: individual id, father id, mother id, sex, affected status. you can use the 'pedigree' function to get the structure of the families and plot the pedigree out. Here is some sample code:
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library(kinship)
attach(data)
ped
Hi, We have been using Haplopainter. It can surely highlight haplotypes or whatever groups you specify. You surely depend on the output file format what you get from a previously run programme in Easy linkage or those kinds. For simply drawing the pedigrees, we use Cyrillic like a base figure .
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