Question

Visualizing pedigrees from Plink files

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12.0 years ago

alexhli ▴ 90

Is there a simple way to visualize the family structure of pedigrees described in PLINK files?

It seems like all the necessary information is in the PED file but I could not find a straightforward way to visualize these families.

plink pedigree plot • 5.8k views

ADD COMMENT • link updated 4.9 years ago by zx8754 12k • written 12.0 years ago by alexhli ▴ 90

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Upvote: I have looked before and had no luck. Started writing an [r] script and got distracted. Seems like something should be out there.

ADD REPLY • link 12.0 years ago by Zev.Kronenberg 12k

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You'll have to do some reformatting to get the PLINK ped file to be read into a format compatible with programs like Madeline (UMich), Cranefoot, or Pedfiddler

ADD REPLY • link 12.0 years ago by jxchong ▴ 160

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Thanks, I ended up writing a simple script that converts the PLINK peds to the Madeline peds. Thanks for making me aware of this software. I also don't know how to mark this as resolved since you posted as a comment :)

ADD REPLY • link 12.0 years ago by alexhli ▴ 90

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Related post, which links back to this post:

Visualize PLINK pedigree files

ADD REPLY • link 4.9 years ago by zx8754 12k

score 5 · Answer 1 · 2013-01-05

For a quick and simple overview of the tree, I scan the .ped file twice with awk to generate a graphviz dot file (first to get the individuals, second to get the relationships) and I grab the X/Y positions of the nodes before transfroming it to SVG. It's far from being perfect ( order of the siblings, etc...) but that works. See my old post: http://plindenbaum.blogspot.fr/2006/01/drawing-pedigrees.html

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