Visualizing pedigrees from Plink files
1
2
Entering edit mode
8.6 years ago
alexhli ▴ 80

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 • 4.0k views
ADD COMMENT
0
Entering edit mode

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
0
Entering edit mode

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
1
Entering edit mode

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
0
Entering edit mode

Related post, which links back to this post:

ADD REPLY
5
Entering edit mode
8.6 years ago

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

enter image description here

ADD COMMENT

Login before adding your answer.

Traffic: 1720 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6