Question: (Closed) Visualizing Pedigrees From Plink Files
1
gravatar for alexhli
6.9 years ago by
alexhli70
United States
alexhli70 wrote:

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.

Thanks

• 3.3k views
ADD COMMENTlink modified 6.9 years ago by Pierre Lindenbaum124k • written 6.9 years ago by alexhli70

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 REPLYlink written 6.9 years ago by Zev.Kronenberg11k

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 REPLYlink written 6.9 years ago by jxchong160
1

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 REPLYlink written 6.8 years ago by alexhli70
4
gravatar for Pierre Lindenbaum
6.9 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum124k wrote:

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 COMMENTlink written 6.9 years ago by Pierre Lindenbaum124k

I will have to give it a try!

ADD REPLYlink written 6.9 years ago by Zev.Kronenberg11k

looks promising, thanks for the link!

ADD REPLYlink written 6.9 years ago by alexhli70
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