Obsidian Canvas, Pedigree Visualization

SO I have a specific problem and looking at the early videos on the new Obsidian 1.1.3 (early access beta) and it’s implementation of a JSON based Canvas for drawing I thought it might work for my needs.

The issue is we’re working on a graphical way to calculate inbreeding coefficients by using the path medhod. This is a common way that folks are taught in college but no one ever tries to do a complex pedigree this way but with some innovative Python code it is something that can be done.

The code is working for simple pedigrees with few inbred common ancestors but is failing on a very complex pedigree of a very highly inbred individual going into an infinite loop for some reason.

My task for the weekend was to draw a path diagram of the pedigree so that we can use it as we trace the program doing its calculation.

After looking at several options I decided to go ahead and install the new version of Obsidian and use that.

This is the final pedigree of Desert Weyr Brownie.

What is amazing is how easy it was to create the file.

If anyone wants to actually play with it I’ll be glad to send you the .canvas file. It won’t all fit in readable form in a single frame I can do a screenshot of.

You really have to zoom in to see the individuals. I decided to color code male founders, female founders, sires and dams.

For those that are interested Brownie had (she has passed on) an inbreeding coefficient of 0.34957

Not the most inbred individual in the North American Welsh Mountain sheep populaton but darned close.

My next one is going to be the most inbred individual in my database, a ewe yearling with an inbreeding coefficient of 0.48828.


This is really clever – and that is absolutely a benefit of structuring data a tool like this in json: it can be created or modified with code.

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