Entering edit mode

7 months ago

Whirlingdaf
▴
40

OK, I have a question that I feel has a quite simple solution, but my brain has just hit a wall...

I would like to plot the output from :

```
vcftools -relatedness2
```

into a plot where the samples are nodes and the edges show the values of relatedness. I would also like to be able to filter this relatedness to only show relatedness edges with values >0.01.

Example relatedness output looks something like:

```
INDV1, INDV2, RELATEDNESS_PHI
1, 4, 0.05096620
1, 2, 0.01837480
1, 3, -0.03895280
1, 6, 0.00689972
...
```

Where RELATEDNESS_PHI is the relatedness value. An example output would look something like:

Thanks for any help working past this mental block!

And where exactly is now your mental block? The data you are showing corresponds to the default edge notation useable by e.g. Cytoscape or the geomnet package in R. For traversals through edge graphs (can even be bi-weighted) use dogdr.

Sorry just seeing this, I did end up trying to work through these data with igraph, so it is likely within my scripting in igraph itself... I had: