Automatically annotate figures with pathway strengths

[petercombs]

One nice thing to do would be to automatically take a figure like this one from the Schaap review:

and annotate it by coloring genes by strength of hit.

[petercombs]

Okay, this is starting to work:

7e8af60

Still have some things to work out, such as:

• What do I do if there are multiple loci that all produce the same gene product? Thinking here TgrB and TgrC seem to come from multiple genes, and PKA has both a regulatory and catalytic subunit.

• How do I incorporate this into a single SVG file? Or an HTML file that has the CSS in the header? I'm not sure what's the best way to proceed.

• Several of these have SNPs that are almost as strong towards the Stalk as the spore, but show up only as one or the other.

• Best way to embed a colorscale?

[petercombs]

In lab meeting, it was pointed out that classifying SNPs are "stalk biased" or "spore biased" doesn't make a ton of sense, since if you switch the reference and alternate alleles, the classification switches. So maybe just coloring by the highest p-value, regardless of "direction" is the better way to do it.

Other comments:

• Try using cytoscape to visualize the pathways.
• Try reannotating GO terms by looking at orthologs in closely related organisms (plasmodium? yeast??)