Open petercombs opened 5 years ago
Okay, this is starting to work:
https://github.com/petercombs/dicty/commit/7e8af6045f02e3dcf0f9542028bb869b5c249dbc
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?
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:
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.