Closed j-andrews7 closed 4 months ago
this is a concept I should explain better in the docs and the paper, and I will give that a go
The leaf nodes are colored relative to the original annotation, the purpose is to indicate that annotation is at its maximal granularity (there are no additional nodes under this annotation).
A dark green means that the ontology has no terms that would be even more specific than that annotation.
A light green means there are more specific annotations, but none of the genes were annotated as such,
So the green shade is an indicator of how good/specific the GO annotation were and would not change shade.
Okay, I understand and agree that it could be explained a little more clearly. I think stating that the dark green nodes have no children terms would be helpful.
Additional explanation added to the readme regarding the coloring.
Should the most granular leaf nodes color mapping be changed when filtering is applied? As an example, here's a few genes with all terms included:![image](https://github.com/ialbert/genescape-central/assets/10225716/3c589953-3e95-44c6-90b9-692366555cd2)
All of the leaf nodes are light green, with the leaf nodes containing the most parent terms being dark green (please correct me if I'm interpreting this incorrectly).
If I limit to Biological Process terms, should the "adaptive immune response" node now be a dark green leaf node?