Feature/hucira #901
Draft
Feature/hucira #901
+1,602
−1
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
PR Checklist
docsis updatedDescription of changes
adding new tool.
Technical details
Technically, the most interesting part is the data itself. Most of the methods that come with this tool are wrappers that aid with the enrichment analysis (e.g., help create a ranked list from query data, or help navigate the different levels of the data).
The plotting tools are seaborn heatmap wrappers that are tailored to the output format.
Only the cytokine communication methods are specific to this tool. (get_senders and receivers()). This plotting function is specific to this tool.
Additional context
new feature "hucira". Lukas wants to check if methods are too specific.
Some of the code might actually be redundant.. I had implemented the wrappers to make simple visualizations a click away for users but I can rethink about making the tool more lightweight.
The only dependencies I added (bokeh and pyCirclize) are for visualization tools
The very generic tests that I wrote are not passing. I don't know why, it looks like they're timing out.