[MRG] Add a function to plot the taxonomy output #1607
Conversation
This file contains 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
… identifiers/taxonomy
…into add-taxonomy
…to add-taxonomy
Co-authored-by: C. Titus Brown <titus@idyll.org>
…ames; label --> annotate
Codecov Report
@@ Coverage Diff @@
## latest #1607 +/- ##
==========================================
+ Coverage 84.66% 91.76% +7.09%
==========================================
Files 131 100 -31
Lines 15512 11274 -4238
Branches 2210 2218 +8
==========================================
- Hits 13134 10346 -2788
+ Misses 2085 635 -1450
Partials 293 293
Flags with carried forward coverage won't be shown. Click here to find out more. 📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more |
|
exploring here: https://github.com/bluegenes/2021-sourmash-taxonomy-hackathon/blob/main/plot-lineage.ipynb |
|
@taylorreiter @bluegenes does anyone remember why this didn't get reviewed & merged? |
|
I don't, but looking at the notebook in the previous comment, maybe something to do with squished labels not being worked out when there are many samples? @bluegenes do you remember? |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
Given an abundance csv generated by sourmash tax summarize --output-format lineage_summary,
plot a heatmap that is clustered on the lineage axis. Output as a png file.
Some potential improvement in the viz:
Some design choices that aren't considered here:
plot_composite_matrix(), the saving of the plot is not split out into a different command.So given these things, the exact function I included here might not fit with sourmash, but this PR at leasts preserves the code and gives us a jumping off point. I think the viz improvements can be addressed in a later PR also.
@luizirber @bluegenes ready for review/feedback merge etc.