split.by-like function for the umap to compare gene expression between conditions
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Description
- Additional function parameters / changed functionality / changed defaults?
- New analysis tool: A simple analysis tool you have been using and are missing in
sc.tools? - New plotting function: A kind of plot you would like to seein
sc.pl? - External tools: Do you know an existing package that should go into
sc.external.*? - Other?
...
Currently, to compare gene expressions on the umap between different samples or conditions
I use the for loop and do something like this
for i in ['embryonic day1', 'postnatal day2']:
print(i)
sc.pl.umap(
adata[adata.obs["bulk.ident"] == i], size=20,
color=["gene"],
frameon=False,
)
but i would love to have a function for this that creates multiple umaps in parallel in one row with maybe 'ncol' fxn to decide how many in one row.
could we please add split.by-like function function in the scanpy?
+addendum
Also, simply subplotting multiple umaps per condition could be somewhat missleading as scale for particular gene expression would very per samples. We would need a comprehensive fxn that provides uniform scale of expression for multiple samples..
#1879
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start at the existing sc.pl.umap entry point and review the related discussion in issue #1879. Define how condition-based subplot layout and a uniform expression scale should work, including the ncol behavior. Done means a plotting function supports the requested comparisons without misleading per-sample scaling.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data-visualization
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100