scverse / scverse/scanpy

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

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Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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