scverse / scverse/scanpy

Improve gene expression visualisatio non UMAP

Open
#2,013 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Python
Stars
2.6k
Forks
779
Avg merge
1d 4h
Merged PRs (30d)
27

Description

  • [ x] Additional function parameters / changed functionality / changed defaults?
  • New analysis tool: A simple analysis tool you have been using and are missing in sc.tools?
  • [x ] 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?
    ...
    It would be nice to have something like https://github.com/powellgenomicslab/Nebulosa to plot sparse genes.
    On one hand, ordering with highest value on top (top plot) does not always work as what is below top layer is hidden and decreasing point size to combat this is not always good if different regions of UMAP are differently dense, thus creating white patches. On the other hand, random ordering (middle plot) can be hard to look at for sparse genes.
    The gene on the plot is highly correlated with pattern from the bottom plot, but this is not so clear when plotting the gene alone.

Sort order=True
image
Random cell ordering
image
Strongly correlated with
image

Contributor guide

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 by reviewing the existing plotting functions under sc.pl and the linked Nebulosa approach for sparse-gene visualization. Determine the intended plotting behavior and API changes needed to address occlusion and uneven UMAP density; done should mean sparse genes can be visualized more clearly than with the current ordering options.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics, data-visualization
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
30/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.