scverse / scverse/scanpy

plotting by sc.pl.dpt_timeseries(adata) has no colors

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Description

  • [✔] I have checked that this issue has not already been reported.
  • [✔ ] I have confirmed this bug exists on the latest version of scanpy.
  • [✔] (optional) I have confirmed this bug exists on the master branch of scanpy.

Note: Please read this guide detailing how to provide the necessary information for us to reproduce your bug.
Hello Scanpy,
I'm using the DPT. Every function works fine except sc.pl.dpt_timeseries(adata). I got no colors of the plot.
Could you please help me with this issue?
Thanks!
Best,
YJ
image

Minimal code sample (that we can copy&paste without having any data)
adata = sc.datasets.paul15()
adata
sc.pp.log1p(adata)
sc.pp.neighbors(adata, n_neighbors=20, use_rep='X', method='umap')

sc.tl.diffmap(adata)
sc.tl.dpt(adata, n_dcs=10, n_branchings=1)

sc.pl.diffmap(adata, color=['dpt_pseudotime', 'dpt_groups', 'paul15_clusters'])
sc.pl.dpt_groups_pseudotime(adata)
sc.pl.dpt_timeseries(adata, color_map='viridis', show=True)
Versions

sc.pl.dpt_timeseries(adata, color_map='viridis', show=True)

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 running the provided paul15 example through sc.pl.dpt_timeseries(adata, color_map='viridis', show=True) and inspect the dpt_timeseries plotting entry point. Compare its output with the other plotted DPT fields in the sample; done means the timeseries plot displays the expected colors and a regression check covers the reported case.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data-visualization
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
38/100

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