plotting by sc.pl.dpt_timeseries(adata) has no colors
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 2.6k
- Forks
- 779
- Avg merge
- 1d 4h
- Merged PRs (30d)
- 27
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

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
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 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