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plotting by sc.pl.dpt_timeseries(adata) has no colors #2141

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hyjforesight opened this issue Feb 15, 2022 · 1 comment
Open

plotting by sc.pl.dpt_timeseries(adata) has no colors #2141

hyjforesight opened this issue Feb 15, 2022 · 1 comment

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@hyjforesight
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hyjforesight commented Feb 15, 2022
  • [✔] 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)

@evelyn-schmidt
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I have this exact error!

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