scverse / scanpy

Single-cell analysis in Python. Scales to >1M cells.
https://scanpy.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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plotting by sc.pl.dpt_timeseries(adata) has no colors #2141

Open hyjforesight opened 2 years ago

hyjforesight commented 2 years ago

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 commented 6 months ago

I have this exact error!