Error when repeating the tutorial for diffusion map in v1.9.1 scanpy
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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.
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This is the code I'm using which was copied from the tutorial:
import scanpy as sc
adata = sc.datasets.paul15()
sc.pp.log1p(adata)
sc.pp.neighbors(adata, n_neighbors=20, use_rep='X', method='gauss')
sc.tl.diffmap(adata)
sc.tl.dpt(adata, n_branchings=1, n_dcs=10)
sc.pl.diffmap(adata, color=['dpt_pseudotime', 'dpt_groups', 'paul15_clusters'])
The results I got are:

Which is totally different than in the tutorial:

Can anyone run into this problem ever? Thanks for your help.
Versions
anndata 0.8.0
scanpy 1.9.1
PIL 8.4.0
backcall 0.2.0
beta_ufunc NA
binom_ufunc NA
bottleneck 1.3.2
cffi 1.15.0
colorama 0.4.4
cycler 0.10.0
cython_runtime NA
dateutil 2.8.2
debugpy 1.5.1
decorator 4.4.2
defusedxml 0.6.0
google NA
h5py 3.6.0
ipykernel 6.4.1
ipython_genutils 0.2.0
jedi 0.18.1
joblib 0.17.0
kiwisolver 1.3.1
llvmlite 0.38.0
...
Python 3.9.7 (default, Sep 16 2021, 13:09:58) [GCC 7.5.0]
Linux-3.16.0-11-amd64-x86_64-with-glibc2.19
Session information updated at 2022-05-12 14:59
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First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
Start by rerunning the tutorial code with the reported Scanpy 1.9.1, AnnData 0.8.0, and Python 3.9.7 versions, focusing on sc.tl.diffmap(), sc.tl.dpt(), and sc.pl.diffmap(). Compare the generated plots with the tutorial images and determine whether the discrepancy is reproducible and attributable to the reported environment.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100