Neighbors.compute_transitions() with error 'AnnData' object has no attribute '_connectivities'
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.
Hello,
I would like to derive the transition matrix with the following input:
sc.Neighbors.compute_transitions(adata)
The error below was produced. The anndata object was fine with sc.pp.neighbors(adata) and sc.tl.umap(adata) for UMAP plotting. Thanks
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/root/miniconda3/envs/scVI/lib/python3.8/site-packages/scanpy/neighbors/__init__.py", line 911, in compute_transitions
W = self._connectivities
AttributeError: 'AnnData' object has no attribute '_connectivities'
Versions
[Paste the output of scanpy.logging.print_versions() leaving a blank line after the details tag]
WARNING: If you miss a compact list, please try print_header!
anndata 0.7.5
scanpy 1.8.2
sinfo 0.3.1
PIL 8.0.1
absl NA
anndata 0.7.5
attr 20.3.0
cffi 1.14.4
colorama 0.4.4
cycler 0.10.0
cython_runtime NA
dateutil 2.8.1
deprecate 0.3.0
docrep 0.3.2
fsspec 2022.01.0
google NA
h5py 3.1.0
igraph 0.9.1
joblib 0.17.0
kiwisolver 1.3.1
leidenalg 0.8.3
llvmlite 0.37.0
matplotlib 3.3.3
mkl 2.3.0
mpl_toolkits NA
natsort 7.1.0
numba 0.54.1
numexpr 2.7.1
numpy 1.19.2
opt_einsum v3.3.0
packaging 20.7
pandas 1.1.5
pkg_resources NA
pycparser 2.20
pygments 2.7.3
pynndescent 0.5.5
pyparsing 2.4.7
pyro 1.8.0+0ec1e87
pytorch_lightning 1.3.8
pytz 2020.4
rich NA
scanpy 1.8.2
scipy 1.5.2
scvi 0.14.5
setuptools 49.6.0.post20201009
setuptools_scm NA
sinfo 0.3.1
six 1.15.0
sklearn 1.0.1
sphinxcontrib NA
tables 3.6.1
tensorboard 2.7.0
texttable 1.6.3
threadpoolctl 2.1.0
torch 1.9.0
torchmetrics 0.6.2
tqdm 4.62.3
typing_extensions NA
umap 0.5.2
wcwidth 0.2.5
yaml 5.4.1
Python 3.8.6 | packaged by conda-forge | (default, Nov 27 2020, 19:31:52) [GCC 9.3.0]
Linux-5.4.72-microsoft-standard-WSL2-x86_64-with-glibc2.10
24 logical CPU cores, x86_64
Session information updated at 2022-01-14 13:58
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 with scanpy/neighbors/init.py and inspect Neighbors.compute_transitions alongside the reported call sc.Neighbors.compute_transitions(adata). Reproduce with sc.pp.neighbors(adata) and the listed Scanpy 1.8.2 environment, then verify the method works with the resulting AnnData object without the reported AttributeError.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100