Distance matrix is not always square #72
Description
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Working on the AIDA dataset, I get the following error when trying TotalPseudobulk:
Traceback (most recent call last):
File "/home/michaela.mueller/workspace/immune-v1-scripts/.snakemake/scripts/tmpfflhhssl.pseudobulk.py", line 61, in <module>
sc.pp.neighbors(adata, use_rep='distances', metric='precomputed', transformer='sklearn')
File "/hpc/scratch/project.hca_integration/mambaforge/envs/sample_representation/lib/python3.11/site-packages/scanpy/neighbors/__init__.py", line 191, in neighbors
neighbors.compute_neighbors(
File "/hpc/scratch/project.hca_integration/mambaforge/envs/sample_representation/lib/python3.11/site-packages/scanpy/neighbors/__init__.py", line 576, in compute_neighbors
self._distances = transformer.fit_transform(X)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/hpc/scratch/project.hca_integration/mambaforge/envs/sample_representation/lib/python3.11/site-packages/sklearn/utils/_set_output.py", line 316, in wrapped
data_to_wrap = f(self, X, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/hpc/scratch/project.hca_integration/mambaforge/envs/sample_representation/lib/python3.11/site-packages/sklearn/neighbors/_graph.py", line 482, in fit_transform
return self.fit(X).transform(X)
^^^^^^^^^^^
File "/hpc/scratch/project.hca_integration/mambaforge/envs/sample_representation/lib/python3.11/site-packages/sklearn/base.py", line 1473, in wrapper
return fit_method(estimator, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/hpc/scratch/project.hca_integration/mambaforge/envs/sample_representation/lib/python3.11/site-packages/sklearn/neighbors/_graph.py", line 434, in fit
self._fit(X)
File "/hpc/scratch/project.hca_integration/mambaforge/envs/sample_representation/lib/python3.11/site-packages/sklearn/neighbors/_base.py", line 571, in _fit
raise ValueError(
ValueError: Precomputed matrix must be square. Input is a 1068x1069 matrix.
Is this something that has already been observed? For most other datasets I don't get this error, so I think this might be something numerical.
Version information
Version info via pip list
Package Version Editable project location
------------------------ ----------- -------------------------------------------------------
absl-py 2.1.0
aiohappyeyeballs 2.4.3
aiohttp 3.10.9
aiosignal 1.3.1
anndata 0.10.9
array_api_compat 1.9
asciitree 0.3.3
attrs 24.2.0
autograd 1.7.0
autograd-gamma 0.5.0
beautifulsoup4 4.12.3
blosc 1.11.2
bokeh 3.5.2
Brotli 1.1.0
cached-property 1.5.2
cachetools 5.5.0
causal-learn 0.1.3.8
certifi 2024.8.30
cffi 1.17.1
charset-normalizer 3.3.2
chex 0.1.87
clarabel 0.9.0
click 8.1.7
cloudpickle 3.0.0
colorama 0.4.6
contextlib2 21.6.0
contourpy 1.3.0
cvxpy 1.5.3
cycler 0.12.1
Cython 3.0.11
cytoolz 1.0.0
dask 2024.9.1
dask-expr 1.1.15
dask-glm 0.3.2
dask-ml 2024.4.4
db-dtypes 1.3.0
decorator 5.1.1
Deprecated 1.2.14
DiffusionEMD 0.5.0
dill 0.3.9
distributed 2024.9.1
docrep 0.3.2
dowhy 0.11.1
ecos 2.0.14
ehrapy 0.9.0
et-xmlfile 1.1.0
etils 1.9.4
exceptiongroup 1.2.2
faiss-cpu 1.8.0.post1
fasteners 0.17.3
fhiry 4.0.0
filelock 3.16.1
fknni 1.1.1
flax 0.9.0
fonttools 4.54.1
formulaic 1.0.2
frozenlist 1.4.1
fsspec 2024.9.0
future 1.0.0
gdown 5.2.0
get-annotations 0.1.2
google-api-core 2.20.0
google-auth 2.35.0
google-cloud-bigquery 3.26.0
google-cloud-core 2.4.1
google-crc32c 1.6.0
google-resumable-media 2.7.2
googleapis-common-protos 1.65.0
graphtools 1.5.3
graphviz 0.20.3
grpcio 1.66.2
grpcio-status 1.66.2
h2 4.1.0
h5py 3.10.0
hpack 4.0.0
humanize 4.11.0
hyperframe 6.0.1
idna 3.10
igraph 0.11.6
imbalanced-learn 0.12.4
importlib_metadata 8.5.0
importlib_resources 6.4.5
interface-meta 1.3.0
jax 0.4.34
jaxlib 0.4.34
Jinja2 3.1.4
joblib 1.4.2
kiwisolver 1.4.7
lamin_utils 0.13.6
legacy-api-wrap 1.4
leidenalg 0.10.2
lifelines 0.28.0
lightgbm 4.5.0
lightning 2.4.0
lightning-utilities 0.11.7
llvmlite 0.43.0
locket 1.0.0
lz4 4.3.3
Markdown 3.7
markdown-it-py 3.0.0
MarkupSafe 2.1.5
matplotlib 3.9.2
mdurl 0.1.2
miceforest 5.7.0
missingno 0.5.2
ml_collections 0.1.1
ml_dtypes 0.5.0
mpmath 1.3.0
msgpack 1.1.0
mudata 0.3.1
multidict 6.1.0
multipledispatch 0.6.0
munkres 1.1.4
muon 0.1.6
natsort 8.4.0
nest-asyncio 1.6.0
networkx 3.3
newick 1.0.0
numba 0.60.0
numcodecs 0.13.0
numpy 1.26.4
numpyro 0.15.3
nvidia-cublas-cu12 12.1.3.1
nvidia-cuda-cupti-cu12 12.1.105
nvidia-cuda-nvrtc-cu12 12.1.105
nvidia-cuda-runtime-cu12 12.1.105
nvidia-cudnn-cu12 9.1.0.70
nvidia-cufft-cu12 11.0.2.54
nvidia-curand-cu12 10.3.2.106
nvidia-cusolver-cu12 11.4.5.107
nvidia-cusparse-cu12 12.1.0.106
nvidia-nccl-cu12 2.20.5
nvidia-nvjitlink-cu12 12.6.77
nvidia-nvtx-cu12 12.1.105
openpyxl 3.1.5
openTSNE 1.0.2
opt_einsum 3.4.0
optax 0.2.3
orbax-checkpoint 0.6.4
osqp 0.6.7.post1
packaging 24.1
pandas 1.5.3
partd 1.4.2
patient_representation 0.1.28 /home/michaela.mueller/workspace/patient_representation
patsy 0.5.6
phate 1.0.11
pillow 10.4.0
pip 24.2
plottable 0.1.5
POT 0.9.4
prodict 0.8.18
proto-plus 1.24.0
protobuf 5.28.2
psutil 6.0.0
pyampute 0.0.3
pyarrow 17.0.0
pyarrow-hotfix 0.6
pyasn1 0.6.1
pyasn1_modules 0.4.1
pycparser 2.22
pydot 3.0.2
Pygments 2.18.0
PyGSP 0.5.1
pynndescent 0.5.13
pyparsing 3.1.4
pyro-api 0.1.2
pyro-ppl 1.9.1
PySocks 1.7.1
python-dateutil 2.9.0
pytorch-lightning 2.4.0
pytz 2024.1
PyYAML 6.0.2
qdldl 0.1.7.post4
RapidFuzz 3.10.0
requests 2.32.3
rich 13.9.2
rsa 4.9
s_gd2 1.8.1
scanpy 1.10.3
scArches 0.6.1
scHPL 1.0.5
scikit-learn 1.5.2
scikit-misc 0.5.1
scipy 1.14.1
scprep 1.2.3
scs 3.2.7
scvi-tools 1.2.0
seaborn 0.13.2
session-info 1.0.0
setuptools 75.1.0
six 1.16.0
sortedcontainers 2.4.0
soupsieve 2.6
sparse 0.15.4
statsmodels 0.14.4
stdlib-list 0.10.0
sympy 1.13.3
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tasklogger 1.2.0
tblib 3.0.0
tensorboard 2.18.0
tensorboard-data-server 0.7.2
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timeago 1.0.16
toolz 1.0.0
torch 2.4.1
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triton 3.0.0
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tzdata 2024.2
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WassersteinTSNE 1.1.1
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wheel 0.44.0
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xarray 2024.3.0
xyzservices 2024.9.0
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zict 3.0.0
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