Hello,
I am experiencing an issue with my UMAP plots in Scanpy. When trying to plot my data, the process takes over 20 minutes and does not produce any output. I have updated my Scanpy to the latest version and re-installed it, but the issue persists. Additionally, when running the plotting function, I receive the following warning message:
‘/Users/sei/opt/anaconda3/envs/scvi-env/lib/python3.9/site-packages/scanpy/plotting/_tools/scatterplots.py:392: UserWarning: No data for colormapping provided via ‘c’. Parameters ‘cmap’ will be ignored
cax = scatter(.’
Can someone provide some guidance on how to resolve this issue?
Thank you.
import scanpy
print(scanpy.version) 1.9.3
!python --version Python 3.9.16
Package Version
absl-py 1.4.0
altair 4.2.2
anndata 0.8.0
anyio 3.6.2
appnope 0.1.3
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
arrow 1.2.3
asttokens 2.2.1
attrs 22.2.0
backcall 0.2.0
backports.functools-lru-cache 1.6.4
beautifulsoup4 4.11.2
biothings-client 0.2.6
bleach 6.0.0
brotlipy 0.7.0
cached-property 1.5.2
celltypist 1.3.0
certifi 2022.12.7
cffi 1.15.1
charset-normalizer 2.0.4
chex 0.1.6
click 8.1.3
colorama 0.4.6
contextlib2 21.6.0
contourpy 1.0.7
cryptography 39.0.1
cycler 0.11.0
dataclasses 0.8
debugpy 1.6.6
decorator 5.1.1
defusedxml 0.7.1
dm-tree 0.1.7
docrep 0.3.2
entrypoints 0.4
et-xmlfile 1.1.0
executing 1.2.0
fastjsonschema 2.16.3
flax 0.5.0
flit_core 3.6.0
fonttools 4.39.0
fqdn 1.5.1
fsspec 2023.3.0
h5py 3.7.0
idna 3.4
igraph 0.10.4
importlib-metadata 6.0.0
importlib-resources 5.12.0
ipykernel 6.15.0
ipython 8.11.0
ipython-genutils 0.2.0
isoduration 20.11.0
jax 0.4.1
jaxlib 0.3.25
jedi 0.18.2
Jinja2 3.1.2
joblib 1.2.0
jsonpointer 2.3
jsonschema 4.17.3
jupyter_client 8.0.3
jupyter_core 5.2.0
jupyter-events 0.6.3
jupyter_server 2.4.0
jupyter_server_terminals 0.4.4
jupyterlab-pygments 0.2.2
kiwisolver 1.4.4
leidenalg 0.9.1
lightning-utilities 0.7.0
llvmlite 0.39.1
markdown-it-py 2.2.0
MarkupSafe 2.1.2
matplotlib 3.7.1
matplotlib-inline 0.1.6
mdurl 0.1.0
mistune 2.0.5
mkl-fft 1.3.1
mkl-random 1.2.2
mkl-service 2.4.0
ml-collections 0.1.1
msgpack 1.0.5
mudata 0.2.1
multipledispatch 0.6.0
munkres 1.1.4
mygene 3.2.2
natsort 8.3.1
nbclassic 0.5.3
nbclient 0.7.2
nbconvert 7.2.9
nbformat 5.7.3
nest-asyncio 1.5.6
networkx 3.0
notebook 6.5.3
notebook_shim 0.2.2
numba 0.56.4
numpy 1.23.5
numpyro 0.11.0
openpyxl 3.1.1
opt-einsum 3.3.0
optax 0.1.4
packaging 23.0
pandas 1.5.3
pandocfilters 1.5.0
parso 0.8.3
patsy 0.5.3
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.4.0
pip 21.2.4
platformdirs 3.1.0
pooch 1.7.0
prometheus-client 0.16.0
prompt-toolkit 3.0.38
psutil 5.9.4
ptyprocess 0.7.0
pure-eval 0.2.2
pycparser 2.21
Pygments 2.14.0
pynndescent 0.5.8
pyOpenSSL 23.0.0
pyparsing 3.0.9
pyro-api 0.1.2
pyro-ppl 1.8.4+9ed468d
pyrsistent 0.19.3
PySocks 1.7.1
python-dateutil 2.8.2
python-json-logger 2.0.7
pytorch-lightning 1.9.4
pytz 2022.7.1
PyYAML 6.0
pyzmq 25.0.0
requests 2.28.1
rfc3339-validator 0.1.4
rfc3986-validator 0.1.1
rich 13.3.2
scanpy 1.9.3
scikit-learn 1.2.1
scipy 1.10.0
scvi-tools 0.20.1
seaborn 0.12.2
Send2Trash 1.8.0
session-info 1.0.0
setuptools 65.6.3
six 1.16.0
sniffio 1.3.0
soupsieve 2.4
stack-data 0.6.2
statsmodels 0.13.5
stdlib-list 0.8.0
terminado 0.17.1
texttable 1.6.7
threadpoolctl 3.1.0
tinycss2 1.2.1
toolz 0.12.0
torch 1.13.1
torchaudio 0.13.1
torchmetrics 0.11.3
torchvision 0.14.1
tornado 6.2
tqdm 4.65.0
traitlets 5.9.0
typing_extensions 4.4.0
umap-learn 0.5.3
unicodedata2 15.0.0
uri-template 1.2.0
urllib3 1.26.14
wcwidth 0.2.6
webcolors 1.12
webencodings 0.5.1
websocket-client 1.5.1
wheel 0.38.4
xlrd 1.2.0
zipp 3.15.0