UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored

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

I have the same error. My sc.pl.umap also just does not give an output for over 30 mins, and also breaks the jupyter kernel eventually. First had this issue with scanpy 1.9.1, after uninstalling and reinstalling 1.9.3, I still have the same problem. Any advice will be helpful!

Having similar issues. UMAP taking 18 hours on 200,00 cells. My current workaround is calculating UMAP outside of scanpy using the cuml package from RAPIDS (runs on a GPU in about a minute), and then pasting those UMAP results back into my anndata object.

@rboiar @sruthi-hub Are you guys using the VScode or jupyter notebook?

You aren’t, by any chance, using a svg backend with your notebooks?

Could you try to set it to png explicitly?

%config InlineBackend.figure_formats = ['png']