Hi,
I think this is a very specific issue. I cannot provide data to replicate. So obs has a column containing a continuous data and I want to visualize it. If the column name is "0" or "1", it shows a blank plot while other integers like "2", "3" or others work fine.
An example code to visualize a column.
sdata.pl.render_images("queried_cytassist").pl.render_shapes(
f"{sample_id}_square_00{bin_size}um", color="1",cmap=new_cmap,method="matplotlib",scale=0.8
).pl.show(coordinate_systems="global", title="cluster 1",legend_fontsize=8,figsize=(5,5),dpi=200)
My computer is Mac M1.
aiobotocore 2.5.4
aiohappyeyeballs 2.3.7
aiohttp 3.10.4
aioitertools 0.11.0
aiosignal 1.3.1
anndata 0.10.8
appnope 0.1.4
array_api_compat 1.8
asciitree 0.3.3
asttokens 2.4.1
attrs 24.2.0
botocore 1.31.17
certifi 2024.7.4
charset-normalizer 3.3.2
click 8.1.7
cloudpickle 3.0.0
colorcet 3.1.0
comm 0.2.2
contourpy 1.2.1
csbdeep 0.8.0
cycler 0.12.1
dask 2024.8.1
dask-expr 1.1.11
dask-image 2024.5.3
datashader 0.16.3
debugpy 1.8.5
decorator 5.1.1
distributed 2024.8.1
docrep 0.3.2
et-xmlfile 1.1.0
exceptiongroup 1.2.2
executing 2.0.1
fasteners 0.19
fcsparser 0.2.8
fonttools 4.53.1
frozenlist 1.4.1
fsspec 2023.6.0
geopandas 1.0.1
h5py 3.11.0
idna 3.7
igraph 0.11.6
imagecodecs 2024.6.1
imageio 2.35.1
importlib_metadata 8.2.0
inflect 7.3.1
iniconfig 2.0.0
ipykernel 6.29.5
ipython 8.26.0
jedi 0.19.1
Jinja2 3.1.4
jmespath 1.0.1
joblib 1.4.2
jupyter_client 8.6.2
jupyter_core 5.7.2
kiwisolver 1.4.5
lamin_utils 0.13.2
lazy_loader 0.4
legacy-api-wrap 1.4
leidenalg 0.10.2
llvmlite 0.43.0
locket 1.0.0
markdown-it-py 3.0.0
MarkupSafe 2.1.5
matplotlib 3.9.2
matplotlib-inline 0.1.7
matplotlib-scalebar 0.8.1
mdurl 0.1.2
more-itertools 10.4.0
msgpack 1.0.8
multidict 6.0.5
multipledispatch 1.0.0
multiscale_spatial_image 1.0.1
natsort 8.4.0
nest_asyncio 1.6.0
networkx 3.3
numba 0.60.0
numcodecs 0.13.0
numpy 1.26.4
ome-zarr 0.9.0
omnipath 1.0.8
openpyxl 3.1.5
packaging 24.1
pandas 2.2.2
param 2.1.1
parso 0.8.4
partd 1.4.2
patsy 0.5.6
pexpect 4.9.0
pickleshare 0.7.5
pillow 10.4.0
PIMS 0.7
pip 24.2
platformdirs 4.2.2
pluggy 1.5.0
pooch 1.8.2
prompt_toolkit 3.0.47
psutil 6.0.0
ptyprocess 0.7.0
pure_eval 0.2.3
pyarrow 17.0.0
pyct 0.5.0
Pygments 2.18.0
pynndescent 0.5.13
pyogrio 0.9.0
pyparsing 3.1.2
pyproj 3.6.1
pytest 8.3.2
python-dateutil 2.9.0
pytz 2024.1
PyYAML 6.0.2
pyzmq 26.1.0
readfcs 1.1.8
regex 2024.7.24
requests 2.32.3
rich 13.7.1
s3fs 2023.6.0
scanpy 1.10.2
scikit-image 0.24.0
scikit-learn 1.5.1
scipy 1.14.0
seaborn 0.13.2
session_info 1.0.0
setuptools 72.1.0
shapely 2.0.5
six 1.16.0
slicerator 1.1.0
sortedcontainers 2.4.0
spatial_image 1.1.0
spatialdata 0.2.2
spatialdata-io 0.1.4
spatialdata-plot 0.2.4
squidpy 1.6.0
stack-data 0.6.2
stardist 0.9.1
statsmodels 0.14.2
stdlib-list 0.10.0
tblib 3.0.0
texttable 1.7.0
threadpoolctl 3.5.0
tifffile 2024.8.10
toolz 0.12.1
tornado 6.4.1
tqdm 4.66.5
traitlets 5.14.3
typeguard 4.3.0
typing_extensions 4.12.2
tzdata 2024.1
umap-learn 0.5.6
urllib3 1.26.19
validators 0.33.0
wcwidth 0.2.13
wheel 0.44.0
wrapt 1.16.0
xarray 2024.7.0
xarray-dataclasses 1.8.0
xarray-datatree 0.0.14
xarray-schema 0.0.3
xarray-spatial 0.4.0
yarl 1.9.4
zarr 2.18.2
zict 3.0.0
zipp 3.20.0
Hi,
I think this is a very specific issue. I cannot provide data to replicate. So obs has a column containing a continuous data and I want to visualize it. If the column name is "0" or "1", it shows a blank plot while other integers like "2", "3" or others work fine.
An example code to visualize a column.
sdata.pl.render_images("queried_cytassist").pl.render_shapes(
f"{sample_id}_square_00{bin_size}um", color="1",cmap=new_cmap,method="matplotlib",scale=0.8
).pl.show(coordinate_systems="global", title="cluster 1",legend_fontsize=8,figsize=(5,5),dpi=200)
My computer is Mac M1.