Repository navigation
Issue with set_zero_in_cmap_to_transparent Function Not Making Zero Values Transparent in Spatial Data Plotting #376
Description
Issue Description
I am experiencing an issue with the set_zero_in_cmap_to_transparent function. According to the documentation, using this function should set the positions in the data with a value of 0 to be transparent. However, I found that instead of becoming transparent, these positions turn white after executing the function.
Code
Output without set_zero_in_cmap_to_transparent functions:
sdata_small.pl.render_images("_full_image").pl.render_shapes(
"_square_008um",color="CD3D", cmap="viridis").pl.show(coordinate_systems="global", title="bin_size=8µm", figsize=(5, 5))
Output with set_zero_in_cmap_to_transparent functions:
from spatialdata_plot.pl.utils import set_zero_in_cmap_to_transparent
# let's display the areas where no expression is detected as transparent
new_cmap = set_zero_in_cmap_to_transparent(cmap="viridis")
new_cmap
sdata_small.pl.render_images("_full_image").pl.render_shapes(
"_square_008um",color="CD3D", cmap=new_cmap).pl.show(coordinate_systems="global", title="bin_size=8µm", figsize=(5, 5))
Environment Information
conda list
# packages in environment at /data2/data2_mailab003/biosoft/miniconda3/envs/spatialdata:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main defaults
_openmp_mutex 5.1 1_gnu defaults
aiobotocore 2.5.4 pypi_0 pypi
aiohappyeyeballs 2.4.3 pypi_0 pypi
aiohttp 3.10.10 pypi_0 pypi
aioitertools 0.12.0 pypi_0 pypi
aiosignal 1.3.1 pypi_0 pypi
alabaster 0.7.16 pypi_0 pypi
anndata 0.10.9 pypi_0 pypi
annotated-types 0.7.0 pypi_0 pypi
app-model 0.3.0 pypi_0 pypi
appdirs 1.4.4 pypi_0 pypi
array-api-compat 1.9 pypi_0 pypi
asciitree 0.3.3 pypi_0 pypi
asttokens 2.4.1 pypi_0 pypi
async-timeout 4.0.3 pypi_0 pypi
attrs 24.2.0 pypi_0 pypi
babel 2.16.0 pypi_0 pypi
botocore 1.31.17 pypi_0 pypi
build 1.2.2.post1 pypi_0 pypi
ca-certificates 2024.9.24 h06a4308_0 defaults
cachey 0.2.1 pypi_0 pypi
certifi 2024.8.30 pypi_0 pypi
charset-normalizer 3.4.0 pypi_0 pypi
click 8.1.7 pypi_0 pypi
cloudpickle 3.1.0 pypi_0 pypi
colorcet 3.1.0 pypi_0 pypi
comm 0.2.2 pypi_0 pypi
contourpy 1.3.0 pypi_0 pypi
cycler 0.12.1 pypi_0 pypi
dask 2024.8.0 pypi_0 pypi
dask-expr 1.1.10 pypi_0 pypi
dask-image 2024.5.3 pypi_0 pypi
datashader 0.16.3 pypi_0 pypi
debugpy 1.8.7 pypi_0 pypi
decorator 5.1.1 pypi_0 pypi
distributed 2024.8.0 pypi_0 pypi
docrep 0.3.2 pypi_0 pypi
docstring-parser 0.16 pypi_0 pypi
docutils 0.21.2 pypi_0 pypi
exceptiongroup 1.2.2 pypi_0 pypi
executing 2.1.0 pypi_0 pypi
fasteners 0.19 pypi_0 pypi
fcsparser 0.2.8 pypi_0 pypi
flexcache 0.3 pypi_0 pypi
flexparser 0.3.1 pypi_0 pypi
fonttools 4.54.1 pypi_0 pypi
freetype-py 2.5.1 pypi_0 pypi
frozenlist 1.4.1 pypi_0 pypi
fsspec 2023.6.0 pypi_0 pypi
geopandas 1.0.1 pypi_0 pypi
get-annotations 0.1.2 pypi_0 pypi
h5py 3.12.1 pypi_0 pypi
heapdict 1.0.1 pypi_0 pypi
hsluv 5.0.4 pypi_0 pypi
idna 3.10 pypi_0 pypi
igraph 0.11.6 pypi_0 pypi
imagecodecs 2024.9.22 pypi_0 pypi
imageio 2.36.0 pypi_0 pypi
imagesize 1.4.1 pypi_0 pypi
importlib-metadata 8.5.0 pypi_0 pypi
importlib-resources 6.4.5 pypi_0 pypi
in-n-out 0.2.1 pypi_0 pypi
inflect 7.4.0 pypi_0 pypi
ipykernel 6.29.5 pypi_0 pypi
ipython 8.18.1 pypi_0 pypi
jedi 0.19.1 pypi_0 pypi
jinja2 3.1.4 pypi_0 pypi
jmespath 1.0.1 pypi_0 pypi
joblib 1.4.2 pypi_0 pypi
jsonschema 4.23.0 pypi_0 pypi
jsonschema-specifications 2024.10.1 pypi_0 pypi
jupyter-client 8.6.3 pypi_0 pypi
jupyter-core 5.7.2 pypi_0 pypi
kiwisolver 1.4.7 pypi_0 pypi
lamin-utils 0.13.7 pypi_0 pypi
lazy-loader 0.4 pypi_0 pypi
ld_impl_linux-64 2.40 h12ee557_0 defaults
legacy-api-wrap 1.4 pypi_0 pypi
leidenalg 0.10.2 pypi_0 pypi
libffi 3.4.4 h6a678d5_1 defaults
libgcc-ng 11.2.0 h1234567_1 defaults
libgomp 11.2.0 h1234567_1 defaults
libstdcxx-ng 11.2.0 h1234567_1 defaults
llvmlite 0.43.0 pypi_0 pypi
locket 1.0.0 pypi_0 pypi
loguru 0.7.2 pypi_0 pypi
louvain 0.8.2 pypi_0 pypi
magicgui 0.9.1 pypi_0 pypi
markdown-it-py 3.0.0 pypi_0 pypi
markupsafe 3.0.1 pypi_0 pypi
matplotlib 3.9.2 pypi_0 pypi
matplotlib-inline 0.1.7 pypi_0 pypi
matplotlib-scalebar 0.8.1 pypi_0 pypi
mdurl 0.1.2 pypi_0 pypi
more-itertools 10.5.0 pypi_0 pypi
msgpack 1.1.0 pypi_0 pypi
multidict 6.1.0 pypi_0 pypi
multipledispatch 1.0.0 pypi_0 pypi
multiscale-spatial-image 1.0.1 pypi_0 pypi
napari 0.5.4 pypi_0 pypi
napari-console 0.1.0 pypi_0 pypi
napari-matplotlib 2.0.1 pypi_0 pypi
napari-plugin-engine 0.2.0 pypi_0 pypi
napari-spatialdata 0.5.3 pypi_0 pypi
napari-svg 0.2.0 pypi_0 pypi
natsort 8.4.0 pypi_0 pypi
ncurses 6.4 h6a678d5_0 defaults
nest-asyncio 1.6.0 pypi_0 pypi
networkx 3.2.1 pypi_0 pypi
npe2 0.7.7 pypi_0 pypi
numba 0.60.0 pypi_0 pypi
numcodecs 0.12.1 pypi_0 pypi
numpy 1.26.4 pypi_0 pypi
numpydoc 1.8.0 pypi_0 pypi
ome-zarr 0.9.0 pypi_0 pypi
omnipath 1.0.8 pypi_0 pypi
openssl 3.0.15 h5eee18b_0 defaults
packaging 24.1 pypi_0 pypi
pandas 2.2.3 pypi_0 pypi
param 2.1.1 pypi_0 pypi
parso 0.8.4 pypi_0 pypi
partd 1.4.2 pypi_0 pypi
patsy 0.5.6 pypi_0 pypi
pexpect 4.9.0 pypi_0 pypi
pillow 11.0.0 pypi_0 pypi
pims 0.7 pypi_0 pypi
pint 0.24.3 pypi_0 pypi
pip 24.2 py39h06a4308_0 defaults
platformdirs 4.3.6 pypi_0 pypi
pooch 1.8.2 pypi_0 pypi
prompt-toolkit 3.0.48 pypi_0 pypi
propcache 0.2.0 pypi_0 pypi
psutil 6.0.0 pypi_0 pypi
psygnal 0.11.1 pypi_0 pypi
ptyprocess 0.7.0 pypi_0 pypi
pure-eval 0.2.3 pypi_0 pypi
pyarrow 17.0.0 pypi_0 pypi
pyconify 0.1.6 pypi_0 pypi
pyct 0.5.0 pypi_0 pypi
pydantic 2.9.2 pypi_0 pypi
pydantic-compat 0.1.2 pypi_0 pypi
pydantic-core 2.23.4 pypi_0 pypi
pygments 2.18.0 pypi_0 pypi
pynndescent 0.5.13 pypi_0 pypi
pyogrio 0.10.0 pypi_0 pypi
pyopengl 3.1.7 pypi_0 pypi
pyparsing 3.2.0 pypi_0 pypi
pyproj 3.6.1 pypi_0 pypi
pyproject-hooks 1.2.0 pypi_0 pypi
pyqt5 5.15.11 pypi_0 pypi
pyqt5-qt5 5.15.15 pypi_0 pypi
pyqt5-sip 12.15.0 pypi_0 pypi
python 3.9.20 he870216_1 defaults
python-dateutil 2.9.0.post0 pypi_0 pypi
pytz 2024.2 pypi_0 pypi
pyyaml 6.0.2 pypi_0 pypi
pyzmq 26.2.0 pypi_0 pypi
qtconsole 5.6.0 pypi_0 pypi
qtpy 2.4.1 pypi_0 pypi
readfcs 1.1.8 pypi_0 pypi
readline 8.2 h5eee18b_0 defaults
referencing 0.35.1 pypi_0 pypi
requests 2.32.3 pypi_0 pypi
rich 13.9.2 pypi_0 pypi
rpds-py 0.20.0 pypi_0 pypi
s3fs 2023.6.0 pypi_0 pypi
scanpy 1.10.3 pypi_0 pypi
scikit-image 0.24.0 pypi_0 pypi
scikit-learn 1.5.2 pypi_0 pypi
scipy 1.13.1 pypi_0 pypi
seaborn 0.13.2 pypi_0 pypi
session-info 1.0.0 pypi_0 pypi
setuptools 75.1.0 py39h06a4308_0 defaults
shapely 2.0.6 pypi_0 pypi
shellingham 1.5.4 pypi_0 pypi
six 1.16.0 pypi_0 pypi
slicerator 1.1.0 pypi_0 pypi
snowballstemmer 2.2.0 pypi_0 pypi
sortedcontainers 2.4.0 pypi_0 pypi
spatial-image 1.1.0 pypi_0 pypi
spatialdata 0.2.3 pypi_0 pypi
spatialdata-io 0.1.5 pypi_0 pypi
spatialdata-plot 0.2.6 pypi_0 pypi
sphinx 7.4.7 pypi_0 pypi
sphinxcontrib-applehelp 2.0.0 pypi_0 pypi
sphinxcontrib-devhelp 2.0.0 pypi_0 pypi
sphinxcontrib-htmlhelp 2.1.0 pypi_0 pypi
sphinxcontrib-jsmath 1.0.1 pypi_0 pypi
sphinxcontrib-qthelp 2.0.0 pypi_0 pypi
sphinxcontrib-serializinghtml 2.0.0 pypi_0 pypi
sqlite 3.45.3 h5eee18b_0 defaults
squidpy 1.6.1 pypi_0 pypi
stack-data 0.6.3 pypi_0 pypi
statsmodels 0.14.4 pypi_0 pypi
stdlib-list 0.11.0 pypi_0 pypi
superqt 0.6.7 pypi_0 pypi
tabulate 0.9.0 pypi_0 pypi
tblib 3.0.0 pypi_0 pypi
texttable 1.7.0 pypi_0 pypi
threadpoolctl 3.5.0 pypi_0 pypi
tifffile 2024.8.30 pypi_0 pypi
tinycss2 1.3.0 pypi_0 pypi
tk 8.6.14 h39e8969_0 defaults
tomli 2.0.2 pypi_0 pypi
tomli-w 1.1.0 pypi_0 pypi
toolz 1.0.0 pypi_0 pypi
tornado 6.4.1 pypi_0 pypi
tqdm 4.66.5 pypi_0 pypi
traitlets 5.14.3 pypi_0 pypi
typeguard 4.3.0 pypi_0 pypi
typer 0.12.5 pypi_0 pypi
typing-extensions 4.12.2 pypi_0 pypi
tzdata 2024.2 pypi_0 pypi
umap-learn 0.5.6 pypi_0 pypi
urllib3 1.26.20 pypi_0 pypi
validators 0.34.0 pypi_0 pypi
vispy 0.14.3 pypi_0 pypi
wcwidth 0.2.13 pypi_0 pypi
webencodings 0.5.1 pypi_0 pypi
wheel 0.44.0 py39h06a4308_0 defaults
wrapt 1.16.0 pypi_0 pypi
xarray 2024.7.0 pypi_0 pypi
xarray-dataclasses 1.8.0 pypi_0 pypi
xarray-datatree 0.0.14 pypi_0 pypi
xarray-schema 0.0.3 pypi_0 pypi
xarray-spatial 0.4.0 pypi_0 pypi
xz 5.4.6 h5eee18b_1 defaults
yarl 1.15.3 pypi_0 pypi
zarr 2.18.2 pypi_0 pypi
zict 3.0.0 pypi_0 pypi
zipp 3.20.2 pypi_0 pypi
zlib 1.2.13 h5eee18b_1 defaults
Thank you for your help!
Activity
ConstensouxAlexis commentedon Nov 7, 2024
Hi ! Do you have any update on this issue, or a workaround ? Thank you !
timtreis commentedon Nov 7, 2024
Hey @ConstensouxAlexis, the picture looks correct though, no? Given that your plot background is white, they should show up as white. Or what was the result you expected?
lisch7 commentedon Nov 8, 2024
@timtreis Hi, I expected the background to be transparent so that the underlying HE image would show through, as demonstrated in the tutorial. However, the background is currently solid white.
degrainger commentedon Nov 14, 2024
Hi @ConstensouxAlexis @lisch7,
I was running into the same issue as you with the white background. I managed to solve it. I think the
set_zero_in_cmap_to_transparent()function is running correctly and 0 values are transparent but it appears white because the image of the tissue is not being displayed. For me this was due to thecoordinate_systemsargument not being set correctly (was'global'but for me should have been"downscaled_hires"). I'd recomment inspecting your spatial object and checking that both the image and data you're trying to display together share the same coordinate system.Hope this helps!
Dave
LucaMarconato commentedon Jan 5, 2025
I would also try passing
method='matplotlib'inpl.render_shapes()as datashader may interpret the colormap differently. Please let us know if this is the case; we can ensure the two methods are aligned.timtreis commentedon Jan 7, 2025
@lisch7, does @degrainger s comment solve your question?
lisch7 commentedon Jan 10, 2025
No. Finally I draw the picture with the white background, not the transparent background.
Fix set_zero_in_cmap_to_transparent not working with datashader (#376)
Fix set_zero_in_cmap_to_transparent not working with datashader (#376)