Issue with set_zero_in_cmap_to_transparent Function Not Making Zero Values Transparent in Spatial Data Plotting

[lisch7]

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
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_openmp_mutex 5.1 1_gnu defaults
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Thank you for your help!

[ConstensouxAlexis]

Hi ! Do you have any update on this issue, or a workaround ? Thank you !

[timtreis]

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]

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?

@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]

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 the coordinate_systems argument 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]

I would also try passing method='matplotlib' in pl.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]

@lisch7, does @degrainger s comment solve your question?

[lisch7]

@lisch7, does @degrainger s comment solve your question?

No. Finally I draw the picture with the white background, not the transparent background.