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render_shapes() - problem with cmap alpha #251
Description
The alpha doesn't work for me, what am I missing?
viridis = cm.get_cmap("viridis", 256)
colors = viridis(np.linspace(0, 0.8, 256))
colors[0, :] = [1, 1, 1, 0]
new_cmap = LinearSegmentedColormap.from_list("truncated_viridis", colors)
sdata_small.pl.render_images("Visium_HD_Mouse_Small_Intestine_full_image").pl.render_shapes(
f"Visium_HD_Mouse_Small_Intestine_square_016um", color=gene_name, cmap=new_cmap).pl.show(
coordinate_systems="global", title=gene_name, figsize=(10, 10))
The alpha doesn't work even when I use custon cmap with low alpha all over:
Activity
Bioin-Mixologist commentedon May 2, 2024
I face the same mishap, and open one issue Cannot be shown in transparent colors when Plotting the gene expression data at SpatialData.
don't know why, but guess may be associate "clipping input data to the valid range for imshow with RGB data （[0..1] for floats or [0..255]for integers)"
LucaMarconato commentedon May 2, 2024
Hi, it looks like that the reason is that the fix from this PR #239 didn't make it to a release yet. I will cut a release now.
LucaMarconato commentedon May 2, 2024
I made the release in
pip, please let me know if this fixes your issue.Bioin-Mixologist commentedon May 2, 2024
Thankfully @LucaMarconato , after the update, it is now possible to display transparent colors.
However, i found exp maybe diiferent if chage get_cmap() follow the prompts, and prepare to open a new issue #255 .
melonora commentedon Jul 16, 2024
Thanks for opening the new issue, given that the reason for this issue has been solved I will be closing this one. Currently we are in the process of going through all issues with the repositories related to SpatialData so we will address your new issue:)