spatialdata-plot
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scverse
Static plotting for spatialdata
Morning, Trying to make a side-by-side render_image and render_label plot for my sdata object. My code worked with earlier versions of spatialdata-plot, but since updating to 0.2.8 have found some...
`spatialdata_plot.pl.render._render_labels` still had `sdata.table` , changed to `sdata.tables[table_name]`, otherwise colors passed via .uns where ignored. also in https://github.com/scverse/spatialdata-plot/blob/43f25f654e123ca3a6a5da0e499ef15f22d0ec27/src/spatialdata_plot/pl/utils.py#L854 I would remove the check `cluster_key` in `adata.uns`. Because of this I...
When attempting to `render_shapes` with a color key or a table key that does not exist, spatialdata-plot just plots everything grey. I would expect it to raise a KeyError instead....
Hi， I get an error when I use `spatialdata==0.3.0` and `spatialdata-plot==0.2.9` to plot **Shapes** with `method=="datashader"`, but `method=="matplotlib"` is ok! Here is my code:  I don't know whether it's...
Hey! I've come across an issue when trying to plot some images where one of the channels is an alpha level. This is a visium image that was submitted to...
`scanpy.pl.spatial` has a argument `bw=True` that allows to plot a background image in grayscale. I find that useful when plotting shapes on top of an image because the pink H&E...
Hi Spatialdata team! I have recently discovered a bug when plotting data with affine transformations applied and using `method='datashader`. Below is an example based on the [mouse_liver](https://s3.embl.de/spatialdata/spatialdata-sandbox/mouse_liver.zip) dataset. To reproduce,...
# **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...
``` crop0(xenium_sdata).pl.render_labels(outline_alpha=0.4, fill_alpha=0, color="cell_type", contour_px= None, palette=colors, groups=groups).pl.show(coordinate_systems=["global"]) ```  Same command works for CosMx, but doesn't work for Xenium.
Hi, I plot the cell boundaries with `method='datashader'` and `method='matplotlib'`, they both display the cell distribution without overlapping (total 13899 cells). But the `datashader` plot seems more sparse than `matplotlib`...