spatialdata-plot
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scverse
Static plotting for spatialdata
Code to reproduce: ```python import spatialdata import spatialdata_plot sdata = spatialdata.datasets.blobs() # add some labelling we want to color with a custom defined palette sdata["table"].obs["labelling"] = (sdata["table"].obs["instance_id"]>10).astype('int').astype('str') sdata["table"].obs["labelling"] = sdata["table"].obs["labelling"].astype('category')...
Original comment from @MeyerBender > - normalization of channels: see differences between the two notebooks when plotting all channels but DAPI. I guess it is intentional that no normalization is...
Currently it doesn't seem possible to change the color of the border of labels. For instance, reported by @MeyerBender, using ```python sdata_zoomed.pl.render_images(channel=["DAPI"]).pl.render_labels(outline_alpha=1, fill_alpha=0, color="white").pl.show() ``` shows a black border ([code...
Originally reported by @MeyerBender > - normalization of channels: see differences between the two notebooks when plotting all channels but DAPI. I guess it is intentional that no normalization is...
From @MeyerBender: > - legends: in my opinion, it would be great to show legends for the channels by default. Alternatively, one could consider implementing something like pl.render_legend() to give...
To reproduce, please run [the notebook from this PR](https://github.com/scverse/spatialdata-notebooks/blob/feature/sdata_from_scratch/notebooks/examples/sdata_from_scratch.ipynb), which doesn't require any data (it uses the one from `squidpy`). The code cell ```python fig, axs = plt.subplots(1, 3, figsize=(18,...
Comment originally from @MeyerBender, thanks for the feedback! > documentation: in general, I think it would be good to have one or two notebooks that exclusively focus on visualization. Right...
I think the current implementation doesn't correctly handle images with 3+ channels, for example resulting in the following warning when rendering a 5 channel image: `Clipping input data to the...
This PR now cleanly converts to categorical for strings. I also added logging and the lack of usage of the "xyz_colors" column the user mentioned.