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Description
I have a very simple example. I have a cropped spatialdata object
I am trying to plot shapes 'nucleus_boundaries' with colouring by 'ident_add' column from 'table'. But I get all shapes in grey colour.
Interestingly, if I use another shapes, which is related to another table (not in this example sdata object, but in a larger one, from which this was extracted), it works fine with cropping (using polygon query).
In that full sdata object there are shapes which are related to 'table' (generated by baysor segmentation) and 'nucleus_boundaries' related to 'old table'. Here though, I tried to not filter table and set table_name to old_table. Did not work. Tried to move 'old_table' to 'table' and removed table_name parameter from render_shapes. Then I filtered 'table'
anndata = sdata_cropped['table']
sdata_cropped['table'] = anndata[sdata_cropped['nucleus_boundaries'].index]and then tried to plot as follows:
sdata_cropped.pl.render_shapes('nucleus_boundaries', color='ident_add', table_name='table').pl.show()And get the following
Am I doing something wrong or is there a bug somewhere in the plotting routine? What am I doing wrong?