Updata on plotting categories clusters.

[christophechu]

As those issues mentioned.

#422 (comment)
#391
#414

#423

I think you have already resolved part of the issue, especially for the matplotlib backend — which now correctly handles aspects like coordinate alignment and axis visibility.

However, the current fix appears to be limited to method='matplotlib'. When working with large datasets and switching to method='datashader', the same issues still persist. For example:

File /rsrch8/scratch/genomic_med/tchu1/conda/envs/st-python/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:936, in PlotAccessor.show(self, coordinate_systems, legend_fontsize, legend_fontweight, legend_loc, legend_fontoutline, na_in_legend, colorbar, wspace, hspace, ncols, frameon, figsize, dpi, fig, title, share_extent, pad_extent, ax, return_ax, save)
931 wanted_elements, wanted_shapes_on_this_cs, wants_shapes = _get_wanted_render_elements(
932 sdata, wanted_elements, params_copy, cs, "shapes"
933 )
935 if wanted_shapes_on_this_cs:
--> 936 _render_shapes(
937 sdata=sdata,
938 render_params=params_copy,
939 coordinate_system=cs,
940 ax=ax,
941 fig_params=fig_params,
942 scalebar_params=scalebar_params,
943 legend_params=legend_params,
944 )
946 elif cmd == "render_points" and has_points:
947 wanted_elements, wanted_points_on_this_cs, wants_points = _get_wanted_render_elements(
948 sdata, wanted_elements, params_copy, cs, "points"
949 )

File /rsrch8/scratch/genomic_med/tchu1/conda/envs/st-python/lib/python3.10/site-packages/spatialdata_plot/pl/render.py:262, in _render_shapes(sdata, render_params, coordinate_system, ax, fig_params, scalebar_params, legend_params)
259 if isinstance(ds_cmap, str) and ds_cmap[0] == "#":
260 ds_cmap = ds_cmap[:-2]
--> 262 ds_result = _datashader_map_aggregate_to_color(
263 agg,
264 cmap=ds_cmap,
265 color_key=color_key,
266 min_alpha=np.min([254, render_params.fill_alpha * 255]),
267 ) # prevent min_alpha == 255, bc that led to fully colored test plots instead of just colored points/shapes
268 elif aggregate_with_reduction is not None: # to shut up mypy
269 ds_cmap = render_params.cmap_params.cmap

File /rsrch8/scratch/genomic_med/tchu1/conda/envs/st-python/lib/python3.10/site-packages/spatialdata_plot/pl/utils.py:2332, in _datashader_map_aggregate_to_color(agg, cmap, color_key, min_alpha, span, clip)
2329 stack[stack[:, :, 3] == 0] = img_over[stack[:, :, 3] == 0]
2330 return stack
-> 2332 return ds.tf.shade(agg, cmap=cmap, color_key=color_key, min_alpha=min_alpha, span=span, how="linear")

File /rsrch8/scratch/genomic_med/tchu1/conda/envs/st-python/lib/python3.10/site-packages/datashader/transfer_functions/init.py:720, in shade(agg, cmap, color_key, how, alpha, min_alpha, span, name, color_baseline, rescale_discrete_levels)
717 return _interpolate(agg, cmap, how, alpha, span, min_alpha, name,
718 rescale_discrete_levels)
719 elif agg.ndim == 3:
--> 720 return _colorize(agg, color_key, how, alpha, span, min_alpha, name, color_baseline,
721 rescale_discrete_levels)
722 else:
723 raise ValueError("agg must use 2D or 3D coordinates")

File /rsrch8/scratch/genomic_med/tchu1/conda/envs/st-python/lib/python3.10/site-packages/datashader/transfer_functions/init.py:378, in _colorize(agg, color_key, how, alpha, span, min_alpha, name, color_baseline, rescale_discrete_levels)
374 if len(color_key) < len(cats):
375 raise ValueError(f"Insufficient colors provided ({len(color_key)}) for the categorical "
376 f"fields available ({len(cats)})")
--> 378 colors = [rgb(color_key[c]) for c in cats]
379 rs, gs, bs = map(array, zip(*colors))
381 # Reorient array (transposing the category dimension first)

File /rsrch8/scratch/genomic_med/tchu1/conda/envs/st-python/lib/python3.10/site-packages/datashader/transfer_functions/init.py:378, in (.0)
374 if len(color_key) < len(cats):
375 raise ValueError(f"Insufficient colors provided ({len(color_key)}) for the categorical "
376 f"fields available ({len(cats)})")
--> 378 colors = [rgb(color_key[c]) for c in cats]
379 rs, gs, bs = map(array, zip(*colors))
381 # Reorient array (transposing the category dimension first)

File /rsrch8/scratch/genomic_med/tchu1/conda/envs/st-python/lib/python3.10/site-packages/datashader/colors.py:116, in rgb(x)
114 if isinstance(x, str):
115 if x.startswith('#'):
--> 116 return hex_to_rgb(x)
117 elif x in color_lookup:
118 return hex_to_rgb(color_lookup[x])

File /rsrch8/scratch/genomic_med/tchu1/conda/envs/st-python/lib/python3.10/site-packages/datashader/colors.py:91, in hex_to_rgb(x)
83 """Convert a color hexcode to an rgb tuple.
84
85 Example
(...)
88 (255, 255, 255)
89 """
90 if not (x.startswith('#') and len(x) == 7):
---> 91 raise ValueError("Invalid hex color")
92 x = x.strip('#')
93 try:

ValueError: Invalid hex color

[timtreis]

Hey @christophechu, please add further info to existing issues if it's the same problem instead of opening new issues, thank you :)