scverse
pl.render_shapes do not support normal hex color
Hi,
An normal hex color is a string include seven chars, such as "#DD4958", but pl.render_shapes uses nine chars when using datashader, which is not compatible with palette in stored in sdata["table"].uns["leiden_colors"]:
This is my palette:
['#1f77b4', '#ff7f0e', '#2ca02c', '#d62728', '#9467bd', '#8c564b']
So ian error occurred when using customized palette:
Besides, I must run sdata.pl.render_shapes without groups and palette first , then run sdata.pl.render_shapes with groups and palette for the second time. If I run sdata.pl.render_shapes with groups and palette directly, this error will occur:
Another question, we can only set groups as one "string" or all the categories. Such as if we have "0", "1", "2", "3", "4", "5" categories, we can only set groups="3" or groups=["0", "1","2","3","4","5"], we cannot set groups=["1","2"] and so on.
Thanks for reporting. It seems to be related to https://github.com/scverse/spatialdata-plot/issues/375. @timtreis any take?
The same issue persists. Besides that, why is it mandatory to specify groups when providing a palette? This restriction prevents me from customizing cell group colors freely, which is very inconvenient.
palette
['#F4A582', '#0571B0', '#CA0020', '#92C5DE', '#7BAFDE', '#BBD0DE']
sdata.pl.render_images("he_image").pl.render_shapes(
"cell_boundaries",
color="coarse_celltype_level1",
method="datashader",
groups=sdata["table"].obs['coarse_celltype_level1'].cat.categories.tolist(),
palette=palette
).pl.show(title="Lineage expression over H&E image", coordinate_systems="global", figsize=(10, 5))
File /rsrch8/scratch/genomic_med/tchu1/conda/envs/st-python/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:937, 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)
932 wanted_elements, wanted_shapes_on_this_cs, wants_shapes = _get_wanted_render_elements(
933 sdata, wanted_elements, params_copy, cs, "shapes"
934 )
936 if wanted_shapes_on_this_cs:
--> 937 _render_shapes(
938 sdata=sdata,
939 render_params=params_copy,
940 coordinate_system=cs,
941 ax=ax,
942 fig_params=fig_params,
943 scalebar_params=scalebar_params,
944 legend_params=legend_params,
945 )
947 elif cmd == "render_points" and has_points:
948 wanted_elements, wanted_points_on_this_cs, wants_points = _get_wanted_render_elements(
949 sdata, wanted_elements, params_copy, cs, "points"
950 )
File /rsrch8/scratch/genomic_med/tchu1/conda/envs/st-python/lib/python3.10/site-packages/spatialdata_plot/pl/render.py:259, in _render_shapes(sdata, render_params, coordinate_system, ax, fig_params, scalebar_params, legend_params)
256 if isinstance(ds_cmap, str) and ds_cmap[0] == "#":
257 ds_cmap = ds_cmap[:-2]
--> 259 ds_result = ds.tf.shade(
260 agg,
261 cmap=ds_cmap,
262 color_key=color_key,
263 min_alpha=np.min([254, render_params.fill_alpha * 255]),
264 how="linear",
265 )
266 elif aggregate_with_reduction is not None: # to shut up mypy
267 ds_cmap = render_params.cmap_params.cmap
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 <listcomp>(.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
@LucaMarconato @timtreis
