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Cannot plot continuous var values to labels #165

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#201
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Cannot plot continuous var values to labels#165
#201
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timtreis
Labels
bugSomething isn't workingpriority: high
Milestone
v0.1.0 release

Description

@LucaMarconato
LucaMarconato
opened on Sep 29, 2023

This code tries to plots the var present in the table in the blobs dataset, which is mapped to the labels.

import spatialdata as sd
from spatialdata.datasets import blobs
import spatialdata_plot
from napari_spatialdata import Interactive

sdata = blobs()

sdata.pl.render_labels('blobs_labels', key='channel_0_sum').pl.show()

# Interactive(sdata)

This is the output produced (tried for all the var_names: 'channel_0_sum', 'channel_1_sum', 'channel_2_sum', but all lead to the same plot)
image

This is the output produced by napari_spatialdata
image
).

Activity

  1. LucaMarconato
    added
    bugSomething isn't working
    on Sep 29, 2023

  2. LucaMarconato commented on Sep 29, 2023

    @LucaMarconato
    LucaMarconato
    on Sep 29, 2023
    MemberAuthor

    My mistake, I had to use the parameter color, not key. This leads to another bug: AttributeError: 'SpatialImage' object has no attribute 'index'

    sdata.pl.render_labels('blobs_labels', color='channel_0_sum').pl.show()
    /Users/macbook/embl/projects/basel/spatialdata/src/spatialdata/_core/operations/aggregate.py:244: UserWarning: Converting `region_key: region` to categorical dtype.
  table = TableModel.parse(table, region=shapes_name, region_key=region_key, instance_key=instance_key)
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[26], line 8
      4 from napari_spatialdata import Interactive
      6 sdata = blobs()
----> 8 sdata.pl.render_labels('blobs_labels', color='channel_0_sum').pl.show()
     10 # Interactive(sdata)

File ~/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/basic.py:696, 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)
    689         if is_categorical_dtype(colors):
    690             _maybe_set_colors(
    691                 source=sdata.table,
    692                 target=sdata.table,
    693                 key=params.color,
    694                 palette=params.palette,
    695             )
--> 696     _render_labels(
    697         sdata=sdata,
    698         render_params=params,
    699         coordinate_system=cs,
    700         ax=ax,
    701         fig_params=fig_params,
    702         scalebar_params=scalebar_params,
    703         legend_params=legend_params,
    704     )
    706 if title is not None:
    707     if len(title) == 1:

File ~/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/render.py:448, in _render_labels(sdata, render_params, coordinate_system, ax, fig_params, scalebar_params, legend_params)
    445     instance_id = table.obs[instance_key].values
    447 # get color vector (categorical or continuous)
--> 448 color_source_vector, color_vector, categorical = _set_color_source_vec(
    449     sdata=sdata_filt,
    450     element=sdata_filt.labels[label_key],
    451     element_name=label_key,
    452     value_to_plot=render_params.color,
    453     layer=render_params.layer,
    454     groups=render_params.groups,
    455     palette=render_params.palette,
    456     na_color=render_params.cmap_params.na_color,
    457     alpha=render_params.fill_alpha,
    458 )
    460 if (render_params.fill_alpha != render_params.outline_alpha) and render_params.contour_px is not None:
    461     # First get the labels infill and plot them
    462     labels_infill = _map_color_seg(
    463         seg=label.values,
    464         cell_id=instance_id,
   (...)
    470         na_color=render_params.cmap_params.na_color,
    471     )

File ~/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/utils.py:831, in _set_color_source_vec(sdata, element, value_to_plot, element_name, layer, groups, palette, na_color, alpha)
    826     raise ValueError(
    827         f"Color key '{value_to_plot}' for element '{element_name}' been found in multiple locations: {origins}."
    828     )
    830 if len(origins) == 1:
--> 831     vals = get_values(value_key=value_to_plot, sdata=sdata, element_name=element_name)
    832     color_source_vector = vals[value_to_plot]
    834     # if all([isinstance(x, str) for x in color_source_vector]):
    835     #     raise TypeError(
    836     #         f"Color key '{value_to_plot}' for element '{element_name}' has string values, "
   (...)
    839 
    840     # numerical case, return early

File ~/embl/projects/basel/spatialdata/src/spatialdata/_core/query/relational_query.py:268, in get_values(value_key, element, sdata, element_name)
    266 if sdata is not None:
    267     assert element_name is not None
--> 268     matched_table = match_table_to_element(sdata=sdata, element_name=element_name)
    269     if origin == "obs":
    270         return matched_table.obs[value_key_values]

File ~/embl/projects/basel/spatialdata/src/spatialdata/_core/query/relational_query.py:151, in match_table_to_element(sdata, element_name)
    149 assert element_type in ["labels", "shapes"], f"Element {element_name} ({element_type}) is not supported"
    150 elements_dict = {element_type: {element_name: element}}
--> 151 return _filter_table_by_elements(sdata.table, elements_dict, match_rows=True)

File ~/embl/projects/basel/spatialdata/src/spatialdata/_core/query/relational_query.py:114, in _filter_table_by_elements(table, elements_dict, match_rows)
    112 assert "element" in locals()
    113 assert "name" in locals()
--> 114 n0 = np.setdiff1d(element.index.to_numpy(), table.obs[instance_key].to_numpy())
    115 n1 = np.setdiff1d(table.obs[instance_key].to_numpy(), element.index.to_numpy())
    116 raise ValueError(
    117     f"Instances in the table and in the element don't correspond: found {len(n0)} indices in the "
    118     f"element {name} but not in the table and found {len(n1)} indices in the table but not in the "
    119     "element"
    120 )

File ~/miniconda3/envs/ome/lib/python3.10/site-packages/xarray/core/common.py:278, in AttrAccessMixin.__getattr__(self, name)
    276         with suppress(KeyError):
    277             return source[name]
--> 278 raise AttributeError(
    279     f"{type(self).__name__!r} object has no attribute {name!r}"
    280 )

AttributeError: 'SpatialImage' object has no attribute 'index'

  3. timtreis commented on Oct 4, 2023

    @timtreis
    timtreis
    on Oct 4, 2023
    Member

    This error is in spatialdata though, I'm fighting with it in like 3 different issues :D

  4. LucaMarconato commented on Oct 8, 2023

    @LucaMarconato
    LucaMarconato
    on Oct 8, 2023
    MemberAuthor

    Apologies, I fixed the bug in get_values() and the PR is now merged scverse/spatialdata#367.
    The bug was due to the fact that the labels element contains the background (value 0), but not the table. I fixed this and the values returned by get_values() now never contain the background.

    Anyway, this leads to another bug now, which I think it's due to the fact that spatialdata-plot expects a value also for the background.
    Can you make your code ignore the background and not display anything for it (like showing a color with alpha = 0)?

    Note, to make the task easier, and also to take into account that the labels element could contain non-continuous labels, this new PR (merged) ensures that the dataframe returned by get_values() has the instance_key values in its index. scverse/spatialdata#368

    This is the traceback of the new bug:

    ------------------
ax = plt.gca()
sdata.pl.render_images("blobs_image", cmap="viridis", channel=1).pl.show(ax=ax)
sdata_im.pl.render_labels(color="channel_1_mean", fill_alpha=0.5).pl.show(ax=ax)
------------------
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
File /mnt/repos/spatialdata-plot/src/spatialdata_plot/pl/utils.py:899, in _map_color_seg(seg, cell_id, color_vector, color_source_vector, cmap_params, seg_erosionpx, seg_boundaries, na_color)
    898 try:
--> 899     cols = cmap_params.cmap(cmap_params.norm(color_vector))
    900 except TypeError:
TypeError: 'NoneType' object is not callable
During handling of the above exception, another exception occurred:
AssertionError                            Traceback (most recent call last)
Cell In[8], line 3
      1 ax = plt.gca()
      2 sdata.pl.render_images("blobs_image", cmap="viridis", channel=1).pl.show(ax=ax)
----> 3 sdata_im.pl.render_labels(color="channel_1_mean", fill_alpha=0.5).pl.show(ax=ax)
File /mnt/repos/spatialdata-plot/src/spatialdata_plot/pl/basic.py:704, 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)
    697         if is_categorical_dtype(colors):
    698             _maybe_set_colors(
    699                 source=sdata.table,
    700                 target=sdata.table,
    701                 key=params.color,
    702                 palette=params.palette,
    703             )
--> 704     _render_labels(
    705         sdata=sdata,
    706         render_params=params,
    707         coordinate_system=cs,
    708         ax=ax,
    709         fig_params=fig_params,
    710         scalebar_params=scalebar_params,
    711         legend_params=legend_params,
    712     )
    714 if title is not None:
    715     if len(title) == 1:
File /mnt/repos/spatialdata-plot/src/spatialdata_plot/pl/render.py:508, in _render_labels(sdata, render_params, coordinate_system, ax, fig_params, scalebar_params, legend_params)
    493 color_source_vector, color_vector, categorical = _set_color_source_vec(
    494     sdata=sdata_filt,
    495     element=sdata_filt.labels[label_key],
   (...)
    503     cmap_params=render_params.cmap_params,
    504 )
    506 if (render_params.fill_alpha != render_params.outline_alpha) and render_params.contour_px is not None:
    507     # First get the labels infill and plot them
--> 508     labels_infill = _map_color_seg(
    509         seg=label.values,
    510         cell_id=instance_id,
    511         color_vector=color_vector,
    512         color_source_vector=color_source_vector,
    513         cmap_params=render_params.cmap_params,
    514         seg_erosionpx=None,
    515         seg_boundaries=render_params.outline,
    516         na_color=render_params.cmap_params.na_color,
    517     )
    519     _cax = ax.imshow(
    520         labels_infill,
    521         rasterized=True,
   (...)
    526         # zorder=3,
    527     )
    528     cax = ax.add_image(_cax)
File /mnt/repos/spatialdata-plot/src/spatialdata_plot/pl/utils.py:901, in _map_color_seg(seg, cell_id, color_vector, color_source_vector, cmap_params, seg_erosionpx, seg_boundaries, na_color)
    899         cols = cmap_params.cmap(cmap_params.norm(color_vector))
    900     except TypeError:
--> 901         assert all(colors.is_color_like(c) for c in color_vector), "Not all values are color-like."
    902         cols = colors.to_rgba_array(color_vector)
    904 if seg_erosionpx is not None:
AssertionError: Not all values are color-like.

  5. LucaMarconato commented on Oct 8, 2023

    @LucaMarconato
    LucaMarconato
    on Oct 8, 2023
    MemberAuthor

    Finally in this PR scverse/spatialdata#369, I ensure that for labels, get_values() returns a table whose row are sorted by ascending labels value. Anyway, the safe way to match the returned dataframe to the labels is by looking at the index of the returned dataframe, not by looking at the order.

  6. LucaMarconato
    added
    priority: medium
    on Oct 10, 2023

  7. LucaMarconato commented on Oct 10, 2023

    @LucaMarconato
    LucaMarconato
    on Oct 10, 2023
    MemberAuthor

    Setting medium priority since it shows up in the documentation notebooks.

  8. LucaMarconato commented on Oct 10, 2023

    @LucaMarconato
    LucaMarconato
    on Oct 10, 2023
    MemberAuthor

    The current error AssertionError: Not all values are color-like is also appearing in the last plot of the mibitof notebook (I have just fixed the bug with get_values() in scverse/spatialdata#376.

  9. timtreis commented on Oct 11, 2023

    @timtreis
    timtreis
    on Oct 11, 2023
    Member

    I'd love to wait for @Sonja-Stockhaus' #164 to get started on this because we pulled the get_extent refactor on our end into her multi-scale PR because they had quite some otherwise-conflicting overlap. Once that's merged can follow up with a) figuring out if downstream bugs still exist and b) then solve the ones that do.

  10. LucaMarconato commented on Oct 11, 2023

    @LucaMarconato
    LucaMarconato
    on Oct 11, 2023
    MemberAuthor

    Ok perfect, thanks a lot!

  11. timtreis
    self-assigned this
    on Nov 27, 2023

  12. timtreis commented on Nov 28, 2023

    @timtreis
    timtreis
    on Nov 28, 2023
    Member

    Update: Issue persists, will tackle next.

    ---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
File [~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/utils.py:666](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/utils.py:666), in _map_color_seg(seg, cell_id, color_vector, color_source_vector, cmap_params, seg_erosionpx, seg_boundaries, na_color)
    [665](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/utils.py:665) try:
--> [666](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/utils.py:666)     cols = cmap_params.cmap(cmap_params.norm(color_vector))
    [667](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/utils.py:667) except TypeError:

TypeError: 'NoneType' object is not callable

During handling of the above exception, another exception occurred:

AssertionError                            Traceback (most recent call last)
[/Users/tim.treis/Documents/GitHub/spatialdata-plot/test.ipynb](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/test.ipynb) Cell 2 line <cell line: 7>()
      [3](vscode-notebook-cell:/Users/tim.treis/Documents/GitHub/spatialdata-plot/test.ipynb#X21sZmlsZQ%3D%3D?line=2) import spatialdata_plot
      [5](vscode-notebook-cell:/Users/tim.treis/Documents/GitHub/spatialdata-plot/test.ipynb#X21sZmlsZQ%3D%3D?line=4) sdata = blobs()
----> [7](vscode-notebook-cell:/Users/tim.treis/Documents/GitHub/spatialdata-plot/test.ipynb#X21sZmlsZQ%3D%3D?line=6) sdata.pl.render_labels("blobs_labels", color="channel_0_sum").pl.show()

File [~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/basic.py:774](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/basic.py:774), 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)
    [768](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/basic.py:768)     if len(wanted_labels_on_this_cs) > 0:
    [769](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/basic.py:769)         rasterize = (params.scale is None) or (
    [770](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/basic.py:770)             isinstance(params.scale, str)
    [771](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/basic.py:771)             and params.scale != "full"
    [772](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/basic.py:772)             and (dpi is not None or figsize is not None)
    [773](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/basic.py:773)         )
--> [774](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/basic.py:774)         _render_labels(
    [775](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/basic.py:775)             sdata=sdata,
    [776](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/basic.py:776)             render_params=params,
    [777](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/basic.py:777)             coordinate_system=cs,
    [778](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/basic.py:778)             ax=ax,
    [779](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/basic.py:779)             fig_params=fig_params,
    [780](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/basic.py:780)             scalebar_params=scalebar_params,
    [781](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/basic.py:781)             legend_params=legend_params,
    [782](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/basic.py:782)             rasterize=rasterize,
    [783](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/basic.py:783)         )
    [785](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/basic.py:785) if title is None:
    [786](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/basic.py:786)     t = cs

File [~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:593](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:593), in _render_labels(sdata, render_params, coordinate_system, ax, fig_params, scalebar_params, legend_params, rasterize)
    [578](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:578) color_source_vector, color_vector, categorical = _set_color_source_vec(
    [579](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:579)     sdata=sdata_filt,
    [580](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:580)     element=label,
   (...)
    [588](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:588)     cmap_params=render_params.cmap_params,
    [589](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:589) )
    [591](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:591) if (render_params.fill_alpha != render_params.outline_alpha) and render_params.contour_px is not None:
    [592](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:592)     # First get the labels infill and plot them
--> [593](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:593)     labels_infill = _map_color_seg(
    [594](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:594)         seg=label.values,
    [595](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:595)         cell_id=instance_id,
    [596](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:596)         color_vector=color_vector,
    [597](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:597)         color_source_vector=color_source_vector,
    [598](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:598)         cmap_params=render_params.cmap_params,
    [599](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:599)         seg_erosionpx=None,
    [600](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:600)         seg_boundaries=render_params.outline,
    [601](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:601)         na_color=render_params.cmap_params.na_color,
    [602](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:602)     )
    [604](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:604)     _cax = ax.imshow(
    [605](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:605)         labels_infill,
    [606](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:606)         rasterized=True,
   (...)
    [610](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:610)         origin="lower",
    [611](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:611)     )
    [612](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/render.py:612)     _cax.set_transform(trans_data)

File [~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/utils.py:668](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/utils.py:668), in _map_color_seg(seg, cell_id, color_vector, color_source_vector, cmap_params, seg_erosionpx, seg_boundaries, na_color)
    [666](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/utils.py:666)         cols = cmap_params.cmap(cmap_params.norm(color_vector))
    [667](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/utils.py:667)     except TypeError:
--> [668](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/utils.py:668)         assert all(colors.is_color_like(c) for c in color_vector), "Not all values are color-like."
    [669](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/utils.py:669)         cols = colors.to_rgba_array(color_vector)
    [671](https://file+.vscode-resource.vscode-cdn.net/Users/tim.treis/Documents/GitHub/spatialdata-plot/~/Documents/GitHub/spatialdata-plot/src/spatialdata_plot/pl/utils.py:671) if seg_erosionpx is not None:

AssertionError: Not all values are color-like.
  13. timtreis
    added
    priority: high
    and removed
    priority: medium
    on Dec 7, 2023
  14. timtreis
    added this to the v0.1.0 release milestone on Dec 8, 2023
  15. Sonja-Stockhaus
    linked a pull request that will close this issuePlotting of continuous values when norm=None #201on Dec 12, 2023
  16. timtreis
    closed this as completedin #201on Jan 9, 2024
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