Missing colormap values during 3D reconstruction from multiple slices #342
Description
Dear developer team of Spateo,
Thank you so much for developing such an impressive tool for spatial transcriptomics data!
I was trying to follow the official tutorial in Section 5 to reconstruct a 3D plot from aligned multiple slices, but encountered a few errors.
As I used a different set of data for exploring the tool, I am not sure how to deal with the missing color map in the PyVista step.
point_cloud, _ = st.tdr.construct_pc(
adata = aligned_adata,
#spatial_key = "spatial_3D",
spatial_key = "aligned_spatial_3D",
groupby = cluster_key,
key_added = "tissue",
colormap = palette,
)
point_cloudThe point_cloud data looks like this:
Compared to the one in the tutorial, the key tissue_rgba is missing in the object.
This caused an error message during the visualization step
# show the aligned drosophila in 3D
st.pl.three_d_plot(
model = point_cloud,
key = "tissue",
model_style = 'points',
model_size = 8,
show_axes = True,
jupyter = "static",
window_size = (1200, 1200),
show_outline = True,
outline_kwargs = {'show_labels': False, 'outline_width': 3},
# plotter_filename='./results/Drosophila_8_9_rigid_alignment_reconstruction.html', # uncomment this for saving the interactive 3D visualization
)Error message:
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
Cell In[64], line 2
1 # show the aligned drosophila in 3D
----> 2 st.pl.three_d_plot(
3 model = point_cloud,
4 key = "tissue",
5 model_style = 'points',
6 model_size = 8,
7 show_axes = True,
8 jupyter = "static",
9 window_size = (1200, 1200),
10 show_outline = True,
11 outline_kwargs = {'show_labels': False, 'outline_width': 3},
12 # plotter_filename='./results/Drosophila_8_9_rigid_alignment_reconstruction.html', # uncomment this for saving the interactive 3D visualization
13 )
File <full_path_not_shown_here_due_to_security_concern>/miniforge3/envs/Spateo/lib/python3.9/site-packages/spateo/plotting/static/three_d_plot/three_dims_plots.py:324, in three_d_plot(model, key, filename, jupyter, off_screen, window_size, background, cpo, colormap, ambient, opacity, model_style, model_size, show_legend, legend_kwargs, show_outline, outline_kwargs, text, text_kwargs, view_up, framerate, plotter_filename, show_axes)
322 # Create a plotting object to display pyvista/vtk model.
323 p = create_plotter(off_screen=off_screen1, **plotter_kws)
--> 324 wrap_to_plotter(plotter=p, model=model, key=key, cpo=cpo, **model_kwargs)
325 cpo = p.show(return_cpos=True, jupyter_backend="none", cpos=cpo)
327 # Create another plotting object to save pyvista/vtk model.
File <full_path_not_shown_here_due_to_security_concern>/miniforge3/envs/Spateo/lib/python3.9/site-packages/spateo/plotting/static/three_d_plot/three_dims_plots.py:115, in wrap_to_plotter(plotter, model, key, background, cpo, colormap, ambient, opacity, model_style, model_size, show_legend, legend_kwargs, show_outline, outline_kwargs, text, text_kwargs)
112 cbg_rgb = (1 - bg_rgb[0], 1 - bg_rgb[1], 1 - bg_rgb[2])
114 # Add model(s) to the plotter.
--> 115 add_model(
116 plotter=plotter,
117 model=model,
118 key=key,
119 colormap=colormap,
120 ambient=ambient,
121 opacity=opacity,
122 model_size=model_size,
123 model_style=model_style,
124 )
126 # Set the camera position of plotter.
127 plotter.camera_position = cpo
File <full_path_not_shown_here_due_to_security_concern>/miniforge3/envs/Spateo/lib/python3.9/site-packages/spateo/plotting/static/three_d_plot/three_dims_plotter.py:209, in add_model(plotter, model, key, colormap, ambient, opacity, model_style, model_size)
198 _add_model(
199 _p=plotter,
200 _model=sub_model,
(...)
206 _opacity=sub_op,
207 )
208 else:
--> 209 _add_model(
210 _p=plotter,
211 _model=model,
212 _key=key,
213 _colormap=colormap,
214 _style=model_style,
215 _model_size=model_size,
216 _ambient=ambient,
217 _opacity=opacity,
218 )
File <full_path_not_shown_here_due_to_security_concern>/miniforge3/envs/Spateo/lib/python3.9/site-packages/spateo/plotting/static/three_d_plot/three_dims_plotter.py:173, in add_model.<locals>._add_model(_p, _model, _key, _colormap, _style, _ambient, _opacity, _model_size)
163 added_kwargs = (
164 dict(
165 scalars=_key if _key in _model.array_names else _model.active_scalars_name,
(...)
169 else dict(color=_colormap)
170 )
172 mesh_kwargs.update(added_kwargs)
--> 173 _p.add_mesh(_model, **mesh_kwargs)
File <full_path_not_shown_here_due_to_security_concern>/miniforge3/envs/Spateo/lib/python3.9/site-packages/pyvista/_deprecate_positional_args.py:245, in _deprecate_positional_args.<locals>._inner_deprecate_positional_args.<locals>.inner_f(*args, **kwargs)
241 warnings.warn(msg, PyVistaDeprecationWarning, stacklevel=stack_level)
243 warn_positional_args()
--> 245 return f(*args, **kwargs)
File <full_path_not_shown_here_due_to_security_concern>/miniforge3/envs/Spateo/lib/python3.9/site-packages/pyvista/plotting/plotter.py:3799, in BasePlotter.add_mesh(self, mesh, color, style, scalars, clim, show_edges, edge_color, point_size, line_width, opacity, flip_scalars, lighting, n_colors, interpolate_before_map, cmap, label, reset_camera, scalar_bar_args, show_scalar_bar, multi_colors, name, texture, render_points_as_spheres, render_lines_as_tubes, smooth_shading, split_sharp_edges, ambient, diffuse, specular, specular_power, nan_color, nan_opacity, culling, rgb, categories, silhouette, use_transparency, below_color, above_color, annotations, pickable, preference, log_scale, pbr, metallic, roughness, render, user_matrix, component, emissive, copy_mesh, backface_params, show_vertices, edge_opacity, **kwargs)
3796 rgb = True
3798 original_scalar_name = scalars
-> 3799 scalars = get_array(mesh, scalars, preference=preference, err=True)
3800 scalar_bar_args.setdefault('title', original_scalar_name)
3801 scalars_name = original_scalar_name
File <full_path_not_shown_here_due_to_security_concern>/miniforge3/envs/Spateo/lib/python3.9/site-packages/pyvista/_deprecate_positional_args.py:245, in _deprecate_positional_args.<locals>._inner_deprecate_positional_args.<locals>.inner_f(*args, **kwargs)
241 warnings.warn(msg, PyVistaDeprecationWarning, stacklevel=stack_level)
243 warn_positional_args()
--> 245 return f(*args, **kwargs)
File <full_path_not_shown_here_due_to_security_concern>/miniforge3/envs/Spateo/lib/python3.9/site-packages/pyvista/core/utilities/arrays.py:436, in get_array(mesh, name, preference, err)
434 elif err:
435 msg = f'Data array ({name}) not present in this dataset.'
--> 436 raise KeyError(msg)
437 else:
438 out = None
KeyError: 'Data array (tissue_rgba) not present in this dataset.'
The aligned aligned_adata looks like:
AnnData object with n_obs × n_vars = 22534 × 27362
obs: 'orig.ident', 'nCount_RNA', 'nFeature_RNA', 'batch', 'seurat_clusters', ... (not shown) ... 'nGenes', 'nCounts', 'pMito', 'pass_basic_filter', 'Size_Factor', 'initial_cell_size', 'ntr'
obsm: ... (not shown) ... 'spatial', 'spatial_3D', 'X_pca', 'X_umap', 'align_spatial', 'aligned_spatial_3D'
And the palette object has the following values
{1: (0.12156862745098039, 0.4666666666666667, 0.7058823529411765),
2: (0.6823529411764706, 0.7803921568627451, 0.9098039215686274),
3: (1.0, 0.4980392156862745, 0.054901960784313725),
4: (1.0, 0.7333333333333333, 0.47058823529411764),
5: (0.17254901960784313, 0.6274509803921569, 0.17254901960784313),
6: (0.596078431372549, 0.8745098039215686, 0.5411764705882353),
7: (0.8392156862745098, 0.15294117647058825, 0.1568627450980392),
8: (1.0, 0.596078431372549, 0.5882352941176471),
9: (0.5803921568627451, 0.403921568627451, 0.7411764705882353),
10: (0.7725490196078432, 0.6901960784313725, 0.8352941176470589),
11: (0.5490196078431373, 0.33725490196078434, 0.29411764705882354),
12: (0.7686274509803922, 0.611764705882353, 0.5803921568627451),
13: (0.8901960784313725, 0.4666666666666667, 0.7607843137254902),
14: (0.9686274509803922, 0.7137254901960784, 0.8235294117647058),
15: (0.4980392156862745, 0.4980392156862745, 0.4980392156862745),
16: (0.7803921568627451, 0.7803921568627451, 0.7803921568627451),
17: (0.7372549019607844, 0.7411764705882353, 0.13333333333333333),
18: (0.8588235294117647, 0.8588235294117647, 0.5529411764705883),
19: (0.09019607843137255, 0.7450980392156863, 0.8117647058823529),
20: (0.6196078431372549, 0.8549019607843137, 0.8980392156862745),
21: (0.12156862745098039, 0.4666666666666667, 0.7058823529411765),
22: (0.6823529411764706, 0.7803921568627451, 0.9098039215686274),
23: (1.0, 0.4980392156862745, 0.054901960784313725),
24: (1.0, 0.7333333333333333, 0.47058823529411764),
25: (0.17254901960784313, 0.6274509803921569, 0.17254901960784313)}
It seems that the key tissue_rgba may need to be manually added to the constructed object after the st.tdr.construct_pc() step?
I sincerely appreciate your help or any advice on how this could be solved ^_^
Thank you very much in advance!
< Package versions >
spateo-release 1.1.1
pyvista 0.46.3
Best regards,
Jason Leong.