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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/spatialdata commit 87bff76d897c5a4277d9987cf26432a18e0458cd-dirty
author iuc
date Sat, 14 Mar 2026 15:15:45 +0000
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-1:000000000000 0:c5928c28e2f0
1 <tool id="spatialdata_plot" name="SpatialData Plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>rich static plotting from SpatialData objects</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="creator" />
8 <command detect_errors="exit_code"><![CDATA[
9 unzip -q '$input_spatialdata' -d input &&
10
11 ## Rename directory to spatialdata if it has a different name
12 dir_name=\$(ls -d input/*/ | head -1 | xargs basename) &&
13 if [ "\$dir_name" != "spatialdata" ]; then
14 mv "input/\$dir_name" input/spatialdata;
15 fi &&
16
17 ## run the plotting pipeline
18 cat 'spdata_plot.py' &&
19 python3 'spdata_plot.py'
20 ]]></command>
21 <configfiles>
22 <configfile name="spdata_plot_config" filename="spdata_plot.py">
23 import spatialdata as sd
24 import spatialdata_plot
25
26 ## Load the SpatialData object
27 spdata = sd.read_zarr("./input/spatialdata")
28
29 print(spdata)
30
31 ## Render images
32 #for $img in $render_images:
33 spdata = spdata.pl.render_images(
34 #if $img.image_element:
35 element='$img.image_element',
36 #else:
37 element=None,
38 #end if
39 #if $img.channel:
40 channel='$img.channel',
41 #end if
42 #if str($img.cmap_or_palette_condi.color_map_type) == 'cmap':
43 #set $cmap_list = [str(x.strip()) for x in str($img.cmap_or_palette_condi.cmap).split(',')]
44 cmap=$cmap_list,
45 #end if
46 #if str($img.normalize_condi.normalize) == 'yes':
47 norm=Normalize(
48 vmin=$img.normalize_condi.vmin if str($img.normalize_condi.vmin) != '' else None,
49 vmax=$img.normalize_condi.vmax if str($img.normalize_condi.vmax) != '' else None,
50 clip=$img.normalize_condi.clip
51 ),
52 #end if
53 #if str($img.cmap_or_palette_condi.color_map_type) == 'palette':
54 #set $palette_list = [str(x.strip()) for x in str($img.cmap_or_palette_condi.palette).split(',')]
55 palette=$palette_list,
56 #end if
57 alpha=$img.alpha,
58 #if $img.scale:
59 scale='$img.scale',
60 #end if
61 )
62 #end for
63
64 ## Render labels
65 #for $lbl in $render_labels:
66 spdata = spdata.pl.render_labels(
67 #if $lbl.labels_element:
68 element='$lbl.labels_element',
69 #else:
70 element=None,
71 #end if
72 #if $lbl.color:
73 color='$lbl.color',
74 #end if
75 #if $lbl.groups:
76 #set $groups_list = [str(x.strip()) for x in str($lbl.groups).split(',')]
77 groups=$groups_list,
78 #end if
79 #if str($lbl.cmap_or_palette_condi.color_map_type) == 'palette':
80 #set $palette_list = [str(x.strip()) for x in str($lbl.cmap_or_palette_condi.palette).split(',')]
81 palette=$palette_list,
82 #end if
83 contour_px=$lbl.contour_px,
84 #if str($lbl.cmap_or_palette_condi.color_map_type) == 'cmap':
85 #set $cmap_list = [str(x.strip()) for x in str($lbl.cmap_or_palette_condi.cmap).split(',')]
86 cmap=$cmap_list,
87 #end if
88 #if str($lbl.normalize_condi.normalize) == 'yes':
89 norm=Normalize(
90 vmin=$lbl.normalize_condi.vmin if str($lbl.normalize_condi.vmin) != '' else None,
91 vmax=$lbl.normalize_condi.vmax if str($lbl.normalize_condi.vmax) != '' else None,
92 clip=$lbl.normalize_condi.clip
93 ),
94 #end if
95 outline_alpha=$lbl.outline_alpha,
96 fill_alpha=$lbl.fill_alpha,
97 #if $lbl.scale:
98 scale='$lbl.scale',
99 #else
100 scale=None,
101 #end if
102 #if $lbl.table_name:
103 table_name='$lbl.table_name',
104 #else
105 table_name=None,
106 #end if
107 #if $lbl.table_layer:
108 table_layer='$lbl.table_layer',
109 #else
110 table_layer=None,
111 #end if
112 )
113 #end for
114
115 ## Render points
116 #for $pt in $render_points:
117 spdata = spdata.pl.render_points(
118 #if $pt.points_element:
119 element='$pt.points_element',
120 #else:
121 element=None,
122 #end if
123 #if $pt.color:
124 color='$pt.color',
125 #end if
126 #if str($pt.alpha) != '':
127 alpha=$pt.alpha,
128 #end if
129 #if $pt.groups:
130 #set $groups_list = [str(x.strip()) for x in str($pt.groups).split(',')]
131 groups=$groups_list,
132 #end if
133 #if str($pt.cmap_or_palette_condi.color_map_type) == 'palette':
134 #set $palette_list = [str(x.strip()) for x in str($pt.cmap_or_palette_condi.palette).split(',')]
135 palette=$palette_list,
136 #end if
137 #if str($pt.cmap_or_palette_condi.color_map_type) == 'cmap':
138 #set $cmap_list = [str(x.strip()) for x in str($pt.cmap_or_palette_condi.cmap).split(',')]
139 cmap=$cmap_list,
140 #end if
141 #if str($pt.normalize_condi.normalize) == 'yes':
142 norm=Normalize(
143 vmin=$pt.normalize_condi.vmin if str($pt.normalize_condi.vmin) != '' else None,
144 vmax=$pt.normalize_condi.vmax if str($pt.normalize_condi.vmax) != '' else None,
145 clip=$pt.normalize_condi.clip
146 ),
147 #end if
148 size=$pt.size,
149 #if $pt.method:
150 method='$pt.method',
151 #else:
152 method=None,
153 #end if
154 #if $pt.table_name:
155 table_name='$pt.table_name',
156 #else
157 table_name=None,
158 #end if
159 #if $pt.table_layer:
160 table_layer='$pt.table_layer',
161 #else
162 table_layer=None,
163 #end if
164
165 )
166 #end for
167
168 ## Render shapes
169 #for $shp in $render_shapes:
170 spdata = spdata.pl.render_shapes(
171 #if $shp.shapes_element:
172 element='$shp.shapes_element',
173 #else:
174 element=None,
175 #end if
176 #if $shp.color:
177 color='$shp.color',
178 #end if
179 #if str($shp.fill_alpha) != '':
180 fill_alpha=$shp.fill_alpha,
181 #end if
182 #if str($shp.groups) != '':
183 #set $groups_list = [str(x.strip()) for x in str($shp.groups).split(',')]
184 groups=$groups_list,
185 #end if
186 #if str($shp.cmap_or_palette_condi.color_map_type) == 'palette':
187 #set $palette_list = [str(x.strip()) for x in str($shp.cmap_or_palette_condi.palette).split(',')]
188 palette=$palette_list,
189 #end if
190
191 #if str($shp.outline_condi.outline_type) == 'no':
192 outline_width=None,
193 outline_color=None,
194 outline_alpha=None,
195 #else if str($shp.outline_condi.outline_type) == 'yes':
196 outline_width=$shp.outline_condi.outline_width1,
197 outline_color='$shp.outline_condi.outline_color1',
198 outline_alpha=$shp.outline_condi.outline_alpha1,
199 #else if str($shp.outline_condi.outline_type) == 'yes2':
200 outline_width=[$shp.outline_condi.outline_width1, $shp.outline_condi.outline_width2],
201 outline_color=['$shp.outline_condi.outline_color1', '$shp.outline_condi.outline_color2'],
202 outline_alpha=[$shp.outline_condi.outline_alpha1, $shp.outline_condi.outline_alpha2],
203 #end if
204
205 #if str($shp.cmap_or_palette_condi.color_map_type) == 'cmap':
206 #set $cmap_list = [str(x.strip()) for x in str($shp.cmap_or_palette_condi.cmap).split(',')]
207 cmap=$cmap_list,
208 #end if
209 #if str($shp.normalize_condi.normalize) == 'yes':
210 norm=Normalize(
211 vmin=$shp.normalize_condi.vmin if str($shp.normalize_condi.vmin) != '' else None,
212 vmax=$shp.normalize_condi.vmax if str($shp.normalize_condi.vmax) != '' else None,
213 clip=$shp.normalize_condi.clip
214 ),
215 #end if
216 scale=$shp.scale,
217 #if $shp.method and str($shp.method) != 'None':
218 method='$shp.method',
219 #else:
220 method=None,
221 #end if
222 #if $shp.table_name:
223 table_name='$shp.table_name',
224 #else
225 table_name=None,
226 #end if
227 #if $shp.table_layer:
228 table_layer='$shp.table_layer',
229 #else
230 table_layer=None,
231 #end if
232 #if $shp.shape and str($shp.shape) != 'None':
233 shape='$shp.shape',
234 #else:
235 shape=None,
236 #end if
237 )
238 #end for
239
240 ## Show the plot
241 spdata.pl.show(
242 #if $show_params.coordinate_systems:
243 #set $coordinate_systems_list = [str(x.strip()) for x in str($show_params.coordinate_systems).split(',')]
244 coordinate_systems=$coordinate_systems_list,
245 #end if
246 figsize=($show_params.figsize_width, $show_params.figsize_height),
247 dpi=$show_params.dpi,
248 ncols=$show_params.ncols,
249 #if str($show_params.legend_fontsize) != '':
250 legend_fontsize=$show_params.legend_fontsize,
251 #end if
252 legend_fontweight='$show_params.legend_fontweight',
253 legend_loc='$show_params.legend_loc',
254 na_in_legend=$show_params.na_in_legend,
255 #if $show_params.title:
256 title='$show_params.title',
257 #end if
258 share_extent=$show_params.share_extent,
259 save='plot.${show_params.format}'
260 )
261
262 print("Plot saved successfully")
263 </configfile>
264 </configfiles>
265 <inputs>
266 <expand macro="input_spatialdata"/>
267 <repeat name="render_images" min="0" title="Render Images">
268 <param name="image_element" type="text" optional="true" label="Image element name" help="Name of the image element to render. Leave empty to render all images.">
269 <expand macro="sanitize_query"/>
270 </param>
271 <param name="channel" type="text" optional="true" label="Channel(s)" help="Comma-separated list of channel names or indices to plot. Leave empty for all channels.">
272 <expand macro="sanitize_query"/>
273 </param>
274 <expand macro="cmap_or_palette_condi"/>
275 <expand macro="normalize_condi"/>
276 <param name="alpha" type="float" value="1.0" min="0.0" max="1.0" label="Alpha (opacity)" help="Transparency level (0=transparent, 1=opaque)"/>
277 <param name="scale" type="text" optional="true" label="Scale" help="Resolution control: leave empty for auto, 'full' for highest resolution, or specify a scale name. Please note that full resolution, takes more time to render.">
278 <expand macro="sanitize_query"/>
279 </param>
280 </repeat>
281
282 <repeat name="render_labels" min="0" title="Render Labels">
283 <param name="labels_element" type="text" optional="true" label="Labels element name" help="Name of the labels element to render. Leave empty to render all labels.">
284 <expand macro="sanitize_query"/>
285 </param>
286 <expand macro="param_color"/>
287 <param name="groups" type="text" optional="true" label="Groups to show" help=" When using color and the key represents discrete labels, groups can be used to show only a subset of them. Other values are set to NA. The list can contain multiple discrete labels to be visualized.">
288 <expand macro="sanitize_query"/>
289 </param>
290 <expand macro="cmap_or_palette_condi"/>
291 <param name="contour_px" type="integer" value="3" min="0" label="Contour width (pixels)" help="Width of contour to draw for each segment. 0 fills entire segment."/>
292 <expand macro="normalize_condi"/>
293 <param name="outline_alpha" type="float" value="0.0" min="0.0" max="1.0" label="Alpha value for the outline of the labels" help=" Invisible by default." />
294 <param name="fill_alpha" type="float" value="0.4" min="0.0" max="1.0" label="Alpha value for the fill of the labels."/>
295 <param name="scale" type="text" optional="true" label="Scale" help="Resolution control: leave empty for auto, 'full' for highest resolution, or specify a scale name. Please note that full resolution, takes more time to render.">
296 <expand macro="sanitize_query"/>
297 </param>
298 <expand macro="param_table_name" value="" optional="true" help="Name of table containing color columns"/>
299 <expand macro="param_table_layer"/>
300 </repeat>
301
302 <repeat name="render_points" min="0" title="Render Points">
303 <param name="points_element" type="text" optional="true" label="Points element name" help="Name of the points element to render. Leave empty to render all points.">
304 <expand macro="sanitize_query"/>
305 </param>
306 <expand macro="param_color"/>
307 <param name="alpha" type="float" optional="true" min="0.0" max="1.0" label="Alpha (opacity)"/>
308 <param name="groups" type="text" optional="true" label="Groups to show" help=" When using color and the key represents discrete labels, groups can be used to show only a subset of them. Other values are set to NA. The list can contain multiple discrete labels to be visualized.">
309 <expand macro="sanitize_query"/>
310 </param>
311 <expand macro="cmap_or_palette_condi"/>
312 <expand macro="normalize_condi"/>
313 <param name="size" type="float" value="1.0" min="0.0" label="Point size"/>
314 <expand macro="param_rendering_method"/>
315 <expand macro="param_table_name" value="" optional="true" help="Name of table containing color columns"/>
316 <expand macro="param_table_layer"/>
317 </repeat>
318
319 <repeat name="render_shapes" min="0" title="Render Shapes">
320 <param name="shapes_element" type="text" optional="true" label="Shapes element name" help="Name of the shapes element to render. Leave empty to render all shapes.">
321 <expand macro="sanitize_query"/>
322 </param>
323 <expand macro="param_color"/>
324 <param name="fill_alpha" type="float" optional="true" min="0.0" max="1.0" label="Fill alpha" help="By default, it is set to 1.0 or, if a color is given that implies an alpha, that value is used for fill_alpha. If an alpha channel is present in a cmap passed by the user, fill_alpha will overwrite the value present in the cmap."/>
325 <param name="groups" type="text" optional="true" label="Groups to show" help=" When using color and the key represents discrete labels, groups can be used to show only a subset of them. Other values are set to NA. The list can contain multiple discrete labels to be visualized.">
326 <expand macro="sanitize_query"/>
327 </param>
328 <expand macro="cmap_or_palette_condi"/>
329 <conditional name="outline_condi">
330 <param name="outline_type" type="select" label="Shape outline type">
331 <option value="no">No outline</option>
332 <option value="yes">Yes, one outline</option>
333 <option value="yes2">Yes, two outlines</option>
334 </param>
335 <when value="no"/>
336 <when value="yes">
337 <param name="outline_width1" type="float" optional="false" value="1.5" min="0.0" label="Outline width"/>
338 <param name="outline_color1" type="text" optional="false" value="#000000" label="Outline color" help="Color name or hex code">
339 <expand macro="sanitize_query"/>
340 </param>
341 <param name="outline_alpha1" type="float" optional="false" value="1.0" min="0.0" max="1.0" label="Outline alpha"/>
342 </when>
343 <when value="yes2">
344 <param name="outline_width1" type="float" optional="false" value="1.5" min="0.0" label="First outline width"/>
345 <param name="outline_color1" type="text" optional="false" value="#000000" label="First outline color" help="Color name or hex code">
346 <expand macro="sanitize_query"/>
347 </param>
348 <param name="outline_alpha1" type="float" optional="false" value="1.0" min="0.0" max="1.0" label="First outline alpha"/>
349 <param name="outline_width2" type="float" optional="false" value="0.5" min="0.0" label="Second outline width"/>
350 <param name="outline_color2" type="text" optional="false" value="#ffffff" label="Second outline color" help="Color name or hex code">
351 <expand macro="sanitize_query"/>
352 </param>
353 <param name="outline_alpha2" type="float" optional="false" value="1.0" min="0.0" max="1.0" label="Second outline alpha"/>
354 </when>
355 </conditional>
356 <expand macro="normalize_condi"/>
357 <param name="scale" type="float" min="0" value="1.0" label="Scale factor" help="Value to scale circles"/>
358 <expand macro="param_rendering_method" help="When Auto, the method is chosen based on the size of the data.">
359 <option value="None">Auto</option>
360 </expand>
361 <expand macro="param_table_name" value="" optional="true"/>
362 <expand macro="param_table_layer"/>
363 <param name="shape" type="select" optional="true" label="Convert shapes to" help="If Auto, the shapes are rendered as they are">
364 <option value="None">Keep original shapes</option>
365 <option value="circle">Circle</option>
366 <option value="hex">Hexagon</option>
367 <option value="visium_hex">Visium hexagon (adjacent)</option>
368 <option value="square">Square</option>
369 </param>
370 </repeat>
371
372 <section name="show_params" title="Plot Display Parameters" expanded="true">
373 <param name="coordinate_systems" type="text" optional="true" label="Coordinate system(s)" help="Comma-separated list of coordinate systems to plot. Leave empty for all. If a coordinate system doesn't contain any relevant elements (as specified in the render_* calls), it is automatically not plotted.">
374 <expand macro="sanitize_query"/>
375 </param>
376 <param name="figsize_width" type="float" value="6.4" min="0.1" label="Figure width (inches)"/>
377 <param name="figsize_height" type="float" value="4.8" min="0.1" label="Figure height (inches)"/>
378 <param name="dpi" type="integer" value="100" min="1" label="DPI (resolution)" help="Dots per inch for the output image"/>
379 <param name="ncols" type="integer" value="4" min="1" label="Number of columns"/>
380 <param name="legend_fontsize" type="integer" optional="true" min="1" label="Legend font size"/>
381 <param name="legend_fontweight" type="select" label="Legend font weight">
382 <option value="bold" selected="true">Bold</option>
383 <option value="normal">Normal</option>
384 <option value="light">Light</option>
385 </param>
386 <param name="legend_loc" type="select" label="Legend location">
387 <option value="right margin" selected="true">Right margin</option>
388 <option value="upper right">Upper right</option>
389 <option value="upper left">Upper left</option>
390 <option value="lower left">Lower left</option>
391 <option value="lower right">Lower right</option>
392 <option value="center">Center</option>
393 </param>
394 <param name="na_in_legend" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show NA values in legend?"/>
395 <param name="title" type="text" optional="true" label="Plot title" help="If not provided the plot will have the name of the coordinate system as title..">
396 <expand macro="sanitize_query"/>
397 </param>
398 <param name="share_extent" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Share extent across subplots?"/>
399 <param name="format" type="select" label="Image format">
400 <option value="eps">EPS</option>
401 <option value="jpg" selected="true">JPG</option>
402 <option value="pdf">PDF</option>
403 <option value="png">PNG</option>
404 <option value="svg">SVG</option>
405 <option value="tiff">TIFF</option>
406 </param>
407 </section>
408 </inputs>
409 <outputs>
410 <data name="plot_output" format="jpg" from_work_dir="figures/plot.jpg" label="${tool.name} on ${on_string}: plot">
411 <change_format>
412 <when input="show_params.format" value="eps" format="eps"/>
413 <when input="show_params.format" value="jpg" format="jpg"/>
414 <when input="show_params.format" value="pdf" format="pdf"/>
415 <when input="show_params.format" value="png" format="png"/>
416 <when input="show_params.format" value="svg" format="svg"/>
417 <when input="show_params.format" value="tiff" format="tiff"/>
418 </change_format>
419 </data>
420 </outputs>
421 <tests>
422 <!-- test 1 - render images -->
423 <test>
424 <param name="input_spatialdata" location="https://zenodo.org/records/18746346/files/xenium_spatialdata.spatialdata.zip"/>
425 <repeat name="render_images">
426 <param name="image_element" value="he_image"/>
427 </repeat>
428 <assert_stdout>
429 <has_text text="spdata.pl.render_images"/>
430 <has_text text="element=&apos;he_image&apos;"/>
431 </assert_stdout>
432 <output name="plot_output" ftype="jpg">
433 <assert_contents>
434 <has_image_center_of_mass center_of_mass="83,245" eps="5"/>
435 <has_image_channels channels="3"/>
436 <has_image_height height="491"/>
437 <has_image_width width="174"/>
438 </assert_contents>
439 </output>
440 </test>
441 <!-- test 2 - render labels -->
442 <test>
443 <param name="input_spatialdata" location="https://zenodo.org/records/18746346/files/xenium_spatialdata.spatialdata.zip"/>
444 <repeat name="render_labels">
445 <param name="labels_element" value="cell_labels"/>
446 <param name="color" value="total_counts"/>
447 <param name="contour_px" value="2"/>
448 <param name="outline_alpha" value="0.5"/>
449 <param name="fill_alpha" value="0.5"/>
450 </repeat>
451 <assert_stdout>
452 <has_text text="spdata.pl.render_labels"/>
453 <has_text text="element=&apos;cell_labels&apos;"/>
454 <has_text text="color=&apos;total_counts&apos;"/>
455 <has_text text="contour_px=2"/>
456 <has_text text="outline_alpha=0.5"/>
457 <has_text text="fill_alpha=0.5"/>
458 </assert_stdout>
459 <output name="plot_output" ftype="jpg">
460 <assert_contents>
461 <has_image_center_of_mass center_of_mass="155,245" eps="5"/>
462 <has_image_channels channels="3"/>
463 <has_image_height height="491"/>
464 <has_image_width width="320"/>
465 </assert_contents>
466 </output>
467 </test>
468 <!-- test 3 - render points -->
469 <test>
470 <param name="input_spatialdata" location="https://zenodo.org/records/18746346/files/merscope_spatialdata.spatialdata.zip"/>
471 <repeat name="render_points">
472 <param name="points_element" value="slide_name_region_transcripts"/>
473 <param name="color" value="fov"/>
474 <param name="alpha" value="0.7"/>
475 <param name="size" value="2.0"/>
476 </repeat>
477 <assert_stdout>
478 <has_text text="spdata.pl.render_points"/>
479 <has_text text="element=&apos;slide_name_region_transcripts&apos;"/>
480 <has_text text="color=&apos;fov&apos;"/>
481 <has_text text="alpha=0.7"/>
482 <has_text text="size=2.0"/>
483 </assert_stdout>
484 <output name="plot_output" ftype="jpg">
485 <assert_contents>
486 <has_image_center_of_mass center_of_mass="295, 245" eps="10"/>
487 <has_image_channels channels="3"/>
488 <has_image_height height="491"/>
489 <has_image_width width="586"/>
490 </assert_contents>
491 </output>
492 </test>
493 <!-- test 4 - render shapes -->
494 <test>
495 <param name="input_spatialdata" location="https://zenodo.org/records/18746346/files/merscope_spatialdata.spatialdata.zip"/>
496 <repeat name="render_shapes">
497 <param name="shapes_element" value="slide_name_region_polygons"/>
498 <param name="color" value="EntityID"/>
499 <param name="fill_alpha" value="0.3"/>
500 <conditional name="outline_condi">
501 <param name="outline_type" value="yes"/>
502 <param name="outline_width1" value="1.0"/>
503 <param name="outline_color1" value="#ff0000"/>
504 <param name="outline_alpha1" value="0.8"/>
505 </conditional>
506 </repeat>
507 <assert_stdout>
508 <has_text text="spdata.pl.render_shapes"/>
509 <has_text text="element=&apos;slide_name_region_polygons&apos;"/>
510 <has_text text="color=&apos;EntityID&apos;"/>
511 <has_text text="fill_alpha=0.3"/>
512 <has_text text="outline_width=1.0"/>
513 <has_text text="outline_color=&apos;#ff0000&apos;"/>
514 <has_text text="outline_alpha=0.8"/>
515 </assert_stdout>
516 <output name="plot_output" ftype="jpg">
517 <assert_contents>
518 <has_image_center_of_mass center_of_mass="290, 247" eps="5"/>
519 <has_image_channels channels="3"/>
520 <has_image_height height="491"/>
521 <has_image_width width="582"/>
522 </assert_contents>
523 </output>
524 </test>
525 <!-- test 5 - combination: image + labels (xenium) -->
526 <test>
527 <param name="input_spatialdata" location="https://zenodo.org/records/18746346/files/xenium_spatialdata.spatialdata.zip"/>
528 <repeat name="render_images">
529 <param name="image_element" value="morphology_focus"/>
530 </repeat>
531 <repeat name="render_labels">
532 <param name="labels_element" value="cell_labels"/>
533 <param name="contour_px" value="1"/>
534 <param name="outline_alpha" value="0.7"/>
535 <param name="fill_alpha" value="0.0"/>
536 </repeat>
537 <assert_stdout>
538 <has_text text="spdata.pl.render_images"/>
539 <has_text text="element=&apos;morphology_focus&apos;"/>
540 <has_text text="spdata.pl.render_labels"/>
541 <has_text text="element=&apos;cell_labels&apos;"/>
542 </assert_stdout>
543 <output name="plot_output" ftype="jpg">
544 <assert_contents>
545 <has_image_center_of_mass center_of_mass="81, 247" eps="5"/>
546 <has_image_channels channels="3"/>
547 <has_image_height height="491"/>
548 <has_image_width width="248"/>
549 </assert_contents>
550 </output>
551 </test>
552 <!-- test 6 - combination: points + shapes (merscope) -->
553 <test>
554 <param name="input_spatialdata" location="https://zenodo.org/records/18746346/files/merscope_spatialdata.spatialdata.zip"/>
555 <repeat name="render_points">
556 <param name="points_element" value="slide_name_region_transcripts"/>
557 <param name="alpha" value="0.5"/>
558 <param name="size" value="1.5"/>
559 </repeat>
560 <repeat name="render_shapes">
561 <param name="shapes_element" value="slide_name_region_polygons"/>
562 <param name="fill_alpha" value="0.0"/>
563 <conditional name="outline_condi">
564 <param name="outline_type" value="yes"/>
565 <param name="outline_width1" value="0.5"/>
566 <param name="outline_color1" value="#ffffff"/>
567 <param name="outline_alpha1" value="1.0"/>
568 </conditional>
569 </repeat>
570 <assert_stdout>
571 <has_text text="spdata.pl.render_points"/>
572 <has_text text="element=&apos;slide_name_region_transcripts&apos;"/>
573 <has_text text="spdata.pl.render_shapes"/>
574 <has_text text="element=&apos;slide_name_region_polygons&apos;"/>
575 </assert_stdout>
576 <output name="plot_output" ftype="jpg">
577 <assert_contents>
578 <has_image_center_of_mass center_of_mass="245, 244" eps="5"/>
579 <has_image_channels channels="3"/>
580 <has_image_height height="491"/>
581 <has_image_width width="492"/>
582 </assert_contents>
583 </output>
584 </test>
585 <!-- test 7 - combination: image + points + shapes (merscope) -->
586 <test>
587 <param name="input_spatialdata" location="https://zenodo.org/records/18746346/files/merscope_spatialdata.spatialdata.zip"/>
588 <repeat name="render_images">
589 <param name="image_element" value="slide_name_region_z3"/>
590 </repeat>
591 <repeat name="render_points">
592 <param name="points_element" value="slide_name_region_transcripts"/>
593 <param name="alpha" value="0.6"/>
594 <param name="size" value="2.0"/>
595 </repeat>
596 <repeat name="render_shapes">
597 <param name="shapes_element" value="slide_name_region_polygons"/>
598 <param name="fill_alpha" value="0.0"/>
599 <conditional name="outline_condi">
600 <param name="outline_type" value="yes"/>
601 <param name="outline_width1" value="1.0"/>
602 <param name="outline_color1" value="#00ff00"/>
603 <param name="outline_alpha1" value="0.8"/>
604 </conditional>
605 </repeat>
606 <assert_stdout>
607 <has_text text="spdata.pl.render_images"/>
608 <has_text text="element=&apos;slide_name_region_z3&apos;"/>
609 <has_text text="spdata.pl.render_points"/>
610 <has_text text="element=&apos;slide_name_region_transcripts&apos;"/>
611 <has_text text="spdata.pl.render_shapes"/>
612 <has_text text="element=&apos;slide_name_region_polygons&apos;"/>
613 </assert_stdout>
614 <output name="plot_output" ftype="jpg">
615 <assert_contents>
616 <has_image_center_of_mass center_of_mass="242, 244" eps="5"/>
617 <has_image_channels channels="3"/>
618 <has_image_height height="491"/>
619 <has_image_width width="492"/>
620 </assert_contents>
621 </output>
622 </test>
623 </tests>
624 <help><![CDATA[
625 **What it does**
626
627 This tool creates rich static plots from SpatialData objects. It provides comprehensive visualization capabilities for spatial omics data, including images, labels (segmentation masks), point data (e.g., transcripts), and geometric shapes (e.g., cell boundaries).
628
629 -----
630
631 **Rendering Options**
632
633 The tool supports four types of spatial elements:
634
635 **1. Images**: Render microscopy images, H&E stains, or fluorescence channels
636 - Select specific channels or view all
637 - Apply colormaps and adjust transparency
638 - Control resolution and rendering quality
639
640 **2. Labels**: Visualize segmentation masks (cells, nuclei, tissues)
641 - Color by categorical or continuous variables from annotation tables
642 - Adjust contour width and fill transparency
643 - Show only specific groups/categories
644
645 **3. Points**: Display point-based data (e.g., transcript locations)
646 - Color by features or metadata
647 - Adjust point size and transparency
648 - Choose between matplotlib (smaller datasets) or datashader (large datasets) rendering
649
650 **4. Shapes**: Render geometric shapes (circles, polygons, boundaries)
651 - Color by annotations or use solid colors
652 - Control outline and fill properties
653 - Convert shapes to standard geometries (circles, hexagons, squares)
654
655 -----
656
657 **Display Parameters**
658
659 - **Coordinate Systems**: Select which spatial coordinate systems to visualize
660 - **Figure Layout**: Control subplot arrangement, figure size, and resolution
661 - **Legend**: Customize font, position, and content
662 - **Title**: Add custom titles to plots
663
664 -----
665
666 **Usage Tips**
667
668 1. **Layer Multiple Elements**: Enable multiple render options (e.g., images + labels + points) to create overlay visualizations
669 2. **Color by Annotations**: Use the 'color' parameter to visualize gene expression or cell type labels from annotation tables
670 3. **Performance**: For large datasets, consider using datashader rendering method for points and shapes
671 4. **Resolution**: Use 'scale' parameter to balance between rendering speed and image quality
672
673 -----
674
675 **Output**
676
677 The tool generates a static plot image in the selected format (JPG, PNG, PDF, SVG, EPS, or TIFF) containing the rendered visualization(s). Multiple coordinate systems will be displayed as separate subplots arranged in a grid.
678
679 -----
680
681 **More Information**
682
683 - `SpatialData Plot documentation <https://spatialdata.scverse.org/projects/plot/en/stable/>`__
684 - `SpatialData documentation <https://spatialdata.scverse.org/>`__
685
686 ]]></help>
687 <expand macro="citations" />
688 </tool>