Mercurial > repos > iuc > scanpy_plot

comparison plot.xml @ 12:1f380e8a6aec draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
author iuc
date Wed, 31 Jul 2024 18:07:15 +0000
parents c6b7bb9eb72f
children 084c74890a1f
comparison
equal deleted inserted replaced
11:69a12ab93cdd 12:1f380e8a6aec
1 <tool id="scanpy_plot" name="Plot" version="1.7.1+galaxy1" profile="@profile@"> 1 <tool id="scanpy_plot" name="Plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">
2 <description> with scanpy</description> 2 <description> with scanpy</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <stdio> 8 <stdio>
9 <regex match="... storing" source="stderr" level="warning"/> 9 <regex match="... storing" source="stderr" level="warning"/>
10 </stdio> 10 </stdio>
11 <expand macro="version_command"/> 11 <expand macro="version_command"/>
19 19
20 sc.settings.figdir = '.' 20 sc.settings.figdir = '.'
21 21
22 #if $method.method == 'pl.scatter' 22 #if $method.method == 'pl.scatter'
23 23
24 #if $method.type.type == 'xy':
25 x_field='$method.type.x'
26 y_field='$method.type.y'
27
28 #if $method.type.log:
29 if x_field in adata.obs or x_field in adata.var:
30 if x_field in adata.obs:
31 adata.obs[f"log_{x_field}"] = np.log10(adata.obs[x_field])
32 elif x_field in adata.var:
33 adata.var[f"log_{x_field}"] = np.log10(adata.var[x_field])
34 x_field=f"log_{x_field}"
35
36 if y_field in adata.obs or y_field in adata.var:
37 if y_field in adata.obs:
38 adata.obs[f"log_{y_field}"] = np.log10(adata.obs[y_field])
39 elif y_field in adata.var:
40 adata.var[f"log_{y_field}"] = np.log10(adata.var[y_field])
41 y_field=f"log_{y_field}"
42 #end if
43 #end if
44
24 sc.pl.scatter( 45 sc.pl.scatter(
25 @CMD_param_plot_inputs@ 46 @CMD_param_plot_inputs@
26 #if $method.type.type == 'xy' 47 #if $method.type.type == 'xy':
27 x='$method.type.x', 48 x=x_field,
28 y='$method.type.y', 49 y=y_field,
29 #if str($method.type.color) != '' 50 #if $method.type.color
30 color='$method.type.color', 51 color='$method.type.color',
31 #end if 52 #end if
32 #if str('$method.type.layers.use_layers') == 'true' 53 #if str('$method.type.layers.use_layers') == 'true'
33 layers=('$method.type.layers.layer_x', '$method.type.layers.layer_y', '$method.type.layers.layer_color'), 54 layers=('$method.type.layers.layer_x', '$method.type.layers.layer_y', '$method.type.layers.layer_color'),
34 #end if 55 #end if
35 #else 56 #else
36 basis='$method.type.basis', 57 basis='$method.type.basis',
37 #if str($method.type.color) != '' 58 #if $method.type.color
38 #set $color = ([x.strip() for x in str($method.type.color).split(',')]) 59 #set $color = ([x.strip() for x in str($method.type.color).split(',')])
39 color=$color, 60 color=$color,
40 #end if 61 #end if
41 #end if 62 #end if
42 use_raw=$method.use_raw, 63 use_raw=$method.use_raw,
43 sort_order=$method.sort_order, 64 sort_order=$method.sort_order,
44 @CMD_params_groups@ 65 @CMD_params_groups@
45 @CMD_params_pl_components@ 66 @CMD_params_pl_components@
46 projection='$method.plot.projection', 67 projection='$method.plot.projection',
47 legend_loc='$method.plot.legend_loc', 68 legend_loc='$method.plot.legend_loc',
48 #if $method.plot.palette != 'default' 69 #if $method.plot.palette
49 palette=['$method.plot.palette'], 70 palette=['$method.plot.palette'],
50 #end if 71 #end if
51 #if $method.plot.color_map != 'None' 72 #if $method.plot.color_map
52 color_map='$method.plot.color_map', 73 color_map='$method.plot.color_map',
53 #end if 74 #end if
54 @CMD_param_legend_fontsize@ 75 @CMD_param_legend_fontsize@
55 legend_fontweight='$method.plot.legend_fontweight', 76 legend_fontweight='$method.plot.legend_fontweight',
56 @CMD_param_title@ 77 @CMD_param_title@
58 frameon=$method.plot.frameon) 79 frameon=$method.plot.frameon)
59 80
60 #else if $method.method == 'pl.heatmap' 81 #else if $method.method == 'pl.heatmap'
61 sc.pl.heatmap( 82 sc.pl.heatmap(
62 @CMD_param_plot_inputs@ 83 @CMD_param_plot_inputs@
63 #if str($method.gene_symbols) != '' 84 #if $method.gene_symbols
64 gene_symbols='$method.gene_symbols', 85 gene_symbols='$method.gene_symbols',
65 #end if 86 #end if
66 @CMD_params_inputs@ 87 @CMD_params_inputs@
67 @CMD_params_plots@ 88 @CMD_params_plots@
68 @CMD_pl_heatmap@) 89 @CMD_pl_heatmap@)
69 90
70 #else if $method.method == 'pl.dotplot' 91 #else if $method.method == 'pl.dotplot'
71 sc.pl.dotplot( 92 sc.pl.dotplot(
72 @CMD_param_plot_inputs@ 93 @CMD_param_plot_inputs@
73 #if str($method.gene_symbols) != '' 94 #if $method.gene_symbols
74 gene_symbols='$method.gene_symbols', 95 gene_symbols='$method.gene_symbols',
75 #end if 96 #end if
76 @CMD_params_inputs@ 97 @CMD_params_inputs@
77 @CMD_params_plots@ 98 @CMD_params_plots@
78 @CMD_pl_dotplot@) 99 @CMD_pl_dotplot@)
100 #end if 121 #end if
101 scale='$method.violin_plot.scale', 122 scale='$method.violin_plot.scale',
102 #if $method.xlabel 123 #if $method.xlabel
103 xlabel='$method.xlabel', 124 xlabel='$method.xlabel',
104 #end if 125 #end if
105 #if $method.rotation 126 #if str($method.rotation) != ''
106 rotation=$method.rotation, 127 rotation=$method.rotation,
107 #end if 128 #end if
108 @CMD_params_seaborn_violinplot@) 129 @CMD_params_seaborn_violinplot@)
109 130
110 #else if $method.method == 'pl.stacked_violin' 131 #else if $method.method == 'pl.stacked_violin'
111 sc.pl.stacked_violin( 132 sc.pl.stacked_violin(
112 @CMD_param_plot_inputs@ 133 @CMD_param_plot_inputs@
113 #if str($method.gene_symbols) != '' 134 #if $method.gene_symbols
114 gene_symbols='$method.gene_symbols', 135 gene_symbols='$method.gene_symbols',
115 #end if 136 #end if
116 @CMD_params_inputs@ 137 @CMD_params_inputs@
117 @CMD_params_plots@ 138 @CMD_params_plots@
118 @CMD_pl_stacked_violin@) 139 @CMD_pl_stacked_violin@)
119 140
120 #else if $method.method == 'pl.matrixplot' 141 #else if $method.method == 'pl.matrixplot'
121 sc.pl.matrixplot( 142 sc.pl.matrixplot(
122 @CMD_param_plot_inputs@ 143 @CMD_param_plot_inputs@
123 #if str($method.gene_symbols) != '' 144 #if $method.gene_symbols
124 gene_symbols='$method.gene_symbols', 145 gene_symbols='$method.gene_symbols',
125 #end if 146 #end if
126 @CMD_params_inputs@ 147 @CMD_params_inputs@
127 @CMD_params_plots@ 148 @CMD_params_plots@
128 @CMD_pl_matrixplot@) 149 @CMD_pl_matrixplot@)
133 adata=adata.X, 154 adata=adata.X,
134 #else 155 #else
135 adata=adata, 156 adata=adata,
136 #end if 157 #end if
137 show=False, 158 show=False,
138 #if str($method.obs_keys) != '' 159 #if $method.obs_keys
139 obs_keys='$method.obs_keys', 160 obs_keys='$method.obs_keys',
140 #end if 161 #end if
141 use_raw=$method.use_raw, 162 use_raw=$method.use_raw,
142 method='$method.seaborn_clustermap.method', 163 method='$method.seaborn_clustermap.method',
143 metric='$method.seaborn_clustermap.metric', 164 metric='$method.seaborn_clustermap.metric',
152 173
153 #else if $method.method == 'pl.highest_expr_genes' 174 #else if $method.method == 'pl.highest_expr_genes'
154 sc.pl.highest_expr_genes( 175 sc.pl.highest_expr_genes(
155 @CMD_param_plot_inputs@ 176 @CMD_param_plot_inputs@
156 n_top=$method.n_top, 177 n_top=$method.n_top,
157 #if str($method.gene_symbols) != '' 178 #if $method.gene_symbols
158 gene_symbols='$method.gene_symbols', 179 gene_symbols='$method.gene_symbols',
159 #end if 180 #end if
160 #if str($method.setseaborn_boxplot.color) != '' 181 #if $method.setseaborn_boxplot.color
161 color='$method.setseaborn_boxplot.color', 182 color='$method.setseaborn_boxplot.color',
162 #end if 183 #end if
163 #if str($method.setseaborn_boxplot.palette) != 'None' 184 #if $method.setseaborn_boxplot.palette
164 palette='$method.setseaborn_boxplot.palette', 185 palette='$method.setseaborn_boxplot.palette',
165 #end if 186 #end if
166 saturation=$method.setseaborn_boxplot.saturation) 187 saturation=$method.setseaborn_boxplot.saturation)
167 188
168 #else if $method.method == 'pl.highly_variable_genes' 189 #else if $method.method == 'pl.highly_variable_genes'
246 267
247 #else if $method.method == 'pl.draw_graph' 268 #else if $method.method == 'pl.draw_graph'
248 sc.pl.draw_graph( 269 sc.pl.draw_graph(
249 @CMD_param_plot_inputs@ 270 @CMD_param_plot_inputs@
250 @CMD_param_color@ 271 @CMD_param_color@
251 #if str($method.gene_symbols) != '' 272 #if $method.gene_symbols
252 gene_symbols='$method.gene_symbols', 273 gene_symbols='$method.gene_symbols',
253 #end if 274 #end if
254 use_raw=$method.use_raw, 275 use_raw=$method.use_raw,
255 layout='$method.layout', 276 layout='$method.layout',
256 edges=$method.edges.edges, 277 edges=$method.edges.edges,
263 @CMD_params_groups@ 284 @CMD_params_groups@
264 @CMD_params_pl_components@ 285 @CMD_params_pl_components@
265 @CMD_pl_attribute_section@ 286 @CMD_pl_attribute_section@
266 @CMD_params_matplotlib_pyplot_scatter@) 287 @CMD_params_matplotlib_pyplot_scatter@)
267 288
289 #else if $method.method == 'pl.embedding_density'
290 sc.pl.embedding_density(
291 @CMD_param_plot_inputs@
292 basis='$method.basis',
293 #if $method.key
294 key='$method.key',
295 #end if
296 #if $method.groupby
297 groupby='$method.groupby',
298 #end if
299 #if $method.group
300 #set $group = ([x.strip() for x in str($method.group).split(',')])
301 group=$group,
302 #end if
303 #if $method.color_map
304 color_map='$method.color_map',
305 #end if
306 bg_dotsize=$method.bg_dotsize,
307 fg_dotsize=$method.fg_dotsize,
308 ncols=$method.ncols,
309 wspace=$method.wspace,
310 hspace=$method.hspace)
311
268 #else if $method.method == 'pl.dpt_groups_pseudotime' 312 #else if $method.method == 'pl.dpt_groups_pseudotime'
269 sc.pl.dpt_groups_pseudotime( 313 sc.pl.dpt_groups_pseudotime(
270 @CMD_param_plot_inputs@ 314 @CMD_param_plot_inputs@
271 #if str($method.color_map) != '' 315 #if $method.color_map
272 color_map='$method.color_map' 316 color_map='$method.color_map'
273 #end if 317 #end if
274 ) 318 )
275 319
276 #else if $method.method == 'pl.dpt_timeseries' 320 #else if $method.method == 'pl.dpt_timeseries'
277 sc.pl.dpt_timeseries( 321 sc.pl.dpt_timeseries(
278 @CMD_param_plot_inputs@ 322 @CMD_param_plot_inputs@
279 #if $method.heatmap.as_heatmap == "True" 323 #if $method.heatmap.as_heatmap == "True"
280 #if str($method.heatmap.color_map) != '' 324 #if $method.heatmap.color_map
281 color_map='$method.heatmap.color_map', 325 color_map='$method.heatmap.color_map',
282 #end if 326 #end if
283 #end if 327 #end if
284 as_heatmap=$method.heatmap.as_heatmap) 328 as_heatmap=$method.heatmap.as_heatmap)
285 329
299 #set $nodes = ([int(x.strip()) for x in str($method.nodes).split(',')]) 343 #set $nodes = ([int(x.strip()) for x in str($method.nodes).split(',')])
300 nodes=$nodes, 344 nodes=$nodes,
301 #set $keys=([x.strip() for x in str($method.keys).split(',')]) 345 #set $keys=([x.strip() for x in str($method.keys).split(',')])
302 keys=$keys, 346 keys=$keys,
303 use_raw=$method.use_raw, 347 use_raw=$method.use_raw,
304 #if str($method.annotations) != '' 348 #if $method.annotations
305 #set $annotations=([x.strip() for x in str($method.annotations).split(',')]) 349 #set $annotations=([x.strip() for x in str($method.annotations).split(',')])
306 annotations=$annotations, 350 annotations=$annotations,
307 #end if 351 #end if
308 #if str($method.color_map) != '' 352 #if $method.color_map
309 color_map='$method.color_map', 353 color_map='$method.color_map',
310 #end if 354 #end if
311 n_avg=$method.n_avg, 355 n_avg=$method.n_avg,
312 #if str($method.annotations) != '' 356 #if $method.annotations
313 groups_key='$method.groups_key', 357 groups_key='$method.groups_key',
314 #end if 358 #end if
315 as_heatmap=$method.as_heatmap, 359 as_heatmap=$method.as_heatmap,
316 show_node_names=$method.show_node_names, 360 show_node_names=$method.show_node_names,
317 show_colorbar=$method.show_colorbar, 361 show_colorbar=$method.show_colorbar,
321 #else if $method.method == 'pl.rank_genes_groups' 365 #else if $method.method == 'pl.rank_genes_groups'
322 sc.pl.rank_genes_groups( 366 sc.pl.rank_genes_groups(
323 @CMD_param_plot_inputs@ 367 @CMD_param_plot_inputs@
324 @CMD_params_groups@ 368 @CMD_params_groups@
325 n_genes=$method.n_genes, 369 n_genes=$method.n_genes,
326 #if str($method.gene_symbols) != '' 370 #if $method.gene_symbols
327 gene_symbols='$method.gene_symbols', 371 gene_symbols='$method.gene_symbols',
328 #end if 372 #end if
329 fontsize=$method.fontsize, 373 fontsize=$method.fontsize,
330 ncols=$method.ncols, 374 ncols=$method.ncols,
331 sharey=$method.sharey) 375 sharey=$method.sharey)
338 n_genes=$method.genes.n_genes, 382 n_genes=$method.genes.n_genes,
339 #else 383 #else
340 #set $gene_names = ([x.strip() for x in str($method.genes.gene_names).split(',')]) 384 #set $gene_names = ([x.strip() for x in str($method.genes.gene_names).split(',')])
341 gene_names=$gene_names, 385 gene_names=$gene_names,
342 #end if 386 #end if
343 #if str($method.gene_symbols) != '' 387 #if $method.gene_symbols
344 gene_symbols='$method.gene_symbols', 388 gene_symbols='$method.gene_symbols',
345 #end if 389 #end if
346 use_raw=$method.use_raw, 390 use_raw=$method.use_raw,
347 split=$method.split, 391 split=$method.split,
348 strip=$method.violin_plot.stripplot.stripplot, 392 strip=$method.violin_plot.stripplot.stripplot,
356 400
357 #else if $method.method == 'pl.rank_genes_groups_dotplot' 401 #else if $method.method == 'pl.rank_genes_groups_dotplot'
358 sc.pl.rank_genes_groups_dotplot( 402 sc.pl.rank_genes_groups_dotplot(
359 @CMD_param_plot_inputs@ 403 @CMD_param_plot_inputs@
360 @CMD_pl_rank_genes_groups_ext@ 404 @CMD_pl_rank_genes_groups_ext@
405 #if $method.gene_symbols
406 gene_symbols='$method.gene_symbols',
407 #end if
361 @CMD_params_plots@ 408 @CMD_params_plots@
362 @CMD_pl_dotplot@) 409 @CMD_pl_dotplot@)
363 410
364 #else if $method.method == 'pl.rank_genes_groups_heatmap' 411 #else if $method.method == 'pl.rank_genes_groups_heatmap'
365 sc.pl.rank_genes_groups_heatmap( 412 sc.pl.rank_genes_groups_heatmap(
366 @CMD_param_plot_inputs@ 413 @CMD_param_plot_inputs@
367 @CMD_pl_rank_genes_groups_ext@ 414 @CMD_pl_rank_genes_groups_ext@
368 @CMD_params_plots@ 415 @CMD_params_plots@
416 #if $method.gene_symbols
417 gene_symbols='$method.gene_symbols',
418 #end if
369 @CMD_pl_heatmap@) 419 @CMD_pl_heatmap@)
370 420
371 #else if $method.method == 'pl.rank_genes_groups_matrixplot' 421 #else if $method.method == 'pl.rank_genes_groups_matrixplot'
372 sc.pl.rank_genes_groups_matrixplot( 422 sc.pl.rank_genes_groups_matrixplot(
373 @CMD_param_plot_inputs@ 423 @CMD_param_plot_inputs@
374 @CMD_pl_rank_genes_groups_ext@ 424 @CMD_pl_rank_genes_groups_ext@
375 @CMD_params_plots@ 425 @CMD_params_plots@
426 #if $method.gene_symbols
427 gene_symbols='$method.gene_symbols',
428 #end if
376 @CMD_pl_matrixplot@) 429 @CMD_pl_matrixplot@)
377 430
378 #else if $method.method == 'pl.rank_genes_groups_stacked_violin' 431 #else if $method.method == 'pl.rank_genes_groups_stacked_violin'
379 sc.pl.rank_genes_groups_stacked_violin( 432 sc.pl.rank_genes_groups_stacked_violin(
380 @CMD_param_plot_inputs@ 433 @CMD_param_plot_inputs@
381 @CMD_pl_rank_genes_groups_ext@ 434 @CMD_pl_rank_genes_groups_ext@
382 @CMD_params_plots@ 435 @CMD_params_plots@
436 #if $method.gene_symbols
437 gene_symbols='$method.gene_symbols',
438 #end if
383 @CMD_pl_stacked_violin@) 439 @CMD_pl_stacked_violin@)
384 440
385 #end if 441 #end if
386 ]]></configfile> 442 ]]></configfile>
387 </configfiles> 443 </configfiles>
395 <option value="pl.dotplot">Generic: Makes a dot plot of the expression values, using 'pl.dotplot'</option> 451 <option value="pl.dotplot">Generic: Makes a dot plot of the expression values, using 'pl.dotplot'</option>
396 <option value="pl.violin">Generic: Violin plot, using 'pl.violin'</option> 452 <option value="pl.violin">Generic: Violin plot, using 'pl.violin'</option>
397 <option value="pl.stacked_violin">Generic: Stacked violin plots, using 'pl.stacked_violin'</option> 453 <option value="pl.stacked_violin">Generic: Stacked violin plots, using 'pl.stacked_violin'</option>
398 <option value="pl.matrixplot">Generic: Heatmap of the mean expression values per cluster, using 'pl.matrixplot'</option> 454 <option value="pl.matrixplot">Generic: Heatmap of the mean expression values per cluster, using 'pl.matrixplot'</option>
399 <option value="pl.clustermap">Generic: Hierarchically-clustered heatmap, using 'pl.clustermap'</option> 455 <option value="pl.clustermap">Generic: Hierarchically-clustered heatmap, using 'pl.clustermap'</option>
400 <!--<option value="pl.ranking">Generic: </option>!-->
401 <option value="pl.highest_expr_genes">Preprocessing: Plot the fraction of counts assigned to each gene over all cells, using 'pl.highest_expr_genes'</option> 456 <option value="pl.highest_expr_genes">Preprocessing: Plot the fraction of counts assigned to each gene over all cells, using 'pl.highest_expr_genes'</option>
402 <!--<option value="pl.filter_genes_dispersion">Preprocessing: Plot dispersions versus means for genes, using 'pl.filter_genes_dispersion'</option>--> 457 <!--<option value="pl.filter_genes_dispersion">Preprocessing: Plot dispersions versus means for genes, using 'pl.filter_genes_dispersion'</option>-->
403 <option value="pl.highly_variable_genes">Preprocessing: Plot dispersions versus means for genes, using 'pl.highly_variable_genes'</option> 458 <option value="pl.highly_variable_genes">Preprocessing: Plot dispersions versus means for genes, using 'pl.highly_variable_genes'</option>
404 <option value="pl.pca">PCA: Scatter plot in PCA coordinates, using 'pl.pca'</option> 459 <option value="pl.pca">PCA: Scatter plot in PCA coordinates, using 'pl.pca'</option>
405 <option value="pl.pca_loadings">PCA: Rank genes according to contributions to PCs, using 'pl.pca_loadings'</option> 460 <option value="pl.pca_loadings">PCA: Rank genes according to contributions to PCs, using 'pl.pca_loadings'</option>
407 <option value="pl.pca_overview">PCA: Plot PCA results, using 'pl.pca_overview'</option> 462 <option value="pl.pca_overview">PCA: Plot PCA results, using 'pl.pca_overview'</option>
408 <option value="pl.tsne">Embeddings: Scatter plot in tSNE basis, using 'pl.tsne'</option> 463 <option value="pl.tsne">Embeddings: Scatter plot in tSNE basis, using 'pl.tsne'</option>
409 <option value="pl.umap">Embeddings: Scatter plot in UMAP basis, using 'pl.umap'</option> 464 <option value="pl.umap">Embeddings: Scatter plot in UMAP basis, using 'pl.umap'</option>
410 <option value="pl.diffmap">Embeddings: Scatter plot in Diffusion Map basis, using 'pl.diffmap'</option> 465 <option value="pl.diffmap">Embeddings: Scatter plot in Diffusion Map basis, using 'pl.diffmap'</option>
411 <option value="pl.draw_graph">Embeddings: Scatter plot in graph-drawing basis, using 'pl.draw_graph'</option> 466 <option value="pl.draw_graph">Embeddings: Scatter plot in graph-drawing basis, using 'pl.draw_graph'</option>
467 <option value="pl.embedding_density">Embeddings: Plot the density of cells in an embedding (per condition), using 'pl.embedding_density'</option>
412 <option value="pl.dpt_groups_pseudotime">Branching trajectories and pseudotime, clustering: Plot groups and pseudotime, using 'pl.dpt_groups_pseudotime'</option> 468 <option value="pl.dpt_groups_pseudotime">Branching trajectories and pseudotime, clustering: Plot groups and pseudotime, using 'pl.dpt_groups_pseudotime'</option>
413 <option value="pl.dpt_timeseries">Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series, using 'pl.dpt_timeseries'</option> 469 <option value="pl.dpt_timeseries">Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series, using 'pl.dpt_timeseries'</option>
414 <option value="pl.paga">Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges, using 'pl.paga'</option> 470 <option value="pl.paga">Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges, using 'pl.paga'</option>
415 <option value="pl.paga_compare">Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side, using 'pl.paga_compare'</option> 471 <option value="pl.paga_compare">Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side, using 'pl.paga_compare'</option>
416 <option value="pl.paga_path">Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths, using 'pl.paga_path'</option> 472 <option value="pl.paga_path">Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths, using 'pl.paga_path'</option>
417 <option value="pl.rank_genes_groups">Marker genes: Plot ranking of genes using dotplot plot, using 'pl.rank_genes_groups'</option> 473 <option value="pl.rank_genes_groups">Marker genes: Plot ranking of genes using dotplot plot, using 'pl.rank_genes_groups'</option>
418 <!-- doesn't currenty work: https://github.com/galaxyproject/tools-iuc/pull/3485#issuecomment-800055967
419 <option value="pl.rank_genes_groups_violin">Marker genes: Plot ranking of genes as violin plot, using 'pl.rank_genes_groups_violin'</option> 474 <option value="pl.rank_genes_groups_violin">Marker genes: Plot ranking of genes as violin plot, using 'pl.rank_genes_groups_violin'</option>
420 -->
421 <option value="pl.rank_genes_groups_dotplot">Marker genes: Plot ranking of genes as dotplot plot, using 'pl.rank_genes_groups_dotplot'</option> 475 <option value="pl.rank_genes_groups_dotplot">Marker genes: Plot ranking of genes as dotplot plot, using 'pl.rank_genes_groups_dotplot'</option>
422 <option value="pl.rank_genes_groups_heatmap">Marker genes: Plot ranking of genes as heatmap plot, using 'pl.rank_genes_groups_heatmap'</option> 476 <option value="pl.rank_genes_groups_heatmap">Marker genes: Plot ranking of genes as heatmap plot, using 'pl.rank_genes_groups_heatmap'</option>
423 <option value="pl.rank_genes_groups_matrixplot">Marker genes: Plot ranking of genes as matrixplot plot, using 'pl.rank_genes_groups_matrixplot'</option> 477 <option value="pl.rank_genes_groups_matrixplot">Marker genes: Plot ranking of genes as matrixplot plot, using 'pl.rank_genes_groups_matrixplot'</option>
424 <option value="pl.rank_genes_groups_stacked_violin">Marker genes: Plot ranking of genes as stacked violin plot, using 'pl.rank_genes_groups_stacked_violin'</option> 478 <option value="pl.rank_genes_groups_stacked_violin">Marker genes: Plot ranking of genes as stacked violin plot, using 'pl.rank_genes_groups_stacked_violin'</option>
425 </param> 479 </param>
434 <expand macro="sanitize_query" /> 488 <expand macro="sanitize_query" />
435 </param> 489 </param>
436 <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either '.obs' or '.var'"> 490 <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either '.obs' or '.var'">
437 <expand macro="sanitize_query" /> 491 <expand macro="sanitize_query" />
438 </param> 492 </param>
493 <expand macro="param_log"/>
439 <param argument="color" type="text" value="" label="Color by" help="Color points by single variable in `.obs` or `.var`"> 494 <param argument="color" type="text" value="" label="Color by" help="Color points by single variable in `.obs` or `.var`">
440 <expand macro="sanitize_query" /> 495 <expand macro="sanitize_query" />
441 </param> 496 </param>
442 <conditional name="layers"> 497 <conditional name="layers">
443 <param argument="use_layers" type="select" label="Use the layers attribute?"> 498 <param argument="use_layers" type="select" label="Use the layers attribute?">
664 <expand macro="param_sort_order"/> 719 <expand macro="param_sort_order"/>
665 <expand macro="param_groups"/> 720 <expand macro="param_groups"/>
666 <expand macro="pl_attribute_section"/> 721 <expand macro="pl_attribute_section"/>
667 <expand macro="section_matplotlib_pyplot_scatter"/> 722 <expand macro="section_matplotlib_pyplot_scatter"/>
668 </when> 723 </when>
724 <when value="pl.embedding_density">
725 <param argument="basis" type="text" value="umap" label="The embedding over which the density was calculated." help="This embedded representation should be found in adata.obsm['X_[basis]']">
726 <expand macro="sanitize_query" />
727 </param>
728 <param argument="key" type="text" optional="true" value="" label="Name of the .obs covariate that contains the density estimates" help="Alternatively, pass _groupby_.">
729 <expand macro="sanitize_query" />
730 </param>
731 <param argument="groupby" type="text" optional="true" value="" label="Name of the condition used in tl.embedding_density" help="Alternatively, pass _key_.">
732 <expand macro="sanitize_query" />
733 </param>
734 <param argument="group" type="text" optional="all" value="" label="The category in the categorical observation annotation to be plotted"
735 help="For example, 'G1' in the cell cycle 'phase' covariate. If multiple categories want to be plotted use a comma separated list">
736 <expand macro="sanitize_query" />
737 </param>
738 <expand macro="param_color_map"/>
739 <param argument="bg_dotsize" type="integer" min="0" value="80" label="Dot size for background data points not in the group"/>
740 <param argument="fg_dotsize" type="integer" min="0" value="180" label="Dot size for foreground data points in the group"/>
741 <expand macro="param_ncols"/>
742 <expand macro="param_wspace"/>
743 <expand macro="param_hspace"/>
744 </when>
669 <when value="pl.dpt_groups_pseudotime"> 745 <when value="pl.dpt_groups_pseudotime">
670 <expand macro="param_color_map"/> 746 <expand macro="param_color_map"/>
671 </when> 747 </when>
672 <when value="pl.dpt_timeseries"> 748 <when value="pl.dpt_timeseries">
673 <conditional name="heatmap"> 749 <conditional name="heatmap">
728 <when value="n_genes"> 804 <when value="n_genes">
729 <expand macro="param_n_genes"/> 805 <expand macro="param_n_genes"/>
730 </when> 806 </when>
731 <when value="gene_names"> 807 <when value="gene_names">
732 <param argument="gene_names" type="text" value="" label="List of genes to plot" help="A list of comma-separated names"> 808 <param argument="gene_names" type="text" value="" label="List of genes to plot" help="A list of comma-separated names">
733 <expand macro="sanitize_query" /> 809 <expand macro="sanitize_query" />
734 </param> 810 </param>
735 </when> 811 </when>
736 </conditional> 812 </conditional>
737 <expand macro="gene_symbols"/> 813 <expand macro="gene_symbols"/>
738 <expand macro="param_use_raw"/> 814 <expand macro="param_use_raw"/>
743 </section> 819 </section>
744 </when> 820 </when>
745 <when value="pl.rank_genes_groups_dotplot"> 821 <when value="pl.rank_genes_groups_dotplot">
746 <expand macro="pl_rank_genes_groups_ext"/> 822 <expand macro="pl_rank_genes_groups_ext"/>
747 <expand macro="params_plots"/> 823 <expand macro="params_plots"/>
824 <expand macro="gene_symbols"/>
748 <expand macro="pl_dotplot"/> 825 <expand macro="pl_dotplot"/>
749 </when> 826 </when>
750 <when value="pl.rank_genes_groups_heatmap"> 827 <when value="pl.rank_genes_groups_heatmap">
751 <expand macro="pl_rank_genes_groups_ext"/> 828 <expand macro="pl_rank_genes_groups_ext"/>
752 <expand macro="params_plots"/> 829 <expand macro="params_plots"/>
830 <expand macro="gene_symbols"/>
753 <expand macro="pl_heatmap"/> 831 <expand macro="pl_heatmap"/>
754 </when> 832 </when>
755 <when value="pl.rank_genes_groups_matrixplot"> 833 <when value="pl.rank_genes_groups_matrixplot">
756 <expand macro="pl_rank_genes_groups_ext"/> 834 <expand macro="pl_rank_genes_groups_ext"/>
757 <expand macro="params_plots"/> 835 <expand macro="params_plots"/>
836 <expand macro="gene_symbols"/>
758 <expand macro="pl_matrixplot"/> 837 <expand macro="pl_matrixplot"/>
759 </when> 838 </when>
760 <when value="pl.rank_genes_groups_stacked_violin"> 839 <when value="pl.rank_genes_groups_stacked_violin">
761 <expand macro="pl_rank_genes_groups_ext"/> 840 <expand macro="pl_rank_genes_groups_ext"/>
762 <expand macro="params_plots"/> 841 <expand macro="params_plots"/>
842 <expand macro="gene_symbols"/>
763 <expand macro="pl_stacked_violin"/> 843 <expand macro="pl_stacked_violin"/>
764 </when> 844 </when>
765 </conditional> 845 </conditional>
766 <expand macro="inputs_common_advanced"/> 846 <expand macro="inputs_common_advanced"/>
767 </inputs> 847 </inputs>
768 <outputs> 848 <outputs>
769 <data name="out_png" format="png" from_work_dir="*.png" label="${tool.name} (${method.method}) on ${on_string}"> 849 <data name="out_png" format="png" from_work_dir="*.png" label="PNG plot from ${tool.name} (${method.method}) on ${on_string}">
770 <filter>format == 'png' and method['method'] != 'pl.rank_genes_groups_violin'</filter> 850 <filter>format == 'png' and method['method'] != 'pl.rank_genes_groups_violin'</filter>
771 </data> 851 </data>
772 <collection name="collection_png" type="list" label="${tool.name} (${method.method}) on ${on_string}"> 852 <collection name="collection_png" type="list" label="PNG plots from ${tool.name} (${method.method}) on ${on_string}">
773 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).png" format="png"/> 853 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).png" format="png"/>
774 <filter>format == 'png' and method['method'] == 'pl.rank_genes_groups_violin'</filter> 854 <filter>format == 'png' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
775 </collection> 855 </collection>
776 <data name="out_pdf" format="pdf" from_work_dir="*.pdf" label="${tool.name} (${method.method}) on ${on_string}"> 856 <data name="out_pdf" format="pdf" from_work_dir="*.pdf" label="PDF plot from ${tool.name} (${method.method}) on ${on_string}">
777 <filter>format == 'pdf' and method['method'] != pl.rank_genes_groups_violin</filter> 857 <filter>format == 'pdf' and method['method'] != 'pl.rank_genes_groups_violin'</filter>
778 </data> 858 </data>
779 <collection name="collection_pdf" type="list" label="${tool.name} (${method.method}) on ${on_string}"> 859 <collection name="collection_pdf" type="list" label="PDF plots from ${tool.name} (${method.method}) on ${on_string}">
780 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).pdf" format="pdf"/> 860 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).pdf" format="pdf"/>
781 <filter>format == 'pdf' and method['method'] == 'pl.rank_genes_groups_violin'</filter> 861 <filter>format == 'pdf' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
782 </collection> 862 </collection>
783 <data name="out_svg" format="svg" from_work_dir="*.svg" label="${tool.name} (${method.method}) on ${on_string}"> 863 <data name="out_svg" format="svg" from_work_dir="*.svg" label="SVG plot from ${tool.name} (${method.method}) on ${on_string}">
784 <filter>format == 'svg' and method['method'] != pl.rank_genes_groups_violin</filter> 864 <filter>format == 'svg' and method['method'] != pl.rank_genes_groups_violin</filter>
785 </data> 865 </data>
786 <collection name="collection_svg" type="list" label="${tool.name} (${method.method}) on ${on_string}"> 866 <collection name="collection_svg" type="list" label="SVG plots from ${tool.name} (${method.method}) on ${on_string}">
787 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).svg" format="svg"/> 867 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).svg" format="svg"/>
788 <filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter> 868 <filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
789 </collection> 869 </collection>
790 <data name="hidden_output" format="txt" label="Log file" hidden="true" > 870 <data name="hidden_output" format="txt" label="Log file" hidden="true" >
791 <filter>advanced_common['show_log']</filter> 871 <filter>advanced_common['show_log']</filter>
792 </data> 872 </data>
793 </outputs> 873 </outputs>
794 <tests> 874 <tests>
795 <test> 875 <test expect_num_outputs="2">
796 <!-- test 0: pl.scatter !--> 876 <!-- test 1: pl.scatter -->
797 <param name="adata" value="pbmc68k_reduced.h5ad" /> 877 <param name="adata" value="pbmc68k_reduced.h5ad" />
798 <param name="format" value="png"/> 878 <param name="format" value="png"/>
799 <conditional name="method"> 879 <conditional name="method">
800 <param name="method" value="pl.scatter"/> 880 <param name="method" value="pl.scatter"/>
801 <conditional name="type"> 881 <conditional name="type">
835 <has_text_matching expression="size=1.0"/> 915 <has_text_matching expression="size=1.0"/>
836 </assert_contents> 916 </assert_contents>
837 </output> 917 </output>
838 <output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="sim_size"/> 918 <output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="sim_size"/>
839 </test> 919 </test>
840 <test> 920 <test expect_num_outputs="2">
841 <!-- test 1: pl.scatter !--> 921 <!-- test 2: pl.scatter -->
842 <param name="adata" value="krumsiek11.h5ad" /> 922 <param name="adata" value="krumsiek11.h5ad" />
843 <param name="format" value="png"/> 923 <param name="format" value="png"/>
844 <conditional name="method"> 924 <conditional name="method">
845 <param name="method" value="pl.scatter"/> 925 <param name="method" value="pl.scatter"/>
846 <conditional name="type"> 926 <conditional name="type">
868 <param name="show_log" value="true" /> 948 <param name="show_log" value="true" />
869 </section> 949 </section>
870 <output name="hidden_output"> 950 <output name="hidden_output">
871 <assert_contents> 951 <assert_contents>
872 <has_text_matching expression="sc.pl.scatter"/> 952 <has_text_matching expression="sc.pl.scatter"/>
873 <has_text_matching expression="x='EKLF'" /> 953 <has_text_matching expression="x_field='EKLF'" />
874 <has_text_matching expression="y='Cebpa'"/> 954 <has_text_matching expression="y_field='Cebpa'"/>
875 <has_text_matching expression="use_raw=False"/> 955 <has_text_matching expression="use_raw=False"/>
876 <has_text_matching expression="sort_order=True"/> 956 <has_text_matching expression="sort_order=True"/>
877 <has_text_matching expression="projection='2d'"/> 957 <has_text_matching expression="projection='2d'"/>
878 <has_text_matching expression="legend_loc='right margin'"/> 958 <has_text_matching expression="legend_loc='right margin'"/>
879 <has_text_matching expression="legend_fontsize=1"/> 959 <has_text_matching expression="legend_fontsize=1"/>
883 <has_text_matching expression="title='A title'"/> 963 <has_text_matching expression="title='A title'"/>
884 </assert_contents> 964 </assert_contents>
885 </output> 965 </output>
886 <output name="out_png" file="pl.scatter.krumsiek11.png" ftype="png" compare="sim_size"/> 966 <output name="out_png" file="pl.scatter.krumsiek11.png" ftype="png" compare="sim_size"/>
887 </test> 967 </test>
888 <test> 968 <test expect_num_outputs="2">
889 <!-- test 2: pl.heatmap !--> 969 <!-- test 3: pl.heatmap -->
890 <param name="adata" value="krumsiek11.h5ad" /> 970 <param name="adata" value="krumsiek11.h5ad" />
891 <param name="format" value="png"/> 971 <param name="format" value="png"/>
892 <conditional name="method"> 972 <conditional name="method">
893 <param name="method" value="pl.heatmap"/> 973 <param name="method" value="pl.heatmap"/>
894 <conditional name="var_names"> 974 <conditional name="var_names">
931 <has_text_matching expression="origin='upper'"/> 1011 <has_text_matching expression="origin='upper'"/>
932 </assert_contents> 1012 </assert_contents>
933 </output> 1013 </output>
934 <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="sim_size"/> 1014 <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="sim_size"/>
935 </test> 1015 </test>
936 <test> 1016 <test expect_num_outputs="2">
937 <!-- test 2.1: pl.heatmap with symbols !--> 1017 <!-- test 4: pl.heatmap with symbols -->
938 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" /> 1018 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
939 <param name="format" value="png"/> 1019 <param name="format" value="png"/>
940 <conditional name="method"> 1020 <conditional name="method">
941 <param name="method" value="pl.heatmap"/> 1021 <param name="method" value="pl.heatmap"/>
942 <conditional name="var_names"> 1022 <conditional name="var_names">
981 <has_text_matching expression="cmap='YlGnBu'"/> 1061 <has_text_matching expression="cmap='YlGnBu'"/>
982 <has_text_matching expression="origin='upper'"/> 1062 <has_text_matching expression="origin='upper'"/>
983 </assert_contents> 1063 </assert_contents>
984 </output> 1064 </output>
985 </test> 1065 </test>
986 <test> 1066 <test expect_num_outputs="2">
987 <!-- test 3: pl.dotplot !--> 1067 <!-- test 5: pl.dotplot -->
988 <param name="adata" value="pbmc68k_reduced.h5ad" /> 1068 <param name="adata" value="pbmc68k_reduced.h5ad" />
989 <param name="format" value="png"/> 1069 <param name="format" value="png"/>
990 <conditional name="method"> 1070 <conditional name="method">
991 <param name="method" value="pl.dotplot"/> 1071 <param name="method" value="pl.dotplot"/>
992 <conditional name="var_names"> 1072 <conditional name="var_names">
1034 <has_text_matching expression="var_group_positions=\[\(0, 1\), \(11, 12\)\]"/> 1114 <has_text_matching expression="var_group_positions=\[\(0, 1\), \(11, 12\)\]"/>
1035 <has_text_matching expression="var_group_labels=\['B cells', 'dendritic'\]"/> 1115 <has_text_matching expression="var_group_labels=\['B cells', 'dendritic'\]"/>
1036 <has_text_matching expression="color_map='hot'"/> 1116 <has_text_matching expression="color_map='hot'"/>
1037 <has_text_matching expression="dot_max=0.7"/> 1117 <has_text_matching expression="dot_max=0.7"/>
1038 <has_text_matching expression="dot_min=0.1"/> 1118 <has_text_matching expression="dot_min=0.1"/>
1039 <has_text_matching expression="linewidths=0.0"/> 1119 <has_text_matching expression="lw=0.0"/>
1040 <has_text_matching expression="edgecolors='face'"/> 1120 <has_text_matching expression="ec='face'"/>
1041 </assert_contents> 1121 </assert_contents>
1042 </output> 1122 </output>
1043 <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="sim_size"/> 1123 <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="sim_size"/>
1044 </test> 1124 </test>
1045 <test> 1125 <test expect_num_outputs="2">
1046 <!-- test 3.1: pl.dotplot with symbols !--> 1126 <!-- test 6: pl.dotplot with symbols -->
1047 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" /> 1127 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
1048 <param name="format" value="png"/> 1128 <param name="format" value="png"/>
1049 <conditional name="method"> 1129 <conditional name="method">
1050 <param name="method" value="pl.dotplot"/> 1130 <param name="method" value="pl.dotplot"/>
1051 <conditional name="var_names"> 1131 <conditional name="var_names">
1078 <has_text_matching expression="num_categories=7"/> 1158 <has_text_matching expression="num_categories=7"/>
1079 <has_text_matching expression="dendrogram=True"/> 1159 <has_text_matching expression="dendrogram=True"/>
1080 </assert_contents> 1160 </assert_contents>
1081 </output> 1161 </output>
1082 </test> 1162 </test>
1083 <test> 1163 <test expect_num_outputs="2">
1084 <!-- test 4: pl.violin !--> 1164 <!-- test 7: pl.violin -->
1085 <param name="adata" value="pbmc68k_reduced.h5ad" /> 1165 <param name="adata" value="pbmc68k_reduced.h5ad" />
1086 <param name="format" value="png"/> 1166 <param name="format" value="png"/>
1087 <conditional name="method"> 1167 <conditional name="method">
1088 <param name="method" value="pl.violin"/> 1168 <param name="method" value="pl.violin"/>
1089 <conditional name="key_variables"> 1169 <conditional name="key_variables">
1135 <has_text_matching expression="saturation=0.75"/> 1215 <has_text_matching expression="saturation=0.75"/>
1136 </assert_contents> 1216 </assert_contents>
1137 </output> 1217 </output>
1138 <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="sim_size"/> 1218 <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="sim_size"/>
1139 </test> 1219 </test>
1140 <test> 1220 <test expect_num_outputs="2">
1141 <!-- test 5: pl.stacked_violin !--> 1221 <!-- test 8: pl.stacked_violin -->
1142 <param name="adata" value="krumsiek11.h5ad" /> 1222 <param name="adata" value="krumsiek11.h5ad" />
1143 <param name="format" value="png"/> 1223 <param name="format" value="png"/>
1144 <conditional name="method"> 1224 <conditional name="method">
1145 <param name="method" value="pl.stacked_violin"/> 1225 <param name="method" value="pl.stacked_violin"/>
1146 <conditional name="var_names"> 1226 <conditional name="var_names">
1195 <has_text_matching expression="saturation=0.75"/> 1275 <has_text_matching expression="saturation=0.75"/>
1196 </assert_contents> 1276 </assert_contents>
1197 </output> 1277 </output>
1198 <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="sim_size"/> 1278 <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="sim_size"/>
1199 </test> 1279 </test>
1200 <test> 1280 <test expect_num_outputs="2">
1201 <!-- test 5.1: pl.stacked_violin with symbols !--> 1281 <!-- test 9: pl.stacked_violin with symbols -->
1202 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" /> 1282 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
1203 <param name="format" value="png"/> 1283 <param name="format" value="png"/>
1204 <conditional name="method"> 1284 <conditional name="method">
1205 <param name="method" value="pl.stacked_violin"/> 1285 <param name="method" value="pl.stacked_violin"/>
1206 <conditional name="var_names"> 1286 <conditional name="var_names">
1230 <has_text_matching expression="dendrogram=True"/> 1310 <has_text_matching expression="dendrogram=True"/>
1231 <has_text_matching expression="swap_axes=True"/> 1311 <has_text_matching expression="swap_axes=True"/>
1232 </assert_contents> 1312 </assert_contents>
1233 </output> 1313 </output>
1234 </test> 1314 </test>
1235 <test> 1315 <test expect_num_outputs="2">
1236 <!-- test 6: pl.matrixplot !--> 1316 <!-- test 10: pl.matrixplot -->
1237 <param name="adata" value="krumsiek11.h5ad" /> 1317 <param name="adata" value="krumsiek11.h5ad" />
1238 <param name="format" value="png"/> 1318 <param name="format" value="png"/>
1239 <conditional name="method"> 1319 <conditional name="method">
1240 <param name="method" value="pl.matrixplot"/> 1320 <param name="method" value="pl.matrixplot"/>
1241 <conditional name="var_names"> 1321 <conditional name="var_names">
1268 <has_text_matching expression="use_raw=False"/> 1348 <has_text_matching expression="use_raw=False"/>
1269 <has_text_matching expression="num_categories=7"/> 1349 <has_text_matching expression="num_categories=7"/>
1270 <has_text_matching expression="dendrogram=True"/> 1350 <has_text_matching expression="dendrogram=True"/>
1271 <has_text_matching expression="swap_axes=True"/> 1351 <has_text_matching expression="swap_axes=True"/>
1272 <has_text_matching expression="cmap='viridis'"/> 1352 <has_text_matching expression="cmap='viridis'"/>
1273 <has_text_matching expression="edgecolors='face'"/> 1353 <has_text_matching expression="ec='face'"/>
1274 <has_text_matching expression="snap=False"/> 1354 <has_text_matching expression="snap=False"/>
1275 </assert_contents> 1355 </assert_contents>
1276 </output> 1356 </output>
1277 <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="sim_size"/> 1357 <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="sim_size"/>
1278 </test> 1358 </test>
1279 <test> 1359 <test expect_num_outputs="2">
1280 <!-- test 6.1: pl.matrixplot with symbols !--> 1360 <!-- test 11: pl.matrixplot with symbols -->
1281 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" /> 1361 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
1282 <param name="format" value="png"/> 1362 <param name="format" value="png"/>
1283 <conditional name="method"> 1363 <conditional name="method">
1284 <param name="method" value="pl.matrixplot"/> 1364 <param name="method" value="pl.matrixplot"/>
1285 <conditional name="var_names"> 1365 <conditional name="var_names">
1314 <has_text_matching expression="dendrogram=True"/> 1394 <has_text_matching expression="dendrogram=True"/>
1315 <has_text_matching expression="swap_axes=False"/> 1395 <has_text_matching expression="swap_axes=False"/>
1316 </assert_contents> 1396 </assert_contents>
1317 </output> 1397 </output>
1318 </test> 1398 </test>
1319 <test> 1399 <test expect_num_outputs="2">
1320 <!-- test 7: pl.clustermap !--> 1400 <!-- test 12: pl.clustermap -->
1321 <param name="adata" value="krumsiek11.h5ad" /> 1401 <param name="adata" value="krumsiek11.h5ad" />
1322 <param name="format" value="png"/> 1402 <param name="format" value="png"/>
1323 <conditional name="method"> 1403 <conditional name="method">
1324 <param name="method" value="pl.clustermap"/> 1404 <param name="method" value="pl.clustermap"/>
1325 <param name="use_raw" value="False"/> 1405 <param name="use_raw" value="False"/>
1346 <has_text_matching expression="row_cluster=False"/> 1426 <has_text_matching expression="row_cluster=False"/>
1347 </assert_contents> 1427 </assert_contents>
1348 </output> 1428 </output>
1349 <output name="out_png" file="pl.clustermap.krumsiek11.png" ftype="png" compare="sim_size"/> 1429 <output name="out_png" file="pl.clustermap.krumsiek11.png" ftype="png" compare="sim_size"/>
1350 </test> 1430 </test>
1351 <test> 1431 <test expect_num_outputs="2">
1352 <!-- test 8: pl.highest_expr_genes !--> 1432 <!-- test 13: pl.highest_expr_genes -->
1353 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" /> 1433 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
1354 <param name="format" value="png"/> 1434 <param name="format" value="png"/>
1355 <conditional name="method"> 1435 <conditional name="method">
1356 <param name="method" value="pl.highest_expr_genes"/> 1436 <param name="method" value="pl.highest_expr_genes"/>
1357 <param name="n_top" value="30"/> 1437 <param name="n_top" value="30"/>
1373 <has_text_matching expression="saturation=0.5"/> 1453 <has_text_matching expression="saturation=0.5"/>
1374 </assert_contents> 1454 </assert_contents>
1375 </output> 1455 </output>
1376 <output name="out_png" file="pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png" ftype="png" compare="sim_size"/> 1456 <output name="out_png" file="pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png" ftype="png" compare="sim_size"/>
1377 </test> 1457 </test>
1378 <test> 1458 <test expect_num_outputs="2">
1379 <!-- test 9: pl.highly_variable_genes !--> 1459 <!-- test 14: pl.highly_variable_genes -->
1380 <param name="adata" value="pp.highly_variable_genes.seurat.blobs.h5ad" /> 1460 <param name="adata" value="pp.highly_variable_genes.seurat.blobs.h5ad" />
1381 <param name="format" value="png"/> 1461 <param name="format" value="png"/>
1382 <conditional name="method"> 1462 <conditional name="method">
1383 <param name="method" value="pl.highly_variable_genes"/> 1463 <param name="method" value="pl.highly_variable_genes"/>
1384 <param name="log" value="false"/> 1464 <param name="log" value="false"/>
1395 <has_text_matching expression="highly_variable_genes=True"/> 1475 <has_text_matching expression="highly_variable_genes=True"/>
1396 </assert_contents> 1476 </assert_contents>
1397 </output> 1477 </output>
1398 <output name="out_png" file="pl.highly_variable_genes.seurat.blobs.png" ftype="png" compare="sim_size"/> 1478 <output name="out_png" file="pl.highly_variable_genes.seurat.blobs.png" ftype="png" compare="sim_size"/>
1399 </test> 1479 </test>
1400 <test> 1480 <test expect_num_outputs="2">
1401 <!-- test 10: pl.pca !--> 1481 <!-- test 15: pl.pca -->
1402 <param name="adata" value="pbmc68k_reduced.h5ad" /> 1482 <param name="adata" value="pbmc68k_reduced.h5ad" />
1403 <param name="format" value="pdf"/> 1483 <param name="format" value="pdf"/>
1404 <conditional name="method"> 1484 <conditional name="method">
1405 <param name="method" value="pl.pca"/> 1485 <param name="method" value="pl.pca"/>
1406 <param name="color" value="CD3D,CD79A"/> 1486 <param name="color" value="CD3D,CD79A"/>
1450 <has_text_matching expression="palette='viridis'" /> 1530 <has_text_matching expression="palette='viridis'" />
1451 <has_text_matching expression="frameon=True" /> 1531 <has_text_matching expression="frameon=True" />
1452 <has_text_matching expression="ncols=2" /> 1532 <has_text_matching expression="ncols=2" />
1453 <has_text_matching expression="wspace=0.1" /> 1533 <has_text_matching expression="wspace=0.1" />
1454 <has_text_matching expression="hspace=0.25" /> 1534 <has_text_matching expression="hspace=0.25" />
1455 <has_text_matching expression="linewidths=0.0" /> 1535 <has_text_matching expression="lw=0.0" />
1456 <has_text_matching expression="edgecolors='face" /> 1536 <has_text_matching expression="ec='face'" />
1457 </assert_contents> 1537 </assert_contents>
1458 </output> 1538 </output>
1459 <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/> 1539 <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/>
1460 </test> 1540 </test>
1461 <test> 1541 <test expect_num_outputs="2">
1462 <!-- test 11: pl.pca_loadings !--> 1542 <!-- test 16: pl.pca_loadings -->
1463 <param name="adata" value="pp.pca.krumsiek11.h5ad" /> 1543 <param name="adata" value="pp.pca.krumsiek11.h5ad" />
1464 <param name="format" value="png"/> 1544 <param name="format" value="png"/>
1465 <conditional name="method"> 1545 <conditional name="method">
1466 <param name="method" value="pl.pca_loadings"/> 1546 <param name="method" value="pl.pca_loadings"/>
1467 <param name="components" value="1,2,3"/> 1547 <param name="components" value="1,2,3"/>
1475 <has_text_matching expression="components=\[1, 2, 3\]" /> 1555 <has_text_matching expression="components=\[1, 2, 3\]" />
1476 </assert_contents> 1556 </assert_contents>
1477 </output> 1557 </output>
1478 <output name="out_png" file="pl.pca_loadings.pp.pca.krumsiek11.png" compare="sim_size"/> 1558 <output name="out_png" file="pl.pca_loadings.pp.pca.krumsiek11.png" compare="sim_size"/>
1479 </test> 1559 </test>
1480 <test> 1560 <test expect_num_outputs="2">
1481 <!-- test 12: pl.pca_variance_ratio !--> 1561 <!-- test 17: pl.pca_variance_ratio -->
1482 <param name="adata" value="pp.pca.krumsiek11.h5ad" /> 1562 <param name="adata" value="pp.pca.krumsiek11.h5ad" />
1483 <param name="format" value="png"/> 1563 <param name="format" value="png"/>
1484 <conditional name="method"> 1564 <conditional name="method">
1485 <param name="method" value="pl.pca_variance_ratio"/> 1565 <param name="method" value="pl.pca_variance_ratio"/>
1486 <param name="n_pcs" value="5"/> 1566 <param name="n_pcs" value="5"/>
1496 <has_text_matching expression="log=False" /> 1576 <has_text_matching expression="log=False" />
1497 </assert_contents> 1577 </assert_contents>
1498 </output> 1578 </output>
1499 <output name="out_png" file="pl.pca_variance_ratio.pp.pca.krumsiek11.png" compare="sim_size"/> 1579 <output name="out_png" file="pl.pca_variance_ratio.pp.pca.krumsiek11.png" compare="sim_size"/>
1500 </test> 1580 </test>
1501 <test> 1581 <test expect_num_outputs="2">
1502 <!-- test 13: pl.pca_overview !--> 1582 <!-- test 18: pl.pca_overview -->
1503 <param name="adata" value="pp.pca.krumsiek11.h5ad" /> 1583 <param name="adata" value="pp.pca.krumsiek11.h5ad" />
1504 <param name="format" value="png"/> 1584 <param name="format" value="png"/>
1505 <conditional name="method"> 1585 <conditional name="method">
1506 <param name="method" value="pl.pca_overview"/> 1586 <param name="method" value="pl.pca_overview"/>
1507 <param name="use_raw" value="False"/> 1587 <param name="use_raw" value="False"/>
1539 <has_text_matching expression="hspace=0.25"/> 1619 <has_text_matching expression="hspace=0.25"/>
1540 </assert_contents> 1620 </assert_contents>
1541 </output> 1621 </output>
1542 <output name="out_png" file="pl.pca_overview.pp.pca.krumsiek11.png" compare="sim_size"/> 1622 <output name="out_png" file="pl.pca_overview.pp.pca.krumsiek11.png" compare="sim_size"/>
1543 </test> 1623 </test>
1544 <test> 1624 <test expect_num_outputs="2">
1545 <!-- test 14: pl.tsne !--> 1625 <!-- test 19: pl.tsne -->
1546 <param name="adata" value="tl.tsne.krumsiek11.h5ad" /> 1626 <param name="adata" value="tl.tsne.krumsiek11.h5ad" />
1547 <param name="format" value="png"/> 1627 <param name="format" value="png"/>
1548 <conditional name="method"> 1628 <conditional name="method">
1549 <param name="method" value="pl.tsne"/> 1629 <param name="method" value="pl.tsne"/>
1550 <param name="use_raw" value="False"/> 1630 <param name="use_raw" value="False"/>
1588 <has_text_matching expression="palette='viridis'"/> 1668 <has_text_matching expression="palette='viridis'"/>
1589 <has_text_matching expression="frameon=True"/> 1669 <has_text_matching expression="frameon=True"/>
1590 <has_text_matching expression="ncols=4"/> 1670 <has_text_matching expression="ncols=4"/>
1591 <has_text_matching expression="wspace=0.1"/> 1671 <has_text_matching expression="wspace=0.1"/>
1592 <has_text_matching expression="hspace=0.25"/> 1672 <has_text_matching expression="hspace=0.25"/>
1593 <has_text_matching expression="linewidths=0.0"/> 1673 <has_text_matching expression="lw=0.0"/>
1594 <has_text_matching expression="edgecolors='face'"/> 1674 <has_text_matching expression="ec='face'"/>
1595 </assert_contents> 1675 </assert_contents>
1596 </output> 1676 </output>
1597 <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="sim_size"/> 1677 <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="sim_size"/>
1598 </test> 1678 </test>
1599 <test> 1679 <test expect_num_outputs="2">
1600 <!-- test 15: pl.umap !--> 1680 <!-- test 20: pl.umap -->
1601 <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" /> 1681 <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
1602 <param name="format" value="png"/> 1682 <param name="format" value="png"/>
1603 <conditional name="method"> 1683 <conditional name="method">
1604 <param name="method" value="pl.umap"/> 1684 <param name="method" value="pl.umap"/>
1605 <param name="color" value="paul15_clusters"/> 1685 <param name="color" value="paul15_clusters"/>
1648 <has_text_matching expression="palette='viridis'"/> 1728 <has_text_matching expression="palette='viridis'"/>
1649 <has_text_matching expression="frameon=True"/> 1729 <has_text_matching expression="frameon=True"/>
1650 <has_text_matching expression="ncols=4"/> 1730 <has_text_matching expression="ncols=4"/>
1651 <has_text_matching expression="wspace=0.1"/> 1731 <has_text_matching expression="wspace=0.1"/>
1652 <has_text_matching expression="hspace=0.25"/> 1732 <has_text_matching expression="hspace=0.25"/>
1653 <has_text_matching expression="linewidths=0.0"/> 1733 <has_text_matching expression="lw=0.0"/>
1654 <has_text_matching expression="edgecolors='face'"/> 1734 <has_text_matching expression="ec='face'"/>
1655 </assert_contents> 1735 </assert_contents>
1656 </output> 1736 </output>
1657 <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/> 1737 <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
1658 </test> 1738 </test>
1659 <test> 1739 <test expect_num_outputs="2">
1660 <!-- test 16: pl.diffmap !--> 1740 <!-- test 21: pl.diffmap -->
1661 <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" /> 1741 <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
1662 <param name="format" value="png"/> 1742 <param name="format" value="png"/>
1663 <conditional name="method"> 1743 <conditional name="method">
1664 <param name="method" value="pl.diffmap"/> 1744 <param name="method" value="pl.diffmap"/>
1665 <param name="color" value="paul15_clusters"/> 1745 <param name="color" value="paul15_clusters"/>
1699 <has_text_matching expression="palette='viridis'"/> 1779 <has_text_matching expression="palette='viridis'"/>
1700 <has_text_matching expression="frameon=True"/> 1780 <has_text_matching expression="frameon=True"/>
1701 <has_text_matching expression="ncols=4"/> 1781 <has_text_matching expression="ncols=4"/>
1702 <has_text_matching expression="wspace=0.1"/> 1782 <has_text_matching expression="wspace=0.1"/>
1703 <has_text_matching expression="hspace=0.25"/> 1783 <has_text_matching expression="hspace=0.25"/>
1704 <has_text_matching expression="linewidths=0.0"/> 1784 <has_text_matching expression="lw=0.0"/>
1705 <has_text_matching expression="edgecolors='face'"/> 1785 <has_text_matching expression="ec='face'"/>
1706 </assert_contents> 1786 </assert_contents>
1707 </output> 1787 </output>
1708 <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/> 1788 <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
1709 </test> 1789 </test>
1710 <test> 1790 <test expect_num_outputs="2">
1711 <!-- test 17: pl.draw_graph !--> 1791 <!-- test 22: pl.draw_graph -->
1712 <param name="adata" value="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" /> 1792 <param name="adata" value="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
1713 <param name="format" value="png"/> 1793 <param name="format" value="png"/>
1714 <conditional name="method"> 1794 <conditional name="method">
1715 <param name="method" value="pl.draw_graph"/> 1795 <param name="method" value="pl.draw_graph"/>
1716 <param name="use_raw" value="false"/> 1796 <param name="use_raw" value="false"/>
1755 <has_text_matching expression="palette='viridis'"/> 1835 <has_text_matching expression="palette='viridis'"/>
1756 <has_text_matching expression="frameon=True"/> 1836 <has_text_matching expression="frameon=True"/>
1757 <has_text_matching expression="ncols=4"/> 1837 <has_text_matching expression="ncols=4"/>
1758 <has_text_matching expression="wspace=0.1"/> 1838 <has_text_matching expression="wspace=0.1"/>
1759 <has_text_matching expression="hspace=0.25"/> 1839 <has_text_matching expression="hspace=0.25"/>
1760 <has_text_matching expression="linewidths=0.0"/> 1840 <has_text_matching expression="lw=0.0"/>
1761 <has_text_matching expression="edgecolors='face"/> 1841 <has_text_matching expression="ec='face"/>
1762 </assert_contents> 1842 </assert_contents>
1763 </output> 1843 </output>
1764 <output name="out_png" file="pl.draw_graph.png" ftype="png" compare="sim_size"/> 1844 <output name="out_png" file="pl.draw_graph.png" ftype="png" compare="sim_size"/>
1765 </test> 1845 </test>
1766 <!--<test> 1846 <test expect_num_outputs="2">
1767 < test pl.dpt_groups_pseudotime > 1847 <!-- test 23: pl.embedding_density -->
1848 <param name="adata" value="tl.embedding_density.umap.pbmc68k_reduced.h5ad" />
1849 <param name="format" value="png"/>
1850 <conditional name="method">
1851 <param name="method" value="pl.embedding_density"/>
1852 <param name="basis" value="umap"/>
1853 <param name="key" value="umap_density_bulk_labels"/>
1854 </conditional>
1855 <section name="advanced_common">
1856 <param name="show_log" value="true" />
1857 </section>
1858 <output name="hidden_output">
1859 <assert_contents>
1860 <has_text_matching expression="sc.pl.embedding_density"/>
1861 <has_text_matching expression="basis='umap'" />
1862 <has_text_matching expression="key='umap_density_bulk_labels'"/>
1863 </assert_contents>
1864 </output>
1865 <output name="out_png" file="pl.embedding_density.pbmc68k_reduced.png" ftype="png" compare="sim_size"/>
1866 </test>
1867 <test expect_num_outputs="2">
1868 <!-- test 24: pl.dpt_groups_pseudotime -->
1768 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" /> 1869 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
1769 <param name="format" value="png"/> 1870 <param name="format" value="png"/>
1770 <conditional name="method"> 1871 <conditional name="method">
1771 <param name="method" value="pl.dpt_groups_pseudotime"/> 1872 <param name="method" value="pl.dpt_groups_pseudotime"/>
1772 <param name="color_map" value="viridis"/> 1873 <param name="color_map" value="viridis"/>
1773 </conditional> 1874 </conditional>
1774 <assert_stdout> 1875 <section name="advanced_common">
1775 <has_text_matching expression="sc.pl.dpt_groups_pseudotime"/> 1876 <param name="show_log" value="true" />
1776 <has_text_matching expression="color_map='viridis'"/> 1877 </section>
1777 </assert_stdout> 1878 <output name="hidden_output">
1879 <assert_contents>
1880 <has_text_matching expression="sc.pl.dpt_groups_pseudotime"/>
1881 <has_text_matching expression="color_map='viridis'"/>
1882 </assert_contents>
1883 </output>
1778 <output name="out_png" file="pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/> 1884 <output name="out_png" file="pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
1779 </test>!--> 1885 </test>
1780 <test> 1886 <test expect_num_outputs="2">
1781 <!-- test 18: pl.dpt_timeseries !--> 1887 <!-- test 25: pl.dpt_timeseries -->
1782 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" /> 1888 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
1783 <param name="format" value="png"/> 1889 <param name="format" value="png"/>
1784 <conditional name="method"> 1890 <conditional name="method">
1785 <param name="method" value="pl.dpt_timeseries"/> 1891 <param name="method" value="pl.dpt_timeseries"/>
1786 <conditional name="heatmap"> 1892 <conditional name="heatmap">
1798 <has_text_matching expression="as_heatmap=True"/> 1904 <has_text_matching expression="as_heatmap=True"/>
1799 </assert_contents> 1905 </assert_contents>
1800 </output> 1906 </output>
1801 <output name="out_png" file="pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/> 1907 <output name="out_png" file="pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
1802 </test> 1908 </test>
1803 <!--<test> 1909 <test expect_num_outputs="1">
1804 test pl.paga 1910 <!-- test 26: pl.paga -->
1805 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad" /> 1911 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad" />
1806 <param name="format" value="png"/> 1912 <param name="format" value="png"/>
1807 <conditional name="method"> 1913 <conditional name="method">
1808 <param name="method" value="pl.paga"/> 1914 <param name="method" value="pl.paga"/>
1809 <param name="threshold" value="0.01"/> 1915 <param name="threshold" value="0.01"/>
1810 <param name="color" value="paul15_clusters"/> 1916 <param name="color" value="louvain"/>
1811 <param name="labels" value="label" />
1812 <param name="layout" value="fr"/> 1917 <param name="layout" value="fr"/>
1813 <param name="random_state" value="0"/> 1918 <param name="random_state" value="0"/>
1814 <param name="solid_edges" value="connectivities"/> 1919 <param name="solid_edges" value="connectivities"/>
1815 <param name="single_component" value="False"/> 1920 <param name="single_component" value="False"/>
1816 <param name="fontsize" value="1"/> 1921 <param name="fontsize" value="1"/>
1821 <param name="normalize_to_color" value="False"/> 1926 <param name="normalize_to_color" value="False"/>
1822 <param name="cmap" value="viridis"/> 1927 <param name="cmap" value="viridis"/>
1823 <param name="frameon" value="True"/> 1928 <param name="frameon" value="True"/>
1824 </conditional> 1929 </conditional>
1825 <output name="out_png" file="pl.paga.paul15_gauss_braycurtis.png" ftype="png" compare="sim_size"/> 1930 <output name="out_png" file="pl.paga.paul15_gauss_braycurtis.png" ftype="png" compare="sim_size"/>
1826 </test>!--> 1931 </test>
1827 <!--<test> 1932 <test expect_num_outputs="1">
1828 test pl.paga_compare 1933 <!-- test 27: pl.paga_compare -->
1829 </test>!--> 1934 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad" />
1830 <!--<test> 1935 <param name="format" value="png"/>
1936 <conditional name="method">
1937 <param name="method" value="pl.paga_compare"/>
1938 <param name="threshold" value="0.01"/>
1939 <param name="color" value="louvain"/>
1940 <param name="layout" value="fr"/>
1941 <param name="random_state" value="0"/>
1942 <param name="solid_edges" value="connectivities"/>
1943 <param name="single_component" value="False"/>
1944 <param name="fontsize" value="1"/>
1945 <param name="node_size_scale" value="1.0"/>
1946 <param name="node_size_power" value="0.5"/>
1947 <param name="edge_width_scale" value="5"/>
1948 <param name="arrowsize" value="30"/>
1949 <param name="normalize_to_color" value="False"/>
1950 <param name="cmap" value="viridis"/>
1951 <param name="frameon" value="True"/>
1952 </conditional>
1953 <output name="out_png" file="pl.paga_compare.paul15_gauss_braycurtis.png" ftype="png" compare="sim_size"/>
1954 </test>
1955 <!--<test expect_num_outputs="2">
1831 test pl.paga_path 1956 test pl.paga_path
1832 </test>!--> 1957 </test>-->
1833 <test> 1958 <test expect_num_outputs="2">
1834 <!-- test 19: pl.rank_genes_groups !--> 1959 <!-- test 28: pl.rank_genes_groups -->
1835 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> 1960 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
1836 <param name="format" value="png"/> 1961 <param name="format" value="png"/>
1837 <conditional name="method"> 1962 <conditional name="method">
1838 <param name="method" value="pl.rank_genes_groups"/> 1963 <param name="method" value="pl.rank_genes_groups"/>
1964 <param name="gene_symbols" value="symbol"/>
1839 <param name="n_genes" value="10"/> 1965 <param name="n_genes" value="10"/>
1840 <param name="fontsize" value="8"/> 1966 <param name="fontsize" value="8"/>
1841 <param name="ncols" value="4"/> 1967 <param name="ncols" value="4"/>
1842 <param name="sharey" value="true"/> 1968 <param name="sharey" value="true"/>
1843 </conditional> 1969 </conditional>
1853 <has_text_matching expression="sharey=True"/> 1979 <has_text_matching expression="sharey=True"/>
1854 </assert_contents> 1980 </assert_contents>
1855 </output> 1981 </output>
1856 <output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/> 1982 <output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
1857 </test> 1983 </test>
1858 <!-- test 20: pl.rank_genes_groups_violin, currently broken 1984 <test expect_num_outputs="2">
1859 <test> 1985 <!-- test 29: pl.rank_genes_groups_violin -->
1860 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> 1986 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
1861 <param name="format" value="png"/> 1987 <param name="format" value="png"/>
1862 <conditional name="method"> 1988 <conditional name="method">
1863 <param name="method" value="pl.rank_genes_groups_violin"/> 1989 <param name="method" value="pl.rank_genes_groups_violin"/>
1864 <conditional name="genes"> 1990 <conditional name="genes">
1897 <element name="cell_type_Mo" file="pl.rank_genes_groups_violin.Mo.png" ftype="png" compare="sim_size"/> 2023 <element name="cell_type_Mo" file="pl.rank_genes_groups_violin.Mo.png" ftype="png" compare="sim_size"/>
1898 <element name="cell_type_Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="sim_size"/> 2024 <element name="cell_type_Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="sim_size"/>
1899 <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="sim_size"/> 2025 <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="sim_size"/>
1900 </output_collection> 2026 </output_collection>
1901 </test> 2027 </test>
1902 --> 2028 <test expect_num_outputs="2">
1903 <test> 2029 <!-- test 30: pl.rank_genes_groups_dotplot -->
1904 <!-- test 21: pl.rank_genes_groups_dotplot !-->
1905 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> 2030 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
1906 <param name="format" value="png"/> 2031 <param name="format" value="png"/>
1907 <conditional name="method"> 2032 <conditional name="method">
1908 <param name="method" value="pl.rank_genes_groups_dotplot"/> 2033 <param name="method" value="pl.rank_genes_groups_dotplot"/>
2034 <param name="gene_symbols" value="symbol"/>
1909 <param name="n_genes" value="10"/> 2035 <param name="n_genes" value="10"/>
1910 <param name="log" value="False"/> 2036 <param name="log" value="False"/>
1911 <param name="use_raw" value="False"/> 2037 <param name="use_raw" value="False"/>
1912 <param name="dendrogram" value="False"/> 2038 <param name="dendrogram" value="False"/>
1913 <param name="color_map" value="viridis"/> 2039 <param name="color_map" value="viridis"/>
1925 <has_text_matching expression="n_genes=10"/> 2051 <has_text_matching expression="n_genes=10"/>
1926 <has_text_matching expression="log=False"/> 2052 <has_text_matching expression="log=False"/>
1927 <has_text_matching expression="use_raw=False"/> 2053 <has_text_matching expression="use_raw=False"/>
1928 <has_text_matching expression="dendrogram=False"/> 2054 <has_text_matching expression="dendrogram=False"/>
1929 <has_text_matching expression="color_map='viridis'"/> 2055 <has_text_matching expression="color_map='viridis'"/>
1930 <has_text_matching expression="linewidths=0.0"/> 2056 <has_text_matching expression="lw=0.0"/>
1931 <has_text_matching expression="edgecolors='face'"/> 2057 <has_text_matching expression="ec='face'"/>
1932 </assert_contents> 2058 </assert_contents>
1933 </output> 2059 </output>
1934 <output name="out_png" file="pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/> 2060 <output name="out_png" file="pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
1935 </test> 2061 </test>
1936 <test> 2062 <test expect_num_outputs="2">
1937 <!-- test 22: pl.rank_genes_groups_heatmap !--> 2063 <!-- test 31: pl.rank_genes_groups_heatmap -->
1938 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> 2064 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
1939 <param name="format" value="png"/> 2065 <param name="format" value="png"/>
1940 <conditional name="method"> 2066 <conditional name="method">
1941 <param name="method" value="pl.rank_genes_groups_heatmap"/> 2067 <param name="method" value="pl.rank_genes_groups_heatmap"/>
2068 <param name="gene_symbols" value="symbol"/>
1942 <param name="n_genes" value="10"/> 2069 <param name="n_genes" value="10"/>
1943 <param name="log" value="False"/> 2070 <param name="log" value="False"/>
1944 <param name="use_raw" value="False"/> 2071 <param name="use_raw" value="False"/>
1945 <param name="dendrogram" value="False"/> 2072 <param name="dendrogram" value="False"/>
1946 <param name="swap_axes" value="False"/> 2073 <param name="swap_axes" value="False"/>
1967 <has_text_matching expression="origin='upper'"/> 2094 <has_text_matching expression="origin='upper'"/>
1968 </assert_contents> 2095 </assert_contents>
1969 </output> 2096 </output>
1970 <output name="out_png" file="pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/> 2097 <output name="out_png" file="pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
1971 </test> 2098 </test>
1972 <test> 2099 <test expect_num_outputs="2">
1973 <!-- test 23: pl.rank_genes_groups_matrixplot !--> 2100 <!-- test 32: pl.rank_genes_groups_matrixplot -->
1974 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> 2101 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
1975 <param name="format" value="png"/> 2102 <param name="format" value="png"/>
1976 <conditional name="method"> 2103 <conditional name="method">
1977 <param name="method" value="pl.rank_genes_groups_matrixplot"/> 2104 <param name="method" value="pl.rank_genes_groups_matrixplot"/>
2105 <param name="gene_symbols" value="symbol"/>
1978 <param name="n_genes" value="10"/> 2106 <param name="n_genes" value="10"/>
1979 <param name="log" value="False"/> 2107 <param name="log" value="False"/>
1980 <param name="use_raw" value="False"/> 2108 <param name="use_raw" value="False"/>
1981 <param name="dendrogram" value="False"/> 2109 <param name="dendrogram" value="False"/>
1982 <param name="swap_axes" value="False"/> 2110 <param name="swap_axes" value="False"/>
1996 <has_text_matching expression="log=False"/> 2124 <has_text_matching expression="log=False"/>
1997 <has_text_matching expression="use_raw=False"/> 2125 <has_text_matching expression="use_raw=False"/>
1998 <has_text_matching expression="dendrogram=False"/> 2126 <has_text_matching expression="dendrogram=False"/>
1999 <has_text_matching expression="swap_axes=False"/> 2127 <has_text_matching expression="swap_axes=False"/>
2000 <has_text_matching expression="cmap='viridis'"/> 2128 <has_text_matching expression="cmap='viridis'"/>
2001 <has_text_matching expression="edgecolors='face'"/> 2129 <has_text_matching expression="ec='face'"/>
2002 <has_text_matching expression="snap=False"/> 2130 <has_text_matching expression="snap=False"/>
2003 </assert_contents> 2131 </assert_contents>
2004 </output> 2132 </output>
2005 <output name="out_png" file="pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/> 2133 <output name="out_png" file="pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
2006 </test> 2134 </test>
2007 <test> 2135 <test expect_num_outputs="2">
2008 <!-- test 24: pl.rank_genes_groups_stacked_violin !--> 2136 <!-- test 33: pl.rank_genes_groups_stacked_violin -->
2009 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> 2137 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
2010 <param name="format" value="png"/> 2138 <param name="format" value="png"/>
2011 <conditional name="method"> 2139 <conditional name="method">
2012 <param name="method" value="pl.rank_genes_groups_stacked_violin"/> 2140 <param name="method" value="pl.rank_genes_groups_stacked_violin"/>
2141 <param name="gene_symbols" value="symbol"/>
2013 <param name="n_genes" value="10"/> 2142 <param name="n_genes" value="10"/>
2014 <param name="log" value="False"/> 2143 <param name="log" value="False"/>
2015 <param name="use_raw" value="False"/> 2144 <param name="use_raw" value="False"/>
2016 <param name="dendrogram" value="True"/> 2145 <param name="dendrogram" value="True"/>
2017 <param name="swap_axes" value="True"/> 2146 <param name="swap_axes" value="True"/>
2055 <has_text_matching expression="saturation=0.75"/> 2184 <has_text_matching expression="saturation=0.75"/>
2056 </assert_contents> 2185 </assert_contents>
2057 </output> 2186 </output>
2058 <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/> 2187 <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
2059 </test> 2188 </test>
2189 <test expect_num_outputs="2">
2190 <!-- test 34: pl.scatter log !-->
2191 <param name="adata" value="pbmc68k_reduced.h5ad" />
2192 <param name="format" value="png"/>
2193 <conditional name="method">
2194 <param name="method" value="pl.scatter"/>
2195 <conditional name="type">
2196 <param name="type" value="xy"/>
2197 <param name="x" value="n_genes"/>
2198 <param name="y" value="n_counts"/>
2199 <param name="log" value="True"/>
2200 <conditional name="layers">
2201 <param name="use_layers" value="false"/>
2202 </conditional>
2203 </conditional>
2204 <param name="use_raw" value="False"/>
2205 <param name="sort_order" value="True"/>
2206 <section name="plot">
2207 <param name="projection" value="2d"/>
2208 <param name="legend_loc" value="right margin"/>
2209 <param name="legend_fontsize" value="1"/>
2210 <param name="legend_fontweight" value="normal"/>
2211 <param name="palette" value="bwr"/>
2212 <param name="frameon" value="False"/>
2213 <param name="size" value="1"/>
2214 <param name="title" value="A title"/>
2215 </section>
2216 </conditional>
2217 <section name="advanced_common">
2218 <param name="show_log" value="true" />
2219 </section>
2220 <output name="hidden_output">
2221 <assert_contents>
2222 <has_text_matching expression="sc.pl.scatter"/>
2223 <has_text_matching expression="use_raw=False"/>
2224 <has_text_matching expression="sort_order=True"/>
2225 <has_text_matching expression="projection='2d'"/>
2226 <has_text_matching expression="legend_loc='right margin'"/>
2227 <has_text_matching expression="legend_fontsize=1"/>
2228 <has_text_matching expression="legend_fontweight='normal'"/>
2229 <has_text_matching expression="frameon=False"/>
2230 <has_text_matching expression="size=1.0"/>
2231 <has_text_matching expression="title='A title'"/>
2232 </assert_contents>
2233 </output>
2234 <output name="out_png" file="pl.scatter.pbmc68k_reduced.png" ftype="png" compare="sim_size"/>
2235 </test>
2060 </tests> 2236 </tests>
2061 <help><![CDATA[ 2237 <help><![CDATA[
2062 Generic: Scatter plot along observations or variables axes (`pl.scatter`) 2238 Generic: Scatter plot along observations or variables axes (`pl.scatter`)
2063 ========================================================================= 2239 =========================================================================
2064 2240
2065 Color the plot using annotations of observations (`.obs`), variables 2241 Color the plot using annotations of observations (`.obs`), variables
2066 (`.var`) or expression of genes (`.var_names`). 2242 (`.var`) or expression of genes (`.var_names`).
2067 2243
2068 More details on the `scanpy documentation 2244 More details on the `scanpy documentation
2069 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.scatter.html>`__ 2245 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.scatter.html>`__
2070 2246
2071 Generic: Heatmap of the expression values of set of genes (`pl.heatmap`) 2247 Generic: Heatmap of the expression values of set of genes (`pl.heatmap`)
2072 ======================================================================== 2248 ========================================================================
2073 2249
2074 If `groupby` is given, the heatmap is ordered by the respective group. For 2250 If `groupby` is given, the heatmap is ordered by the respective group. For
2076 the `groupby` observation annotation is not categorical the observation 2252 the `groupby` observation annotation is not categorical the observation
2077 annotation is turned into a categorical by binning the data into the number 2253 annotation is turned into a categorical by binning the data into the number
2078 specified in `num_categories`. 2254 specified in `num_categories`.
2079 2255
2080 More details on the `scanpy documentation 2256 More details on the `scanpy documentation
2081 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.heatmap.html>`__ 2257 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.heatmap.html>`__
2082 2258
2083 Generic: Makes a dot plot of the expression values (`pl.dotplot`) 2259 Generic: Makes a dot plot of the expression values (`pl.dotplot`)
2084 ================================================================= 2260 =================================================================
2085 2261
2086 For each var_name and each `groupby` category a dot is plotted. Each dot 2262 For each var_name and each `groupby` category a dot is plotted. Each dot
2093 2269
2094 For instance, for each marker gene, the mean value and the percentage of cells 2270 For instance, for each marker gene, the mean value and the percentage of cells
2095 expressing the gene can be visualized for each cluster. 2271 expressing the gene can be visualized for each cluster.
2096 2272
2097 More details on the `scanpy documentation 2273 More details on the `scanpy documentation
2098 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.dotplot.html>`__ 2274 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.dotplot.html>`__
2099 2275
2100 Generic: Violin plot (`pl.violin`) 2276 Generic: Violin plot (`pl.violin`)
2101 ================================== 2277 ==================================
2102 2278
2103 Wraps `seaborn.violinplot` for `anndata.AnnData`. 2279 Wraps `seaborn.violinplot` for `anndata.AnnData`.
2104 2280
2105 More details on the `scanpy documentation 2281 More details on the `scanpy documentation
2106 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.violin.html>`__ 2282 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.violin.html>`__
2107 2283
2108 Generic: Stacked violin plots (`pl.stacked_violin`) 2284 Generic: Stacked violin plots (`pl.stacked_violin`)
2109 =================================================== 2285 ===================================================
2110 2286
2111 Makes a compact image composed of individual violin plots (from `seaborn.violinplot`) 2287 Makes a compact image composed of individual violin plots (from `seaborn.violinplot`)
2112 stacked on top of each other. Useful to visualize gene expression per cluster. 2288 stacked on top of each other. Useful to visualize gene expression per cluster.
2113 2289
2114 More details on the `scanpy documentation 2290 More details on the `scanpy documentation
2115 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.stacked_violin.html>`__ 2291 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.stacked_violin.html>`__
2116 2292
2117 Generic: Heatmap of the mean expression values per cluster (`pl.matrixplot`) 2293 Generic: Heatmap of the mean expression values per cluster (`pl.matrixplot`)
2118 ============================================================================ 2294 ============================================================================
2119 2295
2120 Creates a heatmap of the mean expression values per cluster of each var_names 2296 Creates a heatmap of the mean expression values per cluster of each var_names
2121 2297
2122 If groupby is not given, the matrixplot assumes that all data belongs to a single 2298 If groupby is not given, the matrixplot assumes that all data belongs to a single
2123 category. 2299 category.
2124 2300
2125 More details on the `scanpy documentation 2301 More details on the `scanpy documentation
2126 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.matrixplot.html>`__ 2302 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.matrixplot.html>`__
2127 2303
2128 Generic: Hierarchically-clustered heatmap (`pl.clustermap`) 2304 Generic: Hierarchically-clustered heatmap (`pl.clustermap`)
2129 =========================================================== 2305 ===========================================================
2130 2306
2131 Wraps `seaborn.clustermap 2307 Wraps `seaborn.clustermap
2139 clustergrid.dendrogram_row.reordered_ind 2315 clustergrid.dendrogram_row.reordered_ind
2140 2316
2141 Column indices, use: clustergrid.dendrogram_col.reordered_ind 2317 Column indices, use: clustergrid.dendrogram_col.reordered_ind
2142 2318
2143 More details on the `scanpy documentation 2319 More details on the `scanpy documentation
2144 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.clustermap.html>`__ 2320 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.clustermap.html>`__
2145 2321
2146 Preprocessing: Plot the fraction of counts assigned to each gene over all cells (`pl.highest_expr_genes`) 2322 Preprocessing: Plot the fraction of counts assigned to each gene over all cells (`pl.highest_expr_genes`)
2147 ========================================================================================================= 2323 =========================================================================================================
2148 2324
2149 Computes, for each gene, the fraction of counts assigned to that gene within 2325 Computes, for each gene, the fraction of counts assigned to that gene within
2151 plotted as boxplots. 2327 plotted as boxplots.
2152 2328
2153 This plot is similar to the `scater` package function `plotHighestExprs(type= "highest-expression")` 2329 This plot is similar to the `scater` package function `plotHighestExprs(type= "highest-expression")`
2154 2330
2155 More details on the `scanpy documentation 2331 More details on the `scanpy documentation
2156 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.highest_expr_genes.html>`__ 2332 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.highest_expr_genes.html>`__
2157 2333
2158 Preprocessing: Plot dispersions versus means for genes (`pl.highly_variable_genes`) 2334 Preprocessing: Plot dispersions versus means for genes (`pl.highly_variable_genes`)
2159 =================================================================================== 2335 ===================================================================================
2160 2336
2161 It produces Supp. Fig. 5c of Zheng et al. (2017) and MeanVarPlot() of Seurat. 2337 It produces Supp. Fig. 5c of Zheng et al. (2017) and MeanVarPlot() of Seurat.
2162 2338
2163 More details on the `scanpy documentation 2339 More details on the `scanpy documentation
2164 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.highly_variable_genes.html>`__ 2340 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.highly_variable_genes.html>`__
2165 2341
2166 PCA: Scatter plot in PCA coordinates (`pl.pca`) 2342 PCA: Scatter plot in PCA coordinates (`pl.pca`)
2167 =============================================== 2343 ===============================================
2168 2344
2169 More details on the `scanpy documentation 2345 More details on the `scanpy documentation
2170 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.pca.html>`__ 2346 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca.html>`__
2171 2347
2172 PCA: Rank genes according to contributions to PCs (`pl.pca_loadings`) 2348 PCA: Rank genes according to contributions to PCs (`pl.pca_loadings`)
2173 ===================================================================== 2349 =====================================================================
2174 2350
2175 More details on the `scanpy documentation 2351 More details on the `scanpy documentation
2176 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.pca_loadings.html>`__ 2352 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca_loadings.html>`__
2177 2353
2178 PCA: Plot the variance ratio (`pl.pca_variance_ratio`) 2354 PCA: Plot the variance ratio (`pl.pca_variance_ratio`)
2179 ====================================================== 2355 ======================================================
2180 2356
2181 More details on the `scanpy documentation 2357 More details on the `scanpy documentation
2182 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.pca_variance_ratio.html>`__ 2358 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca_variance_ratio.html>`__
2183 2359
2184 PCA: Plot PCA results (`pl.pca_overview`) 2360 PCA: Plot PCA results (`pl.pca_overview`)
2185 ========================================= 2361 =========================================
2186 2362
2187 The parameters are the ones of the scatter plot. Call pca_ranking separately 2363 The parameters are the ones of the scatter plot. Call pca_ranking separately
2188 if you want to change the default settings. 2364 if you want to change the default settings.
2189 2365
2190 More details on the `scanpy documentation 2366 More details on the `scanpy documentation
2191 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.pca_overview.html>`__ 2367 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca_overview.html>`__
2192 2368
2193 Embedding: Scatter plot in tSNE basis (`pl.tsne`) 2369 Embedding: Scatter plot in tSNE basis (`pl.tsne`)
2194 ================================================= 2370 =================================================
2195 2371
2196 More details on the `scanpy documentation 2372 More details on the `scanpy documentation
2197 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.tsne.html>`__ 2373 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.tsne.html>`__
2198 2374
2199 Embeddings: Scatter plot in UMAP basis (`pl.umap`) 2375 Embeddings: Scatter plot in UMAP basis (`pl.umap`)
2200 ================================================== 2376 ==================================================
2201 2377
2202 More details on the `scanpy documentation 2378 More details on the `scanpy documentation
2203 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.umap.html>`__ 2379 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.umap.html>`__
2204 2380
2205 Embeddings: Scatter plot in Diffusion Map basis (`pl.diffmap`) 2381 Embeddings: Scatter plot in Diffusion Map basis (`pl.diffmap`)
2206 ============================================================== 2382 ==============================================================
2207 2383
2208 More details on the `scanpy documentation 2384 More details on the `scanpy documentation
2209 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.diffmap.html>`__ 2385 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.diffmap.html>`__
2210 2386
2211 Branching trajectories and pseudotime, clustering: Plot groups and pseudotime (`pl.dpt_groups_pseudotime`) 2387 Branching trajectories and pseudotime, clustering: Plot groups and pseudotime (`pl.dpt_groups_pseudotime`)
2212 =========================================================================================================== 2388 ===========================================================================================================
2213 2389
2214 More details on the `scanpy documentation 2390 More details on the `scanpy documentation
2215 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.dpt_groups_pseudotime.html>`__ 2391 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.dpt_groups_pseudotime.html>`__
2216 2392
2217 Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series (`pl.dpt_timeseries`) 2393 Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series (`pl.dpt_timeseries`)
2218 ===================================================================================================== 2394 =====================================================================================================
2219 2395
2220 More details on the `scanpy documentation 2396 More details on the `scanpy documentation
2221 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.dpt_timeseries.html>`__ 2397 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.dpt_timeseries.html>`__
2222 2398
2223 2399
2224 Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges (`pl.paga`) 2400 Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges (`pl.paga`)
2225 ==================================================================================================================================== 2401 ====================================================================================================================================
2226 2402
2229 When initializing the positions, note that - for some reason - igraph 2405 When initializing the positions, note that - for some reason - igraph
2230 mirrors coordinates along the x axis... that is, you should increase the 2406 mirrors coordinates along the x axis... that is, you should increase the
2231 `maxiter` parameter by 1 if the layout is flipped. 2407 `maxiter` parameter by 1 if the layout is flipped.
2232 2408
2233 More details on the `scanpy documentation 2409 More details on the `scanpy documentation
2234 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.paga.html>`__ 2410 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.paga.html>`__
2235 2411
2236 2412
2237 Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side (`pl.paga_compare`) 2413 Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side (`pl.paga_compare`)
2238 ========================================================================================================== 2414 ==========================================================================================================
2239 2415
2240 More details on the `scanpy documentation 2416 More details on the `scanpy documentation
2241 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.paga_compare.html>`__ 2417 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.paga_compare.html>`__
2242 2418
2243 Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths (`pl.paga_path`) 2419 Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths (`pl.paga_path`)
2244 ====================================================================================================================== 2420 ======================================================================================================================
2245 2421
2246 More details on the `scanpy documentation 2422 More details on the `scanpy documentation
2247 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.paga_path.html>`__ 2423 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.paga_path.html>`__
2248 2424
2249 Marker genes: Plot ranking of genes using dotplot plot (`pl.rank_genes_groups`) 2425 Marker genes: Plot ranking of genes using dotplot plot (`pl.rank_genes_groups`)
2250 =============================================================================== 2426 ===============================================================================
2251 2427
2252 More details on the `scanpy documentation 2428 More details on the `scanpy documentation
2253 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.rank_genes_groups.html>`__ 2429 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups.html>`__
2254 2430
2255 Marker genes: Plot ranking of genes as violin plot (`pl.rank_genes_groups_violin`) 2431 Marker genes: Plot ranking of genes as violin plot (`pl.rank_genes_groups_violin`)
2256 ================================================================================== 2432 ==================================================================================
2257 2433
2258 More details on the `scanpy documentation 2434 More details on the `scanpy documentation
2259 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.rank_genes_groups_violin.html>`__ 2435 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_violin.html>`__
2260 2436
2261 Marker genes: Plot ranking of genes as dotplot plot (`pl.rank_genes_groups_dotplot`) 2437 Marker genes: Plot ranking of genes as dotplot plot (`pl.rank_genes_groups_dotplot`)
2262 ==================================================================================== 2438 ====================================================================================
2263 2439
2264 More details on the `scanpy documentation 2440 More details on the `scanpy documentation
2265 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.rank_genes_groups_dotplot.html>`__ 2441 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_dotplot.html>`__
2266 2442
2267 Marker genes: Plot ranking of genes as heatmap plot (`pl.rank_genes_groups_heatmap`) 2443 Marker genes: Plot ranking of genes as heatmap plot (`pl.rank_genes_groups_heatmap`)
2268 ==================================================================================== 2444 ====================================================================================
2269 2445
2270 More details on the `scanpy documentation 2446 More details on the `scanpy documentation
2271 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.rank_genes_groups_heatmap.html>`__ 2447 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_heatmap.html>`__
2272 2448
2273 Marker genes: Plot ranking of genes as matrixplot plot (`pl.rank_genes_groups_matrixplot`) 2449 Marker genes: Plot ranking of genes as matrixplot plot (`pl.rank_genes_groups_matrixplot`)
2274 ========================================================================================== 2450 ==========================================================================================
2275 2451
2276 More details on the `scanpy documentation 2452 More details on the `scanpy documentation
2277 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.rank_genes_groups_matrixplot.html>`__ 2453 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_matrixplot.html>`__
2278 2454
2279 Marker genes: Plot ranking of genes as stacked violin plot (`pl.rank_genes_groups_stacked_violin`) 2455 Marker genes: Plot ranking of genes as stacked violin plot (`pl.rank_genes_groups_stacked_violin`)
2280 ================================================================================================== 2456 ==================================================================================================
2281 2457
2282 More details on the `scanpy documentation 2458 More details on the `scanpy documentation
2283 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.rank_genes_groups_stacked_violin.html>`__ 2459 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_stacked_violin.html>`__
2284 ]]></help> 2460 ]]></help>
2285 <expand macro="citations"/> 2461 <expand macro="citations"/>
2286 </tool> 2462 </tool>