Mercurial > repos > iuc > scanpy_plot

comparison plot.xml @ 3:22c1b4b70360 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
author iuc
date Thu, 12 Dec 2019 14:18:14 +0000
parents 791469a96577
children f2323ff4e07f
comparison
equal deleted inserted replaced
2:791469a96577 3:22c1b4b70360
35 color=$color, 35 color=$color,
36 #end if 36 #end if
37 #end if 37 #end if
38 use_raw=$method.use_raw, 38 use_raw=$method.use_raw,
39 sort_order=$method.sort_order, 39 sort_order=$method.sort_order,
40 @CMD_params_pl_groups@ 40 @CMD_params_groups@
41 @CMD_params_pl_components@ 41 @CMD_params_pl_components@
42 projection='$method.plot.projection', 42 projection='$method.plot.projection',
43 legend_loc='$method.plot.legend_loc', 43 legend_loc='$method.plot.legend_loc',
44 legend_fontsize=$method.plot.legend_fontsize, 44 @CMD_param_legend_fontsize@
45 legend_fontweight='$method.plot.legend_fontweight', 45 legend_fontweight='$method.plot.legend_fontweight',
46 color_map='$method.plot.color_map', 46 color_map='$method.plot.color_map',
47 #if str($method.plot.palette) != ''
47 palette='$method.plot.palette', 48 palette='$method.plot.palette',
49 #end if
48 frameon=$method.plot.frameon, 50 frameon=$method.plot.frameon,
49 #if $method.plot.title 51 @CMD_param_title@
50 title='$method.plot.title', 52 @CMD_param_size@)
51 #end if
52 size=$method.plot.size)
53 53
54 #else if $method.method == 'pl.heatmap' 54 #else if $method.method == 'pl.heatmap'
55 sc.pl.heatmap( 55 sc.pl.heatmap(
56 @CMD_param_plot_inputs@ 56 @CMD_param_plot_inputs@
57 @CMD_params_inputs@
57 @CMD_params_plots@ 58 @CMD_params_plots@
58 swap_axes=$method.swap_axes, 59 @CMD_pl_heatmap@)
59 show_gene_labels=$method.show_gene_labels,
60 cmap='$method.matplotlib_pyplot_imshow.cmap',
61 #if str($method.matplotlib_pyplot_imshow.interpolation) != 'None'
62 interpolation='$method.matplotlib_pyplot_imshow.interpolation',
63 #end if
64 #if $method.matplotlib_pyplot_imshow.alpha
65 alpha=$method.matplotlib_pyplot_imshow.alpha,
66 #end if
67 #if $method.matplotlib_pyplot_imshow.vmin
68 vmin=$method.matplotlib_pyplot_imshow.vmin,
69 #end if
70 #if $method.matplotlib_pyplot_imshow.vmax
71 vmax=$method.matplotlib_pyplot_imshow.vmax,
72 #end if
73 origin='$method.matplotlib_pyplot_imshow.origin')
74 60
75 #else if $method.method == 'pl.dotplot' 61 #else if $method.method == 'pl.dotplot'
76 sc.pl.dotplot( 62 sc.pl.dotplot(
77 @CMD_param_plot_inputs@ 63 @CMD_param_plot_inputs@
64 @CMD_params_inputs@
78 @CMD_params_plots@ 65 @CMD_params_plots@
79 color_map='$method.color_map', 66 @CMD_pl_dotplot@)
80 #if $method.dot_max
81 dot_max=$method.dot_max,
82 #end if
83 #if $method.dot_min
84 dot_min=$method.dot_min,
85 #end if
86 @CMD_params_matplotlib_pyplot_scatter@)
87 67
88 #else if $method.method == 'pl.violin' 68 #else if $method.method == 'pl.violin'
89 sc.pl.violin( 69 sc.pl.violin(
90 @CMD_param_plot_inputs@ 70 @CMD_param_plot_inputs@
91 #if $method.key_variables.type == "var_names" 71 #if $method.key_variables.type == "var_names"
116 @CMD_params_seaborn_violinplot@) 96 @CMD_params_seaborn_violinplot@)
117 97
118 #else if $method.method == 'pl.stacked_violin' 98 #else if $method.method == 'pl.stacked_violin'
119 sc.pl.stacked_violin( 99 sc.pl.stacked_violin(
120 @CMD_param_plot_inputs@ 100 @CMD_param_plot_inputs@
101 @CMD_params_inputs@
121 @CMD_params_plots@ 102 @CMD_params_plots@
122 swap_axes=$method.swap_axes, 103 @CMD_pl_stacked_violin@)
123 @CMD_conditional_stripplot@
124 scale='$method.violin_plot.scale',
125 row_palette='$method.row_palette',
126 #if str($method.standard_scale) != 'None'
127 standard_scale='$method.standard_scale',
128 #end if
129 @CMD_params_seaborn_violinplot@)
130 104
131 #else if $method.method == 'pl.matrixplot' 105 #else if $method.method == 'pl.matrixplot'
132 sc.pl.matrixplot( 106 sc.pl.matrixplot(
133 @CMD_param_plot_inputs@ 107 @CMD_param_plot_inputs@
108 @CMD_params_inputs@
134 @CMD_params_plots@ 109 @CMD_params_plots@
135 swap_axes=$method.swap_axes, 110 @CMD_pl_matrixplot@)
136 cmap='$method.matplotlib_pyplot_pcolor.cmap',
137 #if $method.matplotlib_pyplot_pcolor.vmin
138 vmin=$method.matplotlib_pyplot_pcolor.vmin,
139 #end if
140 #if $method.matplotlib_pyplot_pcolor.vmax
141 vmax=$method.matplotlib_pyplot_pcolor.vmax,
142 #end if
143 edgecolors='$method.matplotlib_pyplot_pcolor.edgecolors',
144 #if $method.matplotlib_pyplot_pcolor.alpha
145 alpha=$method.matplotlib_pyplot_pcolor.alpha,
146 #end if
147 snap=$method.matplotlib_pyplot_pcolor.snap)
148 111
149 #else if $method.method == 'pl.clustermap' 112 #else if $method.method == 'pl.clustermap'
150 sc.pl.clustermap( 113 sc.pl.clustermap(
151 #if str($method.use_raw) == 'True' 114 #if str($method.use_raw) == 'True'
152 adata=adata.X, 115 adata=adata.X,
188 sc.pl.highly_variable_genes( 151 sc.pl.highly_variable_genes(
189 adata_or_result=adata, 152 adata_or_result=adata,
190 log=$method.log, 153 log=$method.log,
191 save='.$format', 154 save='.$format',
192 show=False, 155 show=False,
193 highly_variable_genes=$method.highly_variable_genes 156 highly_variable_genes=$method.highly_variable_genes)
194 )
195 157
196 #else if $method.method == 'pl.pca' 158 #else if $method.method == 'pl.pca'
197 sc.pl.pca( 159 sc.pl.pca(
198 @CMD_param_plot_inputs@ 160 @CMD_param_plot_inputs@
199 @CMD_param_color@ 161 @CMD_param_color@
200 use_raw=$method.use_raw, 162 use_raw=$method.use_raw,
201 sort_order=$method.sort_order, 163 sort_order=$method.sort_order,
202 @CMD_params_pl_groups@ 164 @CMD_params_groups@
203 @CMD_params_pl_components@ 165 @CMD_params_pl_components@
204 @CMD_pl_attribute_section@ 166 @CMD_pl_attribute_section@
205 @CMD_params_matplotlib_pyplot_scatter@) 167 @CMD_params_matplotlib_pyplot_scatter@)
206 168
207 #else if $method.method == 'pl.pca_loadings' 169 #else if $method.method == 'pl.pca_loadings'
220 sc.pl.pca_overview( 182 sc.pl.pca_overview(
221 @CMD_param_plot_inputs@ 183 @CMD_param_plot_inputs@
222 @CMD_param_color@ 184 @CMD_param_color@
223 use_raw=$method.use_raw, 185 use_raw=$method.use_raw,
224 sort_order=$method.sort_order, 186 sort_order=$method.sort_order,
225 @CMD_params_pl_groups@ 187 @CMD_params_groups@
226 @CMD_params_pl_components@ 188 @CMD_params_pl_components@
227 @CMD_pl_attribute_section@ 189 @CMD_pl_attribute_section@
228 @CMD_params_matplotlib_pyplot_scatter@) 190 @CMD_params_matplotlib_pyplot_scatter@)
229 191
230 #else if $method.method == 'pl.tsne' 192 #else if $method.method == 'pl.tsne'
233 @CMD_param_color@ 195 @CMD_param_color@
234 use_raw=$method.use_raw, 196 use_raw=$method.use_raw,
235 @CMD_pl_edges@ 197 @CMD_pl_edges@
236 arrows=$method.arrows, 198 arrows=$method.arrows,
237 sort_order=$method.sort_order, 199 sort_order=$method.sort_order,
238 @CMD_params_pl_groups@ 200 @CMD_params_groups@
239 @CMD_params_pl_components@ 201 @CMD_params_pl_components@
240 @CMD_pl_attribute_section@ 202 @CMD_pl_attribute_section@
241 @CMD_params_matplotlib_pyplot_scatter@) 203 @CMD_params_matplotlib_pyplot_scatter@)
242 204
243 #else if $method.method == 'pl.umap' 205 #else if $method.method == 'pl.umap'
246 @CMD_param_color@ 208 @CMD_param_color@
247 use_raw=$method.use_raw, 209 use_raw=$method.use_raw,
248 @CMD_pl_edges@ 210 @CMD_pl_edges@
249 arrows=$method.arrows, 211 arrows=$method.arrows,
250 sort_order=$method.sort_order, 212 sort_order=$method.sort_order,
251 @CMD_params_pl_groups@ 213 @CMD_params_groups@
252 @CMD_params_pl_components@ 214 @CMD_params_pl_components@
253 @CMD_pl_attribute_section@ 215 @CMD_pl_attribute_section@
254 @CMD_params_matplotlib_pyplot_scatter@) 216 @CMD_params_matplotlib_pyplot_scatter@)
255 217
256 #else if $method.method == 'pl.diffmap' 218 #else if $method.method == 'pl.diffmap'
257 sc.pl.diffmap( 219 sc.pl.diffmap(
258 @CMD_param_plot_inputs@ 220 @CMD_param_plot_inputs@
259 @CMD_param_color@ 221 @CMD_param_color@
260 use_raw=$method.use_raw, 222 use_raw=$method.use_raw,
261 sort_order=$method.sort_order, 223 sort_order=$method.sort_order,
262 @CMD_params_pl_groups@ 224 @CMD_params_groups@
263 @CMD_params_pl_components@ 225 @CMD_params_pl_components@
264 @CMD_pl_attribute_section@ 226 @CMD_pl_attribute_section@
265 @CMD_params_matplotlib_pyplot_scatter@) 227 @CMD_params_matplotlib_pyplot_scatter@)
266 228
267 #else if $method.method == 'pl.draw_graph' 229 #else if $method.method == 'pl.draw_graph'
280 edges_width=$method.edges.edges_width, 242 edges_width=$method.edges.edges_width,
281 edges_color='$method.edges.edges_color', 243 edges_color='$method.edges.edges_color',
282 #end if 244 #end if
283 arrows=$method.arrows, 245 arrows=$method.arrows,
284 sort_order=$method.sort_order, 246 sort_order=$method.sort_order,
285 @CMD_params_pl_groups@ 247 @CMD_params_groups@
286 @CMD_params_pl_components@ 248 @CMD_params_pl_components@
287 @CMD_pl_attribute_section@ 249 @CMD_pl_attribute_section@
288 @CMD_params_matplotlib_pyplot_scatter@) 250 @CMD_params_matplotlib_pyplot_scatter@)
289 251
290 #else if $method.method == 'pl.dpt_groups_pseudotime' 252 #else if $method.method == 'pl.dpt_groups_pseudotime'
291 sc.pl.dpt_groups_pseudotime( 253 sc.pl.dpt_groups_pseudotime(
292 @CMD_param_plot_inputs@ 254 @CMD_param_plot_inputs@
293 color_map='$method.color_map') 255 #if str($method.color_map) != ''
256 color_map='$method.color_map'
257 #end if
258 )
294 259
295 #else if $method.method == 'pl.dpt_timeseries' 260 #else if $method.method == 'pl.dpt_timeseries'
296 sc.pl.dpt_timeseries( 261 sc.pl.dpt_timeseries(
297 @CMD_param_plot_inputs@ 262 @CMD_param_plot_inputs@
298 #if $method.heatmap.as_heatmap == "True" 263 #if $method.heatmap.as_heatmap == "True"
264 #if str($method.heatmap.color_map) != ''
299 color_map='$method.heatmap.color_map', 265 color_map='$method.heatmap.color_map',
266 #end if
300 #end if 267 #end if
301 as_heatmap=$method.heatmap.as_heatmap) 268 as_heatmap=$method.heatmap.as_heatmap)
302 269
303 #else if $method.method == 'pl.paga' 270 #else if $method.method == 'pl.paga'
304 sc.pl.paga( 271 sc.pl.paga(
320 use_raw=$method.use_raw, 287 use_raw=$method.use_raw,
321 #if str($method.annotations) != '' 288 #if str($method.annotations) != ''
322 #set $annotations=([x.strip() for x in str($method.annotations).split(',')]) 289 #set $annotations=([x.strip() for x in str($method.annotations).split(',')])
323 annotations=$annotations, 290 annotations=$annotations,
324 #end if 291 #end if
292 #if str($method.color_map) != ''
325 color_map='$method.color_map', 293 color_map='$method.color_map',
294 #end if
326 n_avg=$method.n_avg, 295 n_avg=$method.n_avg,
327 #if str($method.annotations) != '' 296 #if str($method.annotations) != ''
328 groups_key='$method.groups_key', 297 groups_key='$method.groups_key',
329 #end if 298 #end if
330 as_heatmap=$method.as_heatmap, 299 as_heatmap=$method.as_heatmap,
334 normalize_to_zero_one=$method.normalize_to_zero_one) 303 normalize_to_zero_one=$method.normalize_to_zero_one)
335 304
336 #else if $method.method == 'pl.rank_genes_groups' 305 #else if $method.method == 'pl.rank_genes_groups'
337 sc.pl.rank_genes_groups( 306 sc.pl.rank_genes_groups(
338 @CMD_param_plot_inputs@ 307 @CMD_param_plot_inputs@
339 @CMD_params_pl_groups@ 308 @CMD_params_groups@
340 n_genes=$method.n_genes, 309 n_genes=$method.n_genes,
341 #if str($method.gene_symbols) != '' 310 #if str($method.gene_symbols) != ''
342 gene_symbols='$method.gene_symbols', 311 gene_symbols='$method.gene_symbols',
343 #end if 312 #end if
344 fontsize=$method.fontsize, 313 fontsize=$method.fontsize,
346 sharey=$method.sharey) 315 sharey=$method.sharey)
347 316
348 #else if $method.method == 'pl.rank_genes_groups_violin' 317 #else if $method.method == 'pl.rank_genes_groups_violin'
349 sc.pl.rank_genes_groups_violin( 318 sc.pl.rank_genes_groups_violin(
350 @CMD_param_plot_inputs@ 319 @CMD_param_plot_inputs@
351 @CMD_params_pl_groups@ 320 @CMD_params_groups@
352 #if $method.genes.select == 'n_genes' 321 #if $method.genes.select == 'n_genes'
353 n_genes=$method.genes.n_genes, 322 n_genes=$method.genes.n_genes,
354 #else 323 #else
355 #set $gene_names = ([x.strip() for x in str($method.genes.gene_names).split(',')]) 324 #set $gene_names = ([x.strip() for x in str($method.genes.gene_names).split(',')])
356 gene_names=$gene_names, 325 gene_names=$gene_names,
357 #end if 326 #end if
327 #if str($method.gene_symbols) != ''
358 gene_symbols='$method.gene_symbols', 328 gene_symbols='$method.gene_symbols',
329 #end if
359 use_raw=$method.use_raw, 330 use_raw=$method.use_raw,
360 split=$method.split, 331 split=$method.split,
361 strip=$method.violin_plot.stripplot.stripplot, 332 strip=$method.violin_plot.stripplot.stripplot,
362 #if $method.violin_plot.stripplot.stripplot == "True" 333 #if $method.violin_plot.stripplot.stripplot == "True"
363 jitter=$method.violin_plot.stripplot.jitter.jitter, 334 jitter=$method.violin_plot.stripplot.jitter.jitter,
365 size=$method.violin_plot.stripplot.jitter.size, 336 size=$method.violin_plot.stripplot.jitter.size,
366 #end if 337 #end if
367 #end if 338 #end if
368 scale='$method.violin_plot.scale') 339 scale='$method.violin_plot.scale')
369 340
341 #else if $method.method == 'pl.rank_genes_groups_dotplot'
342 sc.pl.rank_genes_groups_dotplot(
343 @CMD_param_plot_inputs@
344 @CMD_pl_rank_genes_groups_ext@
345 @CMD_params_plots@
346 @CMD_pl_dotplot@)
347
348 #else if $method.method == 'pl.rank_genes_groups_heatmap'
349 sc.pl.rank_genes_groups_heatmap(
350 @CMD_param_plot_inputs@
351 @CMD_pl_rank_genes_groups_ext@
352 @CMD_params_plots@
353 @CMD_pl_heatmap@)
354
355 #else if $method.method == 'pl.rank_genes_groups_matrixplot'
356 sc.pl.rank_genes_groups_matrixplot(
357 @CMD_param_plot_inputs@
358 @CMD_pl_rank_genes_groups_ext@
359 @CMD_params_plots@
360 @CMD_pl_matrixplot@)
361
362 #else if $method.method == 'pl.rank_genes_groups_stacked_violin'
363 sc.pl.rank_genes_groups_stacked_violin(
364 @CMD_param_plot_inputs@
365 @CMD_pl_rank_genes_groups_ext@
366 @CMD_params_plots@
367 @CMD_pl_stacked_violin@)
368
370 #end if 369 #end if
371 ]]></configfile> 370 ]]></configfile>
372 </configfiles> 371 </configfiles>
373 <inputs> 372 <inputs>
374 <expand macro="inputs_anndata"/> 373 <expand macro="inputs_anndata"/>
375 <expand macro="param_plot_format"/> 374 <expand macro="param_plot_format"/>
376 <conditional name="method"> 375 <conditional name="method">
377 <param argument="method" type="select" label="Method used for plotting"> 376 <param argument="method" type="select" label="Method used for plotting">
378 <option value="pl.scatter">Generic: Scatter plot along observations or variables axes, using `pl.scatter`</option> 377 <option value="pl.scatter">Generic: Scatter plot along observations or variables axes, using 'pl.scatter'</option>
379 <option value="pl.heatmap">Generic: Heatmap of the expression values of set of genes, using `pl.heatmap`</option> 378 <option value="pl.heatmap">Generic: Heatmap of the expression values of set of genes, using 'pl.heatmap'</option>
380 <option value="pl.dotplot">Generic: Makes a dot plot of the expression values, using `pl.dotplot`</option> 379 <option value="pl.dotplot">Generic: Makes a dot plot of the expression values, using 'pl.dotplot'</option>
381 <option value="pl.violin">Generic: Violin plot, using `pl.violin`</option> 380 <option value="pl.violin">Generic: Violin plot, using 'pl.violin'</option>
382 <option value="pl.stacked_violin">Generic: Stacked violin plots, using `pl.stacked_violin`</option> 381 <option value="pl.stacked_violin">Generic: Stacked violin plots, using 'pl.stacked_violin'</option>
383 <option value="pl.matrixplot">Generic: Heatmap of the mean expression values per cluster, using `pl.matrixplot`</option> 382 <option value="pl.matrixplot">Generic: Heatmap of the mean expression values per cluster, using 'pl.matrixplot'</option>
384 <option value="pl.clustermap">Generic: Hierarchically-clustered heatmap, using `pl.clustermap`</option> 383 <option value="pl.clustermap">Generic: Hierarchically-clustered heatmap, using 'pl.clustermap'</option>
385 <!--<option value="pl.ranking">Generic: </option>!--> 384 <!--<option value="pl.ranking">Generic: </option>!-->
386 <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> 385 <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>
387 <!--<option value="pl.filter_genes_dispersion">Preprocessing: Plot dispersions versus means for genes, using `pl.filter_genes_dispersion`</option>--> 386 <!--<option value="pl.filter_genes_dispersion">Preprocessing: Plot dispersions versus means for genes, using 'pl.filter_genes_dispersion'</option>-->
388 <option value="pl.highly_variable_genes">Preprocessing: Plot dispersions versus means for genes, using `pl.highly_variable_genes`</option> 387 <option value="pl.highly_variable_genes">Preprocessing: Plot dispersions versus means for genes, using 'pl.highly_variable_genes'</option>
389 <!--<option value="pl.calculate_qc_metrics">Preprocessing: </option>!--> 388 <option value="pl.pca">PCA: Scatter plot in PCA coordinates, using 'pl.pca'</option>
390 <option value="pl.pca">PCA: Scatter plot in PCA coordinates, using `pl.pca`</option> 389 <option value="pl.pca_loadings">PCA: Rank genes according to contributions to PCs, using 'pl.pca_loadings'</option>
391 <option value="pl.pca_loadings">PCA: Rank genes according to contributions to PCs, using `pl.pca_loadings`</option> 390 <option value="pl.pca_variance_ratio">PCA: Scatter plot in PCA coordinates, using 'pl.pca_variance_ratio'</option>
392 <option value="pl.pca_variance_ratio">PCA: Scatter plot in PCA coordinates, using `pl.pca_variance_ratio`</option> 391 <option value="pl.pca_overview">PCA: Plot PCA results, using 'pl.pca_overview'</option>
393 <option value="pl.pca_overview">PCA: Plot PCA results, using `pl.pca_overview`</option> 392 <option value="pl.tsne">Embeddings: Scatter plot in tSNE basis, using 'pl.tsne'</option>
394 <option value="pl.tsne">Embeddings: Scatter plot in tSNE basis, using `pl.tsne`</option> 393 <option value="pl.umap">Embeddings: Scatter plot in UMAP basis, using 'pl.umap'</option>
395 <option value="pl.umap">Embeddings: Scatter plot in UMAP basis, using `pl.umap`</option> 394 <option value="pl.diffmap">Embeddings: Scatter plot in Diffusion Map basis, using 'pl.diffmap'</option>
396 <option value="pl.diffmap">Embeddings: Scatter plot in Diffusion Map basis, using `pl.diffmap`</option> 395 <option value="pl.draw_graph">Embeddings: Scatter plot in graph-drawing basis, using 'pl.draw_graph'</option>
397 <option value="pl.draw_graph">Embeddings: Scatter plot in graph-drawing basis, using `pl.draw_graph`</option> 396 <option value="pl.dpt_groups_pseudotime">Branching trajectories and pseudotime, clustering: Plot groups and pseudotime, using 'pl.dpt_groups_pseudotime'</option>
398 <option value="pl.dpt_groups_pseudotime">Branching trajectories and pseudotime, clustering: Plot groups and pseudotime, using `pl.dpt_groups_pseudotime`</option> 397 <option value="pl.dpt_timeseries">Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series, using 'pl.dpt_timeseries'</option>
399 <option value="pl.dpt_timeseries">Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series, using `pl.dpt_timeseries`</option> 398 <option value="pl.paga">Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges, using 'pl.paga'</option>
400 <option value="pl.paga">Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges, using `pl.paga`</option> 399 <option value="pl.paga_compare">Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side, using 'pl.paga_compare'</option>
401 <option value="pl.paga_compare">Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side, using `pl.paga_compare`</option> 400 <option value="pl.paga_path">Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths, using 'pl.paga_path'</option>
402 <option value="pl.paga_path">Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths, using `pl.paga_path`</option> 401 <option value="pl.rank_genes_groups">Marker genes: Plot ranking of genes using dotplot plot, using 'pl.rank_genes_groups'</option>
403 <option value="pl.rank_genes_groups">Marker genes: Plot ranking of genes using dotplot plot, using `pl.rank_genes_groups`</option> 402 <option value="pl.rank_genes_groups_violin">Marker genes: Plot ranking of genes as violin plot, using 'pl.rank_genes_groups_violin'</option>
404 <!--<option value="pl.rank_genes_groups_dotplot">Marker genes: </option>!--> 403 <option value="pl.rank_genes_groups_dotplot">Marker genes: Plot ranking of genes as dotplot plot, using 'pl.rank_genes_groups_dotplot'</option>
405 <!--<option value="pl.rank_genes_groups_heatmap">Marker genes: </option>!--> 404 <option value="pl.rank_genes_groups_heatmap">Marker genes: Plot ranking of genes as heatmap plot, using 'pl.rank_genes_groups_heatmap'</option>
406 <!--<option value="pl.rank_genes_groups_matrixplot">Marker genes: </option>!--> 405 <option value="pl.rank_genes_groups_matrixplot">Marker genes: Plot ranking of genes as matrixplot plot, using 'pl.rank_genes_groups_matrixplot'</option>
407 <!--<option value="pl.rank_genes_groups_stacked_violin">Marker genes: </option>!--> 406 <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>
408 <option value="pl.rank_genes_groups_violin">Marker genes: Plot ranking of genes for all tested comparisons, using `pl.rank_genes_groups_violin`</option>
409 <!--<option value="pl.phate">Misc: </option>!-->
410 <!--<option value="pl.matrix">Misc: </option>!-->
411 <!--<option value="pl.paga_adjacency">Misc: </option>!-->
412 <!--<option value="pl.timeseries">Misc: </option>!-->
413 <!--<option value="pl.timeseries_as_heatmap">Misc: </option>!-->
414 <!--<option value="pl.timeseries_subplot">Misc: </option>!-->
415 </param> 407 </param>
416 <when value="pl.scatter"> 408 <when value="pl.scatter">
417 <conditional name="type"> 409 <conditional name="type">
418 <param name="type" type="select" label="Plotting tool that computed coordinates" help=""> 410 <param name="type" type="select" label="Plotting tool that computed coordinates" help="">
419 <option value="xy">Using coordinates</option> 411 <option value="xy">Using coordinates</option>
420 <option value="basis">Using tool that computes coordinates</option> 412 <option value="basis">Using tool that computes coordinates</option>
421 </param> 413 </param>
422 <when value="xy"> 414 <when value="xy">
423 <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either `.obs` or `.var`"/> 415 <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either '.obs' or '.var'"/>
424 <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either `.obs` or `.var`"/> 416 <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either '.obs' or '.var'"/>
425 <conditional name="layers"> 417 <conditional name="layers">
426 <param argument="use_layers" type="select" label="Use the layers attribute?"> 418 <param argument="use_layers" type="select" label="Use the layers attribute?">
427 <option value="true">Yes</option> 419 <option value="true">Yes</option>
428 <option value="false" selected="true">No</option> 420 <option value="false" selected="true">No</option>
429 </param> 421 </param>
430 <when value="true"> 422 <when value="true">
431 <param argument="layer_x" type="text" value="" optional="true" label="Layers for x coordinate" help="Use the `layers` attribute of `adata` if present"/> 423 <param argument="layer_x" type="text" value="" optional="true" label="Layers for x coordinate" help="Use the 'layers' attribute of 'adata' if present"/>
432 <param argument="layer_y" type="text" value="" optional="true" label="Layers for y coordinate" help="Use the `layers` attribute of `adata` if present"/> 424 <param argument="layer_y" type="text" value="" optional="true" label="Layers for y coordinate" help="Use the 'layers' attribute of 'adata' if present"/>
433 <param argument="layer_color" type="text" value="" optional="true" label="Layers for color" help="Use the `layers` attribute of `adata` if present"/> 425 <param argument="layer_color" type="text" value="" optional="true" label="Layers for color" help="Use the 'layers' attribute of 'adata' if present"/>
434 </when> 426 </when>
435 <when value="false"/> 427 <when value="false"/>
436 </conditional> 428 </conditional>
437 </when> 429 </when>
438 <when value="basis"> 430 <when value="basis">
439 <param argument="basis" type="select" label="Plotting tool that computes coordinates" help=""> 431 <param argument="basis" type="select" label="Plotting tool that computes coordinates" help="">
440 <option value="pca">pca (need to run on `tl.pca` output)</option> 432 <option value="pca">pca (need to run on 'tl.pca' output)</option>
441 <option value="tsne">tsne (need to run on `tl.tsne` output)</option> 433 <option value="tsne">tsne (need to run on 'tl.tsne' output)</option>
442 <option value="umap">umap (need to run on `tl.umap` output)</option> 434 <option value="umap">umap (need to run on 'tl.umap' output)</option>
443 <option value="diffmap">diffmap (need to run on `tl.diffmap` output)</option> 435 <option value="diffmap">diffmap (need to run on 'tl.diffmap' output)</option>
444 <option value="draw_graph_fr">draw_graph_fr (need to run on `tl.draw_graph` output)</option> 436 <option value="draw_graph_fr">draw_graph_fr (need to run on 'tl.draw_graph' output)</option>
445 </param> 437 </param>
446 <expand macro="param_color"/> 438 <expand macro="param_color"/>
447 </when> 439 </when>
448 </conditional> 440 </conditional>
449 <expand macro="param_use_raw"/> 441 <expand macro="param_use_raw"/>
450 <param argument="sort_order" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot data points with higher values on top of others?" help="For continuous annotations used as color parameter"/> 442 <param argument="sort_order" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot data points with higher values on top of others?" help="For continuous annotations used as color parameter"/>
451 <expand macro="pl_groups"/> 443 <expand macro="param_groups"/>
452 <section name="plot" title="Plot attributes"> 444 <section name="plot" title="Plot attributes">
453 <expand macro="pl_components"/> 445 <expand macro="pl_components"/>
454 <expand macro="param_projection"/> 446 <expand macro="param_projection"/>
455 <expand macro="param_legend_loc"/> 447 <expand macro="param_legend_loc"/>
456 <expand macro="param_legend_fontsize"/> 448 <expand macro="param_legend_fontsize"/>
461 <expand macro="param_size"/> 453 <expand macro="param_size"/>
462 <expand macro="param_title"/> 454 <expand macro="param_title"/>
463 </section> 455 </section>
464 </when> 456 </when>
465 <when value="pl.heatmap"> 457 <when value="pl.heatmap">
458 <expand macro="params_inputs"/>
466 <expand macro="params_plots"/> 459 <expand macro="params_plots"/>
467 <expand macro="param_swap_axes"/> 460 <expand macro="pl_heatmap"/>
468 <param argument="show_gene_labels" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show gene labels?" help="By default gene labels are shown when there are 50 or less genes. Otherwise the labels are removed."/>
469 <section name="matplotlib_pyplot_imshow" title="Parameters for matplotlib.pyplot.imshow">
470 <expand macro="param_cmap"/>
471 <param name="interpolation" type="select" label="Interpolation method" help="">
472 <option value="None">none</option>
473 <option value="nearest">nearest</option>
474 <option value="bilinear">bilinear</option>
475 <option value="bicubic">bicubic</option>
476 <option value="spline16">spline16</option>
477 <option value="spline36">spline36</option>
478 <option value="hanning">hanning</option>
479 <option value="hamming">hamming</option>
480 <option value="hermite">hermite</option>
481 <option value="kaiser">kaiser</option>
482 <option value="quadric">quadric</option>
483 <option value="catrom">catrom</option>
484 <option value="gaussian">gaussian</option>
485 <option value="bessel">bessel</option>
486 <option value="sinc">sinc</option>
487 <option value="mitchell">mitchell</option>
488 <option value="lanczos">lanczos</option>
489 </param>
490 <expand macro="param_alpha"/>
491 <expand macro="param_vmin"/>
492 <expand macro="param_vmax"/>
493 <param name="origin" type="select" label="Place the [0,0] index of the array in the upper left or lower left corner of the axes" help=" The convention 'upper' is typically used for matrices and images.">
494 <option value="upper">Upper</option>
495 <option value="lower">Lower</option>
496 </param>
497 </section>
498 </when> 461 </when>
499 <when value="pl.dotplot"> 462 <when value="pl.dotplot">
463 <expand macro="params_inputs"/>
500 <expand macro="params_plots"/> 464 <expand macro="params_plots"/>
501 <param argument="color_map" type="select" label="Color palette"> 465 <expand macro="pl_dotplot"/>
502 <expand macro="matplotlib_pyplot_colormap"/>
503 </param>
504 <param argument="dot_max" type="float" value="" min="0" max="1" optional="true" label="Maximum dot size" help="If none, the maximum dot size is set to the maximum fraction value found (e.g. 0.6). If given, the value should be a number between 0 and 1. All fractions larger than dot_max are clipped to this value."/>
505 <param argument="dot_min" type="float" value="" min="0" max="1" optional="true" label="Minimum dot size" help="If none, the minimum dot size is set to 0. If given, the value should be a number between 0 and 1. All fractions smaller than dot_min are clipped to this value."/>
506 <expand macro="section_matplotlib_pyplot_scatter"/>
507 </when> 466 </when>
508 <when value="pl.violin"> 467 <when value="pl.violin">
509 <conditional name="key_variables"> 468 <conditional name="key_variables">
510 <param name="type" type="select" label="Keys for accessing variables"> 469 <param name="type" type="select" label="Keys for accessing variables">
511 <option value="var_names">All variables in `.var_names`</option> 470 <option value="var_names">All variables in '.var_names'</option>
512 <option value="obs">All fields in `.obs`</option> 471 <option value="obs">All fields in '.obs'</option>
513 <option value="custom">Subset of variables in `adata.var_names` or fields of `.obs`</option> 472 <option value="custom">Subset of variables in 'adata.var_names' or fields of '.obs'</option>
514 </param> 473 </param>
515 <when value="var_names"/> 474 <when value="var_names"/>
516 <when value="obs"/> 475 <when value="obs"/>
517 <when value="custom"> 476 <when value="custom">
518 <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from `.var_names` or fields of `.obs`"/> 477 <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'"/>
519 </when> 478 </when>
520 </conditional> 479 </conditional>
521 <expand macro="param_groupby"/> 480 <expand macro="param_groupby"/>
522 <expand macro="param_log"/> 481 <expand macro="param_log"/>
523 <expand macro="param_use_raw"/> 482 <expand macro="param_use_raw"/>
524 <section name="violin_plot" title="Violin plot attributes"> 483 <section name="violin_plot" title="Violin plot attributes">
525 <expand macro="conditional_stripplot"/> 484 <expand macro="conditional_stripplot"/>
526 <conditional name="multi_panel"> 485 <conditional name="multi_panel">
527 <param argument="multi_panel" type="select" label="Display keys in multiple panels" help="Also when `groupby is not provided"> 486 <param argument="multi_panel" type="select" label="Display keys in multiple panels" help="Also when 'groupby is not provided">
528 <option value="True">Yes</option> 487 <option value="True">Yes</option>
529 <option value="False" selected="true">No</option> 488 <option value="False" selected="true">No</option>
530 </param> 489 </param>
531 <when value="True"> 490 <when value="True">
532 <param argument="width" type="integer" min="0" value="" optional="true" label="Width of the figure" help=""/> 491 <param argument="width" type="integer" min="0" value="" optional="true" label="Width of the figure" help=""/>
534 </when> 493 </when>
535 <when value="False"/> 494 <when value="False"/>
536 </conditional> 495 </conditional>
537 <expand macro="param_scale"/> 496 <expand macro="param_scale"/>
538 </section> 497 </section>
539 <param argument="xlabel" type="text" value="" optional="true" label="Label of the x axis" help="Defaults to `groupby` if `rotation` is `None`, otherwise, no label is shown."/> 498 <param argument="xlabel" type="text" value="" optional="true" label="Label of the x axis" help="Defaults to 'groupby' if 'rotation' is 'None', otherwise, no label is shown."/>
540 <param argument="rotation" type="float" value="" optional="true" label="Rotation of xtick labels" help=""/> 499 <param argument="rotation" type="float" value="" optional="true" label="Rotation of xtick labels" help=""/>
541 <expand macro="seaborn_violinplot"/> 500 <expand macro="seaborn_violinplot"/>
542 </when> 501 </when>
543 <when value="pl.stacked_violin"> 502 <when value="pl.stacked_violin">
503 <expand macro="params_inputs"/>
544 <expand macro="params_plots"/> 504 <expand macro="params_plots"/>
545 <expand macro="param_swap_axes"/> 505 <expand macro="pl_stacked_violin"/>
546 <section name="violin_plot" title="Violin plot attributes">
547 <expand macro="conditional_stripplot"/>
548 <expand macro="param_scale"/>
549 </section>
550 <param argument="row_palette" type="select" label="Colors to use in each of the stacked violin plots">
551 <option value="muted">muted</option>
552 <expand macro="seaborn_color_palette_options"/>
553 </param>
554 <param argument="standard_scale" type="select" label="Standardize a dimension between 0 and 1" help="Each variable or observation is subtracted by the minimum and divided each by its maximum.">
555 <option value="None">No standardization</option>
556 <option value="var">Standardization on variable</option>
557 <option value="obs">Standardization on observation</option>
558 </param>
559 <expand macro="seaborn_violinplot"/>
560 </when> 506 </when>
561 <when value="pl.matrixplot"> 507 <when value="pl.matrixplot">
508 <expand macro="params_inputs"/>
562 <expand macro="params_plots"/> 509 <expand macro="params_plots"/>
563 <expand macro="param_swap_axes"/> 510 <expand macro="pl_matrixplot"/>
564 <section name="matplotlib_pyplot_pcolor" title="Parameters for matplotlib.pyplot.pcolor">
565 <param argument="cmap" type="select" label="Color palette">
566 <expand macro="seaborn_color_palette_options"/>
567 </param>
568 <param argument="vmin" type="float" value="" optional="true" label="Minimum value to anchor the colormap" help=""/>
569 <param argument="vmax" type="float" value="" optional="true" label="Maximum value to anchor the colormap" help=""/>
570 <expand macro="param_matplotlib_pyplot_edgecolors"/>
571 <expand macro="param_alpha"/>
572 <param argument="snap" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Snap the mesh to pixel boundaries?" help=""/>
573 </section>
574 </when> 511 </when>
575 <when value="pl.clustermap"> 512 <when value="pl.clustermap">
576 <param argument="obs_keys" type="text" value="" optional="true" label="Categorical annotation to plot with a different color map" help="Currently, only a single key is supported."/> 513 <param argument="obs_keys" type="text" value="" optional="true" label="Categorical annotation to plot with a different color map" help="Currently, only a single key is supported."/>
577 <expand macro="param_use_raw"/> 514 <expand macro="param_use_raw"/>
578 <section name="seaborn_clustermap" title="Parameters for seaborn.clustermap"> 515 <section name="seaborn_clustermap" title="Parameters for seaborn.clustermap">
606 <expand macro="param_log"/> 543 <expand macro="param_log"/>
607 <param argument="highly_variable_genes" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot highly variable genes or gene subset?"/> 544 <param argument="highly_variable_genes" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot highly variable genes or gene subset?"/>
608 </when> 545 </when>
609 <when value="pl.highest_expr_genes"> 546 <when value="pl.highest_expr_genes">
610 <param argument="n_top" type="integer" min="0" value="30" label="Number of top genes" help=""/> 547 <param argument="n_top" type="integer" min="0" value="30" label="Number of top genes" help=""/>
611 <param argument="gene_symbols" type="text" optional="true" label="Key for field in `.var` that stores gene symbols" help="Fill it if you do not want to use `.var_names`."/> 548 <param argument="gene_symbols" type="text" optional="true" label="Key for field in '.var' that stores gene symbols" help="Fill it if you do not want to use '.var_names'."/>
612 <section name="setseaborn_boxplot" title="Plot settings" expanded="false"> 549 <section name="setseaborn_boxplot" title="Plot settings" expanded="false">
613 <param argument="color" type="text" value="" optional="true" label="Color for all of the elements, or seed for a gradient palette" help=""/> 550 <param argument="color" type="text" value="" optional="true" label="Color for all of the elements, or seed for a gradient palette" help=""/>
614 <param argument="palette" type="select" optional="true" label="Colors to use for the different levels of the hue variable" help="See https://seaborn.pydata.org/tutorial/color_palettes.html for more details."> 551 <param argument="palette" type="select" optional="true" label="Colors to use for the different levels of the hue variable" help="See https://seaborn.pydata.org/tutorial/color_palettes.html for more details.">
615 <expand macro="seaborn_color_palette_options"/> 552 <expand macro="seaborn_color_palette_options"/>
616 </param> 553 </param>
619 </when> 556 </when>
620 <when value="pl.pca"> 557 <when value="pl.pca">
621 <expand macro="param_color"/> 558 <expand macro="param_color"/>
622 <expand macro="param_use_raw"/> 559 <expand macro="param_use_raw"/>
623 <expand macro="param_sort_order"/> 560 <expand macro="param_sort_order"/>
624 <expand macro="pl_groups"/> 561 <expand macro="param_groups"/>
625 <expand macro="pl_attribute_section"/> 562 <expand macro="pl_attribute_section"/>
626 <expand macro="section_matplotlib_pyplot_scatter"/> 563 <expand macro="section_matplotlib_pyplot_scatter"/>
627 </when> 564 </when>
628 <when value="pl.pca_loadings"> 565 <when value="pl.pca_loadings">
629 <param argument="components" type="text" value="1,2,3" label="Lsit of comma-separated components" help="1, 2, 3 means first, second and third principal components"/> 566 <param argument="components" type="text" value="1,2,3" label="List of comma-separated components" help="1, 2, 3 means first, second and third principal components"/>
630 </when> 567 </when>
631 <when value="pl.pca_variance_ratio"> 568 <when value="pl.pca_variance_ratio">
632 <param argument="n_pcs" type="integer" min="0" value="30" label="Number of PCs to show" help=""/> 569 <param argument="n_pcs" type="integer" min="0" value="30" label="Number of PCs to show" help=""/>
633 <expand macro="param_log"/> 570 <expand macro="param_log"/>
634 </when> 571 </when>
635 <when value="pl.pca_overview"> 572 <when value="pl.pca_overview">
636 <expand macro="param_color"/> 573 <expand macro="param_color"/>
637 <expand macro="param_use_raw"/> 574 <expand macro="param_use_raw"/>
638 <expand macro="param_sort_order"/> 575 <expand macro="param_sort_order"/>
639 <expand macro="pl_groups"/> 576 <expand macro="param_groups"/>
640 <expand macro="pl_attribute_section"/> 577 <expand macro="pl_attribute_section"/>
641 <expand macro="section_matplotlib_pyplot_scatter"/> 578 <expand macro="section_matplotlib_pyplot_scatter"/>
642 </when> 579 </when>
643 <when value="pl.tsne"> 580 <when value="pl.tsne">
644 <expand macro="param_color"/> 581 <expand macro="param_color"/>
645 <expand macro="param_use_raw"/> 582 <expand macro="param_use_raw"/>
646 <expand macro="pl_edges"/> 583 <expand macro="pl_edges"/>
647 <expand macro="param_arrows"/> 584 <expand macro="param_arrows"/>
648 <expand macro="param_sort_order"/> 585 <expand macro="param_sort_order"/>
649 <expand macro="pl_groups"/> 586 <expand macro="param_groups"/>
650 <expand macro="pl_attribute_section"/> 587 <expand macro="pl_attribute_section"/>
651 <expand macro="section_matplotlib_pyplot_scatter"/> 588 <expand macro="section_matplotlib_pyplot_scatter"/>
652 </when> 589 </when>
653 <when value="pl.umap"> 590 <when value="pl.umap">
654 <expand macro="param_color"/> 591 <expand macro="param_color"/>
655 <expand macro="param_use_raw"/> 592 <expand macro="param_use_raw"/>
656 <expand macro="pl_edges"/> 593 <expand macro="pl_edges"/>
657 <expand macro="param_arrows"/> 594 <expand macro="param_arrows"/>
658 <expand macro="param_sort_order"/> 595 <expand macro="param_sort_order"/>
659 <expand macro="pl_groups"/> 596 <expand macro="param_groups"/>
660 <expand macro="pl_attribute_section"/> 597 <expand macro="pl_attribute_section"/>
661 <expand macro="section_matplotlib_pyplot_scatter"/> 598 <expand macro="section_matplotlib_pyplot_scatter"/>
662 </when> 599 </when>
663 <when value="pl.diffmap"> 600 <when value="pl.diffmap">
664 <expand macro="param_color"/> 601 <expand macro="param_color"/>
665 <expand macro="param_use_raw"/> 602 <expand macro="param_use_raw"/>
666 <expand macro="param_sort_order"/> 603 <expand macro="param_sort_order"/>
667 <expand macro="pl_groups"/> 604 <expand macro="param_groups"/>
668 <expand macro="pl_attribute_section"/> 605 <expand macro="pl_attribute_section"/>
669 <expand macro="section_matplotlib_pyplot_scatter"/> 606 <expand macro="section_matplotlib_pyplot_scatter"/>
670 </when> 607 </when>
671 <when value="pl.draw_graph"> 608 <when value="pl.draw_graph">
672 <expand macro="param_color"/> 609 <expand macro="param_color"/>
676 <expand macro="options_layout"/> 613 <expand macro="options_layout"/>
677 </param> 614 </param>
678 <expand macro="pl_edges"/> 615 <expand macro="pl_edges"/>
679 <expand macro="param_arrows"/> 616 <expand macro="param_arrows"/>
680 <expand macro="param_sort_order"/> 617 <expand macro="param_sort_order"/>
681 <expand macro="pl_groups"/> 618 <expand macro="param_groups"/>
682 <expand macro="pl_attribute_section"/> 619 <expand macro="pl_attribute_section"/>
683 <expand macro="section_matplotlib_pyplot_scatter"/> 620 <expand macro="section_matplotlib_pyplot_scatter"/>
684 </when> 621 </when>
685 <when value="pl.dpt_groups_pseudotime"> 622 <when value="pl.dpt_groups_pseudotime">
686 <expand macro="param_color_map"/> 623 <expand macro="param_color_map"/>
704 <expand macro="inputs_paga"/> 641 <expand macro="inputs_paga"/>
705 </when> 642 </when>
706 <when value="pl.paga_path"> 643 <when value="pl.paga_path">
707 <param argument="nodes" type="text" value="" label="A path through nodes of the abstracted graph" 644 <param argument="nodes" type="text" value="" label="A path through nodes of the abstracted graph"
708 help="Each node is represented by its indice (within .categories) for the groups that have been used to run PAGA. Comma-separated"/> 645 help="Each node is represented by its indice (within .categories) for the groups that have been used to run PAGA. Comma-separated"/>
709 <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from `.var_names` or fields of `.obs`"/> 646 <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'"/>
710 <expand macro="param_use_raw"/> 647 <expand macro="param_use_raw"/>
711 <param argument="annotations" type="text" value="" optional="true" label="Key to plot" help="Keys for obs, comma-separated"/> 648 <param argument="annotations" type="text" value="" optional="true" label="Key to plot" help="Keys for obs, comma-separated"/>
712 <expand macro="param_color_map"/> 649 <expand macro="param_color_map"/>
713 <param argument="n_avg" type="integer" value="1" label="Number of data points to include in computation of running average"/> 650 <param argument="n_avg" type="integer" value="1" label="Number of data points to include in computation of running average"/>
714 <param argument="groups_key" type="text" value="" optional="true" label="Key of the grouping used to run PAGA" help="If not set, use uns/page/groups"/> 651 <param argument="groups_key" type="text" value="" optional="true" label="Key of the grouping used to run PAGA" help="If not set, use uns/page/groups"/>
717 <param argument="show_colorbar" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the colorbar?"/> 654 <param argument="show_colorbar" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the colorbar?"/>
718 <param argument="show_yticks" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the y ticks?"/> 655 <param argument="show_yticks" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the y ticks?"/>
719 <param argument="normalize_to_zero_one" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Shift and scale the running average to [0, 1] per gene?"/> 656 <param argument="normalize_to_zero_one" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Shift and scale the running average to [0, 1] per gene?"/>
720 </when> 657 </when>
721 <when value="pl.rank_genes_groups"> 658 <when value="pl.rank_genes_groups">
722 <expand macro="pl_groups"/> 659 <expand macro="param_groups"/>
723 <expand macro="n_genes"/> 660 <expand macro="param_n_genes"/>
724 <expand macro="gene_symbols"/> 661 <expand macro="gene_symbols"/>
725 <param argument="fontsize" type="integer" min="0" value="8" label="Font size for gene names"/> 662 <param argument="fontsize" type="integer" min="0" value="8" label="Font size for gene names"/>
726 <expand macro="param_ncols"/> 663 <expand macro="param_ncols"/>
727 <param argument="sharey" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Should the y-axis of each panels be shared?" help="If not, each panel has its own y-axis range"/> 664 <param argument="sharey" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Should the y-axis of each panels be shared?" help="If not, each panel has its own y-axis range"/>
728 </when> 665 </when>
729 <when value="pl.rank_genes_groups_violin"> 666 <when value="pl.rank_genes_groups_violin">
730 <expand macro="pl_groups"/> 667 <expand macro="param_groups"/>
731 <conditional name="genes"> 668 <conditional name="genes">
732 <param argument="select" type="select" label="Which genes to plot?" help=""> 669 <param argument="select" type="select" label="Which genes to plot?" help="">
733 <option value="n_genes">A number of genes</option> 670 <option value="n_genes">A number of genes</option>
734 <option value="gene_names">A custom list of genes</option> 671 <option value="gene_names">A custom list of genes</option>
735 </param> 672 </param>
736 <when value="n_genes"> 673 <when value="n_genes">
737 <expand macro="n_genes"/> 674 <expand macro="param_n_genes"/>
738 </when> 675 </when>
739 <when value="gene_names"> 676 <when value="gene_names">
740 <param argument="gene_names" type="text" value="" label="List of genes to plot" help="A list of comma-separated names"/> 677 <param argument="gene_names" type="text" value="" label="List of genes to plot" help="A list of comma-separated names"/>
741 </when> 678 </when>
742 </conditional> 679 </conditional>
746 <section name="violin_plot" title="Violin plot attributes"> 683 <section name="violin_plot" title="Violin plot attributes">
747 <expand macro="conditional_stripplot"/> 684 <expand macro="conditional_stripplot"/>
748 <expand macro="param_scale"/> 685 <expand macro="param_scale"/>
749 </section> 686 </section>
750 </when> 687 </when>
688 <when value="pl.rank_genes_groups_dotplot">
689 <expand macro="pl_rank_genes_groups_ext"/>
690 <expand macro="params_plots"/>
691 <expand macro="pl_dotplot"/>
692 </when>
693 <when value="pl.rank_genes_groups_heatmap">
694 <expand macro="pl_rank_genes_groups_ext"/>
695 <expand macro="params_plots"/>
696 <expand macro="pl_heatmap"/>
697 </when>
698 <when value="pl.rank_genes_groups_matrixplot">
699 <expand macro="pl_rank_genes_groups_ext"/>
700 <expand macro="params_plots"/>
701 <expand macro="pl_matrixplot"/>
702 </when>
703 <when value="pl.rank_genes_groups_stacked_violin">
704 <expand macro="pl_rank_genes_groups_ext"/>
705 <expand macro="params_plots"/>
706 <expand macro="pl_stacked_violin"/>
707 </when>
751 </conditional> 708 </conditional>
752 </inputs> 709 </inputs>
753 <outputs> 710 <outputs>
754 <data name="out_png" format="png" from_work_dir="*.png" label="${tool.name} (${method.method}) on ${on_string}"> 711 <data name="out_png" format="png" from_work_dir="*.png" label="${tool.name} (${method.method}) on ${on_string}">
755 <filter>format == 'png' and method['method'] != 'pl.rank_genes_groups_violin'</filter> 712 <filter>format == 'png' and method['method'] != 'pl.rank_genes_groups_violin'</filter>
756 </data> 713 </data>
757 <collection name="collection_png" type="list" label="${tool.name} (${method.method}) on ${on_string}"> 714 <collection name="collection_png" type="list" label="${tool.name} (${method.method}) on ${on_string}">
758 <discover_datasets pattern="rank_genes_groups_cell_type_(?P&lt;designation&gt;.*).png" format="png"/> 715 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).png" format="png"/>
759 <filter>format == 'png' and method['method'] == 'pl.rank_genes_groups_violin'</filter> 716 <filter>format == 'png' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
760 </collection> 717 </collection>
761 <data name="out_pdf" format="pdf" from_work_dir="*.pdf" label="${tool.name} (${method.method}) on ${on_string}"> 718 <data name="out_pdf" format="pdf" from_work_dir="*.pdf" label="${tool.name} (${method.method}) on ${on_string}">
762 <filter>format == 'pdf' and method['method'] != pl.rank_genes_groups_violin</filter> 719 <filter>format == 'pdf' and method['method'] != pl.rank_genes_groups_violin</filter>
763 </data> 720 </data>
764 <collection name="collection_pdf" type="list" label="${tool.name} (${method.method}) on ${on_string}"> 721 <collection name="collection_pdf" type="list" label="${tool.name} (${method.method}) on ${on_string}">
765 <discover_datasets pattern="rank_genes_groups_cell_type_(?P&lt;designation&gt;.*).pdf" format="pdf"/> 722 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).pdf" format="pdf"/>
766 <filter>format == 'pdf' and method['method'] == 'pl.rank_genes_groups_violin'</filter> 723 <filter>format == 'pdf' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
767 </collection> 724 </collection>
768 <data name="out_svg" format="svg" from_work_dir="*.svg" label="${tool.name} (${method.method}) on ${on_string}"> 725 <data name="out_svg" format="svg" from_work_dir="*.svg" label="${tool.name} (${method.method}) on ${on_string}">
769 <filter>format == 'svg' and method['method'] != pl.rank_genes_groups_violin</filter> 726 <filter>format == 'svg' and method['method'] != pl.rank_genes_groups_violin</filter>
770 </data> 727 </data>
771 <collection name="collection_svg" type="list" label="${tool.name} (${method.method}) on ${on_string}"> 728 <collection name="collection_svg" type="list" label="${tool.name} (${method.method}) on ${on_string}">
772 <discover_datasets pattern="rank_genes_groups_cell_type_(?P&lt;designation&gt;.*).svg" format="svg"/> 729 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).svg" format="svg"/>
773 <filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter> 730 <filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
774 </collection> 731 </collection>
775 </outputs> 732 </outputs>
776 <tests> 733 <tests>
777 <test> 734 <test>
850 <has_text_matching expression="sort_order=True"/> 807 <has_text_matching expression="sort_order=True"/>
851 <has_text_matching expression="projection='2d'"/> 808 <has_text_matching expression="projection='2d'"/>
852 <has_text_matching expression="legend_loc='right margin'"/> 809 <has_text_matching expression="legend_loc='right margin'"/>
853 <has_text_matching expression="legend_fontsize=1"/> 810 <has_text_matching expression="legend_fontsize=1"/>
854 <has_text_matching expression="legend_fontweight='normal'"/> 811 <has_text_matching expression="legend_fontweight='normal'"/>
855 <has_text_matching expression="color_map='viridis'"/>
856 <has_text_matching expression="palette='bwr'"/> 812 <has_text_matching expression="palette='bwr'"/>
857 <has_text_matching expression="frameon=False"/> 813 <has_text_matching expression="frameon=False"/>
858 <has_text_matching expression="size=1.0"/> 814 <has_text_matching expression="size=1.0"/>
859 <has_text_matching expression="title='A title'"/> 815 <has_text_matching expression="title='A title'"/>
860 </assert_stdout> 816 </assert_stdout>
868 <param name="method" value="pl.heatmap"/> 824 <param name="method" value="pl.heatmap"/>
869 <conditional name="var_names"> 825 <conditional name="var_names">
870 <param name="type" value="all"/> 826 <param name="type" value="all"/>
871 </conditional> 827 </conditional>
872 <param name="groupby" value="cell_type"/> 828 <param name="groupby" value="cell_type"/>
829 <param name="num_categories" value="7"/>
873 <param name="log" value="False"/> 830 <param name="log" value="False"/>
874 <param name="use_raw" value="False"/> 831 <param name="use_raw" value="False"/>
875 <param name="num_categories" value="7"/>
876 <conditional name="figsize"> 832 <conditional name="figsize">
877 <param name="test" value="yes"/> 833 <param name="test" value="yes"/>
878 <param name="width" value="10" /> 834 <param name="width" value="10" />
879 <param name="height" value="3"/> 835 <param name="height" value="3"/>
880 </conditional> 836 </conditional>
912 <conditional name="var_names"> 868 <conditional name="var_names">
913 <param name="type" value="custom"/> 869 <param name="type" value="custom"/>
914 <param name="var_names" value="CD79A, MS4A1, CD8A, CD8B, LYZ, GNLY, NKG7, RP3-467N11.1, FCGR3A, FCER1A, CST3, POU2AF1, LINC00402"/> 870 <param name="var_names" value="CD79A, MS4A1, CD8A, CD8B, LYZ, GNLY, NKG7, RP3-467N11.1, FCGR3A, FCER1A, CST3, POU2AF1, LINC00402"/>
915 </conditional> 871 </conditional>
916 <param name="groupby" value="louvain"/> 872 <param name="groupby" value="louvain"/>
873 <param name="num_categories" value="7"/>
917 <param name="log" value="False"/> 874 <param name="log" value="False"/>
918 <param name="use_raw" value="False"/> 875 <param name="use_raw" value="False"/>
919 <param name="num_categories" value="7"/>
920 <param name="dendrogram" value="True"/> 876 <param name="dendrogram" value="True"/>
921 <repeat name="var_group_positions"> 877 <repeat name="var_group_positions">
922 <param name="start" value="0"/> 878 <param name="start" value="0"/>
923 <param name="end" value="1"/> 879 <param name="end" value="1"/>
924 <param name="label" value="B cells"/> 880 <param name="label" value="B cells"/>
1018 <param name="method" value="pl.stacked_violin"/> 974 <param name="method" value="pl.stacked_violin"/>
1019 <conditional name="var_names"> 975 <conditional name="var_names">
1020 <param name="type" value="all"/> 976 <param name="type" value="all"/>
1021 </conditional> 977 </conditional>
1022 <param name="groupby" value="cell_type"/> 978 <param name="groupby" value="cell_type"/>
979 <param name="num_categories" value="7"/>
1023 <param name="log" value="False"/> 980 <param name="log" value="False"/>
1024 <param name="use_raw" value="False"/> 981 <param name="use_raw" value="False"/>
1025 <param name="num_categories" value="7"/>
1026 <param name="dendrogram" value="True"/> 982 <param name="dendrogram" value="True"/>
1027 <conditional name="figsize"> 983 <conditional name="figsize">
1028 <param name="test" value="no"/> 984 <param name="test" value="no"/>
1029 </conditional> 985 </conditional>
1030 <param name="swap_axes" value="True"/> 986 <param name="swap_axes" value="True"/>
1609 <has_text_matching expression="jitter=True"/> 1565 <has_text_matching expression="jitter=True"/>
1610 <has_text_matching expression="size=1"/> 1566 <has_text_matching expression="size=1"/>
1611 <has_text_matching expression="scale='width'"/> 1567 <has_text_matching expression="scale='width'"/>
1612 </assert_stdout> 1568 </assert_stdout>
1613 <output_collection name="collection_png"> 1569 <output_collection name="collection_png">
1614 <element name="Ery" file="pl.rank_genes_groups_violin.Ery.png" ftype="png" compare="sim_size"/> 1570 <element name="cell_type_Ery" file="pl.rank_genes_groups_violin.Ery.png" ftype="png" compare="sim_size"/>
1615 <element name="Mk" file="pl.rank_genes_groups_violin.Mk.png" ftype="png" compare="sim_size"/> 1571 <element name="cell_type_Mk" file="pl.rank_genes_groups_violin.Mk.png" ftype="png" compare="sim_size"/>
1616 <element name="Mo" file="pl.rank_genes_groups_violin.Mo.png" ftype="png" compare="sim_size"/> 1572 <element name="cell_type_Mo" file="pl.rank_genes_groups_violin.Mo.png" ftype="png" compare="sim_size"/>
1617 <element name="Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="sim_size"/> 1573 <element name="cell_type_Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="sim_size"/>
1618 <element name="progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="sim_size"/> 1574 <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="sim_size"/>
1619 </output_collection> 1575 </output_collection>
1576 </test>
1577 <test>
1578 <!-- test 22: pl.rank_genes_groups_dotplot !-->
1579 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
1580 <param name="format" value="png"/>
1581 <conditional name="method">
1582 <param name="method" value="pl.rank_genes_groups_dotplot"/>
1583 <param name="n_genes" value="10"/>
1584 <param name="log" value="False"/>
1585 <param name="use_raw" value="False"/>
1586 <param name="dendrogram" value="False"/>
1587 <param name="color_map" value="viridis"/>
1588 <section name="matplotlib_pyplot_scatter">
1589 <param name="linewidths" value="0" />
1590 <param name="edgecolors" value="face"/>
1591 </section>
1592 </conditional>
1593 <assert_stdout>
1594 <has_text_matching expression="sc.pl.rank_genes_groups_dotplot"/>
1595 <has_text_matching expression="n_genes=10"/>
1596 <has_text_matching expression="log=False"/>
1597 <has_text_matching expression="use_raw=False"/>
1598 <has_text_matching expression="dendrogram=False"/>
1599 <has_text_matching expression="color_map='viridis'"/>
1600 <has_text_matching expression="linewidths=0.0"/>
1601 <has_text_matching expression="edgecolors='face'"/>
1602 </assert_stdout>
1603 <output name="out_png" file="pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
1604 </test>
1605 <test>
1606 <!-- test 23: pl.rank_genes_groups_heatmap !-->
1607 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
1608 <param name="format" value="png"/>
1609 <conditional name="method">
1610 <param name="method" value="pl.rank_genes_groups_heatmap"/>
1611 <param name="n_genes" value="10"/>
1612 <param name="log" value="False"/>
1613 <param name="use_raw" value="False"/>
1614 <param name="dendrogram" value="False"/>
1615 <param name="swap_axes" value="False"/>
1616 <param name="show_gene_labels" value="False"/>
1617 <section name="matplotlib_pyplot_imshow">
1618 <param name="cmap" value="viridis"/>
1619 <param name="interpolation" value="None"/>
1620 <param name="origin" value="upper"/>
1621 </section>
1622 </conditional>
1623 <assert_stdout>
1624 <has_text_matching expression="sc.pl.rank_genes_groups_heatmap"/>
1625 <has_text_matching expression="n_genes=10"/>
1626 <has_text_matching expression="log=False"/>
1627 <has_text_matching expression="use_raw=False"/>
1628 <has_text_matching expression="dendrogram=False"/>
1629 <has_text_matching expression="swap_axes=False"/>
1630 <has_text_matching expression="show_gene_labels=False"/>
1631 <has_text_matching expression="cmap='viridis'"/>
1632 <has_text_matching expression="origin='upper'"/>
1633 </assert_stdout>
1634 <output name="out_png" file="pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
1635 </test>
1636 <test>
1637 <!-- test 24: pl.rank_genes_groups_matrixplot !-->
1638 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
1639 <param name="format" value="png"/>
1640 <conditional name="method">
1641 <param name="method" value="pl.rank_genes_groups_matrixplot"/>
1642 <param name="n_genes" value="10"/>
1643 <param name="log" value="False"/>
1644 <param name="use_raw" value="False"/>
1645 <param name="dendrogram" value="False"/>
1646 <param name="swap_axes" value="False"/>
1647 <section name="matplotlib_pyplot_pcolor">
1648 <param name="cmap" value="viridis"/>
1649 <param name="edgecolors" value="face"/>
1650 <param name="snap" value="False"/>
1651 </section>
1652 </conditional>
1653 <assert_stdout>
1654 <has_text_matching expression="sc.pl.rank_genes_groups_matrixplot"/>
1655 <has_text_matching expression="n_genes=10"/>
1656 <has_text_matching expression="log=False"/>
1657 <has_text_matching expression="use_raw=False"/>
1658 <has_text_matching expression="dendrogram=False"/>
1659 <has_text_matching expression="swap_axes=False"/>
1660 <has_text_matching expression="cmap='viridis'"/>
1661 <has_text_matching expression="edgecolors='face'"/>
1662 <has_text_matching expression="snap=False"/>
1663 </assert_stdout>
1664 <output name="out_png" file="pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
1665 </test>
1666 <test>
1667 <!-- test 25: pl.rank_genes_groups_stacked_violin !-->
1668 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
1669 <param name="format" value="png"/>
1670 <conditional name="method">
1671 <param name="method" value="pl.rank_genes_groups_stacked_violin"/>
1672 <param name="n_genes" value="10"/>
1673 <param name="log" value="False"/>
1674 <param name="use_raw" value="False"/>
1675 <param name="dendrogram" value="True"/>
1676 <param name="swap_axes" value="True"/>
1677 <section name="violin_plot">
1678 <conditional name="stripplot">
1679 <param name="stripplot" value="True"/>
1680 <param name="jitter" value="True"/>
1681 <param name="size" value="1"/>
1682 </conditional>
1683 <param name="scale" value="width"/>
1684 </section>
1685 <param name="row_palette" value="muted"/>
1686 <param name="standard_scale" value="None"/>
1687 <section name="seaborn_violinplot">
1688 <param name="bw" value="scott"/>
1689 <param name="linewidth" value="0"/>
1690 <param name="color" value="AliceBlue"/>
1691 <param name="palette" value="viridis"/>
1692 <param name="saturation" value="0.75"/>
1693 </section>
1694 </conditional>
1695 <assert_stdout>
1696 <has_text_matching expression="sc.pl.rank_genes_groups_stacked_violin"/>
1697 <has_text_matching expression="n_genes=10"/>
1698 <has_text_matching expression="log=False"/>
1699 <has_text_matching expression="use_raw=False"/>
1700 <has_text_matching expression="dendrogram=True"/>
1701 <has_text_matching expression="swap_axes=True"/>
1702 <has_text_matching expression="stripplot=True"/>
1703 <has_text_matching expression="jitter=True"/>
1704 <has_text_matching expression="size=1"/>
1705 <has_text_matching expression="scale='width'"/>
1706 <has_text_matching expression="bw='scott'"/>
1707 <has_text_matching expression="scale='width'"/>
1708 <has_text_matching expression="linewidth=0.0"/>
1709 <has_text_matching expression="color='AliceBlue'"/>
1710 <has_text_matching expression="palette='viridis'"/>
1711 <has_text_matching expression="saturation=0.75"/>
1712 </assert_stdout>
1713 <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
1620 </test> 1714 </test>
1621 </tests> 1715 </tests>
1622 <help><![CDATA[ 1716 <help><![CDATA[
1623 Generic: Scatter plot along observations or variables axes (`pl.scatter`) 1717 Generic: Scatter plot along observations or variables axes (`pl.scatter`)
1624 ========================================================================= 1718 =========================================================================
1811 =============================================================================== 1905 ===============================================================================
1812 1906
1813 More details on the `scanpy documentation 1907 More details on the `scanpy documentation
1814 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups.html>`__ 1908 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups.html>`__
1815 1909
1816 Marker genes: Plot ranking of genes for all tested comparisons (`pl.rank_genes_groups_violin`) 1910 Marker genes: Plot ranking of genes as violin plot (`pl.rank_genes_groups_violin`)
1817 ============================================================================================== 1911 ==================================================================================
1818 1912
1819 More details on the `scanpy documentation 1913 More details on the `scanpy documentation
1820 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_violin.html>`__ 1914 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_violin.html>`__
1915
1916 Marker genes: Plot ranking of genes as dotplot plot (`pl.rank_genes_groups_dotplot`)
1917 ====================================================================================
1918
1919 More details on the `scanpy documentation
1920 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_dotplot.html>`__
1921
1922 Marker genes: Plot ranking of genes as heatmap plot (`pl.rank_genes_groups_heatmap`)
1923 ====================================================================================
1924
1925 More details on the `scanpy documentation
1926 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_heatmap.html>`__
1927
1928 Marker genes: Plot ranking of genes as matrixplot plot (`pl.rank_genes_groups_matrixplot`)
1929 ==========================================================================================
1930
1931 More details on the `scanpy documentation
1932 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_matrixplot.html>`__
1933
1934 Marker genes: Plot ranking of genes as stacked violin plot (`pl.rank_genes_groups_stacked_violin`)
1935 ==================================================================================================
1936
1937 More details on the `scanpy documentation
1938 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_stacked_violin.html>`__
1821 ]]></help> 1939 ]]></help>
1822 <expand macro="citations"/> 1940 <expand macro="citations"/>
1823 </tool> 1941 </tool>