Mercurial > repos > iuc > scanpy_plot

comparison plot.xml @ 1:e4c0f5ee8e17 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
author iuc
date Wed, 16 Oct 2019 06:28:57 -0400
parents 397d2c97af05
children 4bfb75bb7c8e
comparison
equal deleted inserted replaced
0:397d2c97af05 1:e4c0f5ee8e17
1 <tool id="scanpy_plot" name="Plot with scanpy" version="@galaxy_version@"> 1 <tool id="scanpy_plot" name="Plot" version="@galaxy_version@">
2 <description></description> 2 <description> with scanpy</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <stdio> 7 <stdio>
23 sc.pl.scatter( 23 sc.pl.scatter(
24 @CMD_param_plot_inputs@ 24 @CMD_param_plot_inputs@
25 #if $method.type.type == 'xy' 25 #if $method.type.type == 'xy'
26 x='$method.type.x', 26 x='$method.type.x',
27 y='$method.type.y', 27 y='$method.type.y',
28 layers=('$method.type.layer_x', '$method.type.layer_y', '$method.type.layer_color'), 28 #if str('$method.type.layers.use_layers') == 'true'
29 layers=('$method.type.layers.layer_x', '$method.type.layers.layer_y', '$method.type.layers.layer_color'),
30 #end if
29 #else 31 #else
30 basis='$method.type.basis', 32 basis='$method.type.basis',
31 #if str($method.type.color) != '' 33 #if str($method.type.color) != ''
32 #set $color = ([x.strip() for x in str($method.type.color).split(',')]) 34 #set $color = ([x.strip() for x in str($method.type.color).split(',')])
33 color=$color, 35 color=$color,
34 #else
35 color=None,
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_pl_groups@
49 #if $method.plot.title 49 #if $method.plot.title
50 title='$method.plot.title', 50 title='$method.plot.title',
51 #end if 51 #end if
52 size=$method.plot.size) 52 size=$method.plot.size)
53 53
54 #elif $method.method == 'pl.heatmap' 54 #else if $method.method == 'pl.heatmap'
55 sc.pl.heatmap( 55 sc.pl.heatmap(
56 @CMD_param_plot_inputs@ 56 @CMD_param_plot_inputs@
57 @CMD_params_plots@ 57 @CMD_params_plots@
58 swap_axes=$method.swap_axes, 58 swap_axes=$method.swap_axes,
59 show_gene_labels=$method.show_gene_labels, 59 show_gene_labels=$method.show_gene_labels,
60 cmap='$method.matplotlib_pyplot_imshow.cmap', 60 cmap='$method.matplotlib_pyplot_imshow.cmap',
61 #if str($method.matplotlib_pyplot_imshow.interpolation) != 'None'
61 interpolation='$method.matplotlib_pyplot_imshow.interpolation', 62 interpolation='$method.matplotlib_pyplot_imshow.interpolation',
63 #end if
62 #if $method.matplotlib_pyplot_imshow.alpha 64 #if $method.matplotlib_pyplot_imshow.alpha
63 alpha=$method.matplotlib_pyplot_imshow.alpha, 65 alpha=$method.matplotlib_pyplot_imshow.alpha,
64 #end if 66 #end if
65 #if $method.matplotlib_pyplot_imshow.vmin 67 #if $method.matplotlib_pyplot_imshow.vmin
66 vmin=$method.matplotlib_pyplot_imshow.vmin, 68 vmin=$method.matplotlib_pyplot_imshow.vmin,
68 #if $method.matplotlib_pyplot_imshow.vmax 70 #if $method.matplotlib_pyplot_imshow.vmax
69 vmax=$method.matplotlib_pyplot_imshow.vmax, 71 vmax=$method.matplotlib_pyplot_imshow.vmax,
70 #end if 72 #end if
71 origin='$method.matplotlib_pyplot_imshow.origin') 73 origin='$method.matplotlib_pyplot_imshow.origin')
72 74
73 #elif $method.method == 'pl.dotplot' 75 #else if $method.method == 'pl.dotplot'
74 sc.pl.dotplot( 76 sc.pl.dotplot(
75 @CMD_param_plot_inputs@ 77 @CMD_param_plot_inputs@
76 @CMD_params_plots@ 78 @CMD_params_plots@
77 color_map='$method.color_map', 79 color_map='$method.color_map',
78 #if $method.dot_max 80 #if $method.dot_max
81 #if $method.dot_min 83 #if $method.dot_min
82 dot_min=$method.dot_min, 84 dot_min=$method.dot_min,
83 #end if 85 #end if
84 @CMD_params_matplotlib_pyplot_scatter@) 86 @CMD_params_matplotlib_pyplot_scatter@)
85 87
86 #elif $method.method == 'pl.violin' 88 #else if $method.method == 'pl.violin'
87 sc.pl.violin( 89 sc.pl.violin(
88 @CMD_param_plot_inputs@ 90 @CMD_param_plot_inputs@
89 #if $method.key_variables.type == "var_names" 91 #if $method.key_variables.type == "var_names"
90 #set $key_list = adata.var_names 92 #set $key_list = adata.var_names
91 #elif $method.key_variables.type == "obs" 93 #else if $method.key_variables.type == "obs"
92 #set $key_list = adata.obs.select_dtypes(exclude=['category']).columns 94 #set $key_list = adata.obs.select_dtypes(exclude=['category']).columns
93 #elif $method.key_variables.type == "custom" 95 #else if $method.key_variables.type == "custom"
94 #set $key_list=([x.strip() for x in str($method.key_variables.keys).split(',')]) 96 #set $key_list=([x.strip() for x in str($method.key_variables.keys).split(',')])
95 #end if 97 #end if
96 keys=$key_list, 98 keys=$key_list,
97 #if $method.groupby 99 #if $method.groupby
98 groupby='$method.groupby', 100 groupby='$method.groupby',
99 #end if 101 #end if
100 log=$method.log, 102 log=$method.log,
101 use_raw=$method.use_raw, 103 use_raw=$method.use_raw,
102 sstripplot=$method.violin_plot.stripplot.stripplot, 104 @CMD_conditional_stripplot@
103 #if $method.violin_plot.stripplot.stripplot == "True"
104 jitter=$method.violin_plot.stripplot.jitter.jitter,
105 #if $method.violin_plot.stripplot.jitter.jitter == "True"
106 size=$method.violin_plot.stripplot.jitter.size,
107 #end if
108 #end if
109 multi_panel=$method.violin_plot.multi_panel.multi_panel, 105 multi_panel=$method.violin_plot.multi_panel.multi_panel,
106 #if $method.violin_plot.multi_panel.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != '' and str($method.violin_plot.multi_panel.height) != ''
107 figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height),
108 #end if
110 scale='$method.violin_plot.scale', 109 scale='$method.violin_plot.scale',
111 #if $method.xlabel 110 #if $method.xlabel
112 xlabel='$method.xlabel', 111 xlabel='$method.xlabel',
113 #end if 112 #end if
114 #if $method.rotation 113 #if $method.rotation
115 rotation=$method.rotation, 114 rotation=$method.rotation,
116 #end if 115 #end if
117 @CMD_params_seaborn_violinplot@) 116 @CMD_params_seaborn_violinplot@)
118 117
119 #elif $method.method == 'pl.matrixplot' 118 #else if $method.method == 'pl.stacked_violin'
119 sc.pl.stacked_violin(
120 @CMD_param_plot_inputs@
121 @CMD_params_plots@
122 swap_axes=$method.swap_axes,
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
131 #else if $method.method == 'pl.matrixplot'
120 sc.pl.matrixplot( 132 sc.pl.matrixplot(
121 @CMD_param_plot_inputs@ 133 @CMD_param_plot_inputs@
122 @CMD_params_plots@ 134 @CMD_params_plots@
123 swap_axes=$method.swap_axes, 135 swap_axes=$method.swap_axes,
124 cmap='$method.matplotlib_pyplot_pcolor.cmap', 136 cmap='$method.matplotlib_pyplot_pcolor.cmap',
132 #if $method.matplotlib_pyplot_pcolor.alpha 144 #if $method.matplotlib_pyplot_pcolor.alpha
133 alpha=$method.matplotlib_pyplot_pcolor.alpha, 145 alpha=$method.matplotlib_pyplot_pcolor.alpha,
134 #end if 146 #end if
135 snap=$method.matplotlib_pyplot_pcolor.snap) 147 snap=$method.matplotlib_pyplot_pcolor.snap)
136 148
137 #elif $method.method == 'pl.clustermap' 149 #else if $method.method == 'pl.clustermap'
138 sc.pl.clustermap( 150 sc.pl.clustermap(
139 #if str($method.use_raw) == 'True' 151 #if str($method.use_raw) == 'True'
140 adata=adata.X, 152 adata=adata.X,
141 #else 153 #else
142 adata=adata, 154 adata=adata,
143 #end if 155 #end if
144 show=False, 156 show=False,
157 #if str($method.obs_keys) != ''
145 obs_keys='$method.obs_keys', 158 obs_keys='$method.obs_keys',
159 #end if
146 use_raw=$method.use_raw, 160 use_raw=$method.use_raw,
147 method='$method.seaborn_clustermap.method', 161 method='$method.seaborn_clustermap.method',
148 metric='$method.seaborn_clustermap.metric', 162 metric='$method.seaborn_clustermap.metric',
149 #if str($method.seaborn_clustermap.z_score) == 'None' 163 #if str($method.seaborn_clustermap.z_score) != 'None'
150 z_score=None,
151 #else
152 z_score=$method.seaborn_clustermap.z_score, 164 z_score=$method.seaborn_clustermap.z_score,
153 #end if 165 #end if
154 #if str($method.seaborn_clustermap.standard_scale) == 'None' 166 #if str($method.seaborn_clustermap.standard_scale) != 'None'
155 standard_scale=None,
156 #else
157 standard_scale=$method.seaborn_clustermap.standard_scale, 167 standard_scale=$method.seaborn_clustermap.standard_scale,
158 #end if 168 #end if
159 col_cluster=$method.seaborn_clustermap.col_cluster, 169 col_cluster=$method.seaborn_clustermap.col_cluster,
160 row_cluster=$method.seaborn_clustermap.row_cluster).savefig(fname="output.$format") 170 row_cluster=$method.seaborn_clustermap.row_cluster).savefig(fname="output.$format")
161 171
162 #elif $method.method == 'pl.highest_expr_genes' 172 #else if $method.method == 'pl.highest_expr_genes'
163 sc.pl.highest_expr_genes( 173 sc.pl.highest_expr_genes(
164 @CMD_param_plot_inputs@ 174 @CMD_param_plot_inputs@
165 n_top=$method.n_top, 175 n_top=$method.n_top,
166 #if str($method.gene_symbols) != '' 176 #if str($method.gene_symbols) != ''
167 gene_symbols='$method.gene_symbols', 177 gene_symbols='$method.gene_symbols',
172 #if str($method.setseaborn_boxplot.palette) != 'None' 182 #if str($method.setseaborn_boxplot.palette) != 'None'
173 palette='$method.setseaborn_boxplot.palette', 183 palette='$method.setseaborn_boxplot.palette',
174 #end if 184 #end if
175 saturation=$method.setseaborn_boxplot.saturation) 185 saturation=$method.setseaborn_boxplot.saturation)
176 186
177 #elif $method.method == 'pl.pca' 187 #else if $method.method == 'pl.highly_variable_genes'
188 sc.pl.highly_variable_genes(
189 adata_or_result=adata,
190 log=$method.log,
191 save='.$format',
192 show=False,
193 highly_variable_genes=$method.highly_variable_genes
194 )
195
196 #else if $method.method == 'pl.pca'
178 sc.pl.pca( 197 sc.pl.pca(
179 @CMD_param_plot_inputs@ 198 @CMD_param_plot_inputs@
180 @CMD_param_color@ 199 @CMD_param_color@
181 use_raw=$method.use_raw, 200 use_raw=$method.use_raw,
182 sort_order=$method.sort_order, 201 sort_order=$method.sort_order,
183 @CMD_params_pl_groups@ 202 @CMD_params_pl_groups@
184 @CMD_params_pl_components@ 203 @CMD_params_pl_components@
185 @CMD_pl_attribute_section@ 204 @CMD_pl_attribute_section@
186 @CMD_params_matplotlib_pyplot_scatter@) 205 @CMD_params_matplotlib_pyplot_scatter@)
187 206
188 #elif $method.method == 'pl.pca_loadings' 207 #else if $method.method == 'pl.pca_loadings'
189 sc.pl.pca_loadings( 208 sc.pl.pca_loadings(
190 @CMD_param_plot_inputs@ 209 @CMD_param_plot_inputs@
191 #set $components = ([int(x.strip()) for x in str($method.components).split(',')]) 210 #set $components = ([int(x.strip()) for x in str($method.components).split(',')])
192 components=$components) 211 components=$components)
193 212
194 #elif $method.method == 'pl.pca_variance_ratio' 213 #else if $method.method == 'pl.pca_variance_ratio'
195 sc.pl.pca_variance_ratio( 214 sc.pl.pca_variance_ratio(
196 @CMD_param_plot_inputs@ 215 @CMD_param_plot_inputs@
197 n_pcs=$method.n_pcs, 216 n_pcs=$method.n_pcs,
198 log=$method.log) 217 log=$method.log)
199 218
200 #elif $method.method == 'pl.pca_overview' 219 #else if $method.method == 'pl.pca_overview'
201 sc.pl.pca_overview( 220 sc.pl.pca_overview(
202 @CMD_param_plot_inputs@ 221 @CMD_param_plot_inputs@
203 @CMD_param_color@ 222 @CMD_param_color@
204 use_raw=$method.use_raw, 223 use_raw=$method.use_raw,
205 sort_order=$method.sort_order, 224 sort_order=$method.sort_order,
206 @CMD_params_pl_groups@ 225 @CMD_params_pl_groups@
207 @CMD_params_pl_components@ 226 @CMD_params_pl_components@
208 @CMD_pl_attribute_section@ 227 @CMD_pl_attribute_section@
209 @CMD_params_matplotlib_pyplot_scatter@) 228 @CMD_params_matplotlib_pyplot_scatter@)
210 229
211 #elif $method.method == 'pl.tsne' 230 #else if $method.method == 'pl.tsne'
212 sc.pl.tsne( 231 sc.pl.tsne(
213 @CMD_param_plot_inputs@ 232 @CMD_param_plot_inputs@
214 @CMD_param_color@ 233 @CMD_param_color@
215 use_raw=$method.use_raw, 234 use_raw=$method.use_raw,
216 @CMD_pl_edges@ 235 @CMD_pl_edges@
219 @CMD_params_pl_groups@ 238 @CMD_params_pl_groups@
220 @CMD_params_pl_components@ 239 @CMD_params_pl_components@
221 @CMD_pl_attribute_section@ 240 @CMD_pl_attribute_section@
222 @CMD_params_matplotlib_pyplot_scatter@) 241 @CMD_params_matplotlib_pyplot_scatter@)
223 242
224 #elif $method.method == 'pl.umap' 243 #else if $method.method == 'pl.umap'
225 sc.pl.umap( 244 sc.pl.umap(
226 @CMD_param_plot_inputs@ 245 @CMD_param_plot_inputs@
227 @CMD_param_color@ 246 @CMD_param_color@
228 use_raw=$method.use_raw, 247 use_raw=$method.use_raw,
229 @CMD_pl_edges@ 248 @CMD_pl_edges@
232 @CMD_params_pl_groups@ 251 @CMD_params_pl_groups@
233 @CMD_params_pl_components@ 252 @CMD_params_pl_components@
234 @CMD_pl_attribute_section@ 253 @CMD_pl_attribute_section@
235 @CMD_params_matplotlib_pyplot_scatter@) 254 @CMD_params_matplotlib_pyplot_scatter@)
236 255
237 #elif $method.method == 'pl.diffmap' 256 #else if $method.method == 'pl.diffmap'
238 sc.pl.diffmap( 257 sc.pl.diffmap(
239 @CMD_param_plot_inputs@ 258 @CMD_param_plot_inputs@
240 @CMD_param_color@ 259 @CMD_param_color@
241 use_raw=$method.use_raw, 260 use_raw=$method.use_raw,
242 sort_order=$method.sort_order, 261 sort_order=$method.sort_order,
243 @CMD_params_pl_groups@ 262 @CMD_params_pl_groups@
244 @CMD_params_pl_components@ 263 @CMD_params_pl_components@
245 @CMD_pl_attribute_section@ 264 @CMD_pl_attribute_section@
246 @CMD_params_matplotlib_pyplot_scatter@) 265 @CMD_params_matplotlib_pyplot_scatter@)
247 266
248 #elif $method.method == 'pl.dpt_groups_pseudotime' 267 #else if $method.method == 'pl.draw_graph'
268 sc.pl.draw_graph(
269 @CMD_param_plot_inputs@
270 @CMD_param_color@
271 #if str($method.gene_symbols) != ''
272 gene_symbols='$method.gene_symbols',
273 #end if
274 use_raw=$method.use_raw,
275 #if str($method.layout) != 'None'
276 layout='$method.layout',
277 #end if
278 edges=$method.edges.edges,
279 #if str($method.edges.edges) == 'True'
280 edges_width=$method.edges.edges_width,
281 edges_color='$method.edges.edges_color',
282 #end if
283 arrows=$method.arrows,
284 sort_order=$method.sort_order,
285 @CMD_params_pl_groups@
286 @CMD_params_pl_components@
287 @CMD_pl_attribute_section@
288 @CMD_params_matplotlib_pyplot_scatter@)
289
290 #else if $method.method == 'pl.dpt_groups_pseudotime'
249 sc.pl.dpt_groups_pseudotime( 291 sc.pl.dpt_groups_pseudotime(
250 @CMD_param_plot_inputs@ 292 @CMD_param_plot_inputs@
251 color_map='$method.color_map') 293 color_map='$method.color_map')
252 294
253 #elif $method.method == 'pl.dpt_timeseries' 295 #else if $method.method == 'pl.dpt_timeseries'
254 sc.pl.dpt_timeseries( 296 sc.pl.dpt_timeseries(
255 @CMD_param_plot_inputs@ 297 @CMD_param_plot_inputs@
256 #if $method.heatmap.as_heatmap == "True" 298 #if $method.heatmap.as_heatmap == "True"
257 color_map='$method.heatmap.color_map', 299 color_map='$method.heatmap.color_map',
258 #end if 300 #end if
259 as_heatmap=$method.heatmap.as_heatmap) 301 as_heatmap=$method.heatmap.as_heatmap)
260 302
261 #elif $method.method == 'pl.paga' 303 #else if $method.method == 'pl.paga'
262 sc.pl.paga( 304 sc.pl.paga(
263 @CMD_param_plot_inputs@ 305 @CMD_param_plot_inputs@
264 @CMD_params_pl_paga@) 306 @CMD_params_pl_paga@)
307
308 #else if $method.method == 'pl.paga_compare'
309 sc.pl.paga_compare(
310 @CMD_param_plot_inputs@
311 @CMD_params_pl_paga@)
312
313 #else if $method.method == 'pl.paga_path'
314 sc.pl.paga_path(
315 @CMD_param_plot_inputs@
316 #set $nodes = ([int(x.strip()) for x in str($method.nodes).split(',')])
317 nodes=$nodes,
318 #set $keys=([x.strip() for x in str($method.keys).split(',')])
319 keys=$keys,
320 use_raw=$method.use_raw,
321 #if str($method.annotations) != ''
322 #set $annotations=([x.strip() for x in str($method.annotations).split(',')])
323 annotations=$annotations,
324 #end if
325 color_map='$method.color_map',
326 n_avg=$method.n_avg,
327 #if str($method.annotations) != ''
328 groups_key='$method.groups_key',
329 #end if
330 as_heatmap=$method.as_heatmap,
331 show_node_names=$method.show_node_names,
332 show_colorbar=$method.show_colorbar,
333 show_yticks=$method.show_yticks,
334 normalize_to_zero_one=$method.normalize_to_zero_one)
335
336 #else if $method.method == 'pl.rank_genes_groups'
337 sc.pl.rank_genes_groups(
338 @CMD_param_plot_inputs@
339 @CMD_params_pl_groups@
340 n_genes=$method.n_genes,
341 #if str($method.gene_symbols) != ''
342 gene_symbols='$method.gene_symbols',
343 #end if
344 fontsize=$method.fontsize,
345 ncols=$method.ncols,
346 sharey=$method.sharey)
347
348 #else if $method.method == 'pl.rank_genes_groups_violin'
349 sc.pl.rank_genes_groups_violin(
350 @CMD_param_plot_inputs@
351 @CMD_params_pl_groups@
352 #if $method.genes.select == 'n_genes'
353 n_genes=$method.genes.n_genes,
354 #else
355 #set $gene_names = ([x.strip() for x in str($method.genes.gene_names).split(',')])
356 gene_names=$gene_names,
357 #end if
358 gene_symbols='$method.gene_symbols',
359 use_raw=$method.use_raw,
360 split=$method.split,
361 strip=$method.violin_plot.stripplot.stripplot,
362 #if $method.violin_plot.stripplot.stripplot == "True"
363 jitter=$method.violin_plot.stripplot.jitter.jitter,
364 #if $method.violin_plot.stripplot.jitter.jitter == "True"
365 size=$method.violin_plot.stripplot.jitter.size,
366 #end if
367 #end if
368 scale='$method.violin_plot.scale')
369
265 #end if 370 #end if
266 ]]></configfile> 371 ]]></configfile>
267 </configfiles> 372 </configfiles>
268 <inputs> 373 <inputs>
269 <expand macro="inputs_anndata"/> 374 <expand macro="inputs_anndata"/>
272 <param argument="method" type="select" label="Method used for plotting"> 377 <param argument="method" type="select" label="Method used for plotting">
273 <option value="pl.scatter">Generic: Scatter plot along observations or variables axes, using `pl.scatter`</option> 378 <option value="pl.scatter">Generic: Scatter plot along observations or variables axes, using `pl.scatter`</option>
274 <option value="pl.heatmap">Generic: Heatmap of the expression values of set of genes, using `pl.heatmap`</option> 379 <option value="pl.heatmap">Generic: Heatmap of the expression values of set of genes, using `pl.heatmap`</option>
275 <option value="pl.dotplot">Generic: Makes a dot plot of the expression values, using `pl.dotplot`</option> 380 <option value="pl.dotplot">Generic: Makes a dot plot of the expression values, using `pl.dotplot`</option>
276 <option value="pl.violin">Generic: Violin plot, using `pl.violin`</option> 381 <option value="pl.violin">Generic: Violin plot, using `pl.violin`</option>
277 <!--<option value="pl.stacked_violin">Generic: </option>!--> 382 <option value="pl.stacked_violin">Generic: Stacked violin plots, using `pl.stacked_violin`</option>
278 <option value="pl.matrixplot">Generic: Heatmap of the mean expression values per cluster, using `pl.matrixplot`</option> 383 <option value="pl.matrixplot">Generic: Heatmap of the mean expression values per cluster, using `pl.matrixplot`</option>
279 <option value="pl.clustermap">Generic: Hierarchically-clustered heatmap, using `pl.clustermap`</option> 384 <option value="pl.clustermap">Generic: Hierarchically-clustered heatmap, using `pl.clustermap`</option>
280 <!--<option value="pl.ranking">Generic: </option>!--> 385 <!--<option value="pl.ranking">Generic: </option>!-->
281 <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> 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>
282 <!--<option value="pl.filter_genes_dispersion">Preprocessing: Plot dispersions versus means for genes, using `pl.filter_genes_dispersion`</option>--> 387 <!--<option value="pl.filter_genes_dispersion">Preprocessing: Plot dispersions versus means for genes, using `pl.filter_genes_dispersion`</option>-->
283 <!--<option value="pl.highly_variable_genes">Preprocessing: </option>!--> 388 <option value="pl.highly_variable_genes">Preprocessing: Plot dispersions versus means for genes, using `pl.highly_variable_genes`</option>
284 <!--<option value="pl.calculate_qc_metrics">Preprocessing: </option>!--> 389 <!--<option value="pl.calculate_qc_metrics">Preprocessing: </option>!-->
285 <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>
286 <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>
287 <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>
288 <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>
289 <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>
290 <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>
291 <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>
292 <!--<option value="pl.draw_graph">Embeddings: </option>!--> 397 <option value="pl.draw_graph">Embeddings: Scatter plot in graph-drawing basis, using `pl.draw_graph`</option>
293 <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>
294 <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>
295 <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>
296 <!--<option value="pl.paga_compare">Branching trajectories and pseudotime, clustering: </option>!--> 401 <option value="pl.paga_compare">Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side, using `pl.paga_compare`</option>
297 <!--<option value="pl.paga_path">Branching trajectories and pseudotime, clustering: </option>!--> 402 <option value="pl.paga_path">Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths, using `pl.paga_path`</option>
298 <!--<option value="pl.rank_gene_groups">Marker genes: Plot ranking of genes using dotplot plot, using `pl.rank_gene_groups`</option>!--> 403 <option value="pl.rank_genes_groups">Marker genes: Plot ranking of genes using dotplot plot, using `pl.rank_genes_groups`</option>
299 <!--<option value="pl.rank_genes_groups_dotplot">Marker genes: </option>!--> 404 <!--<option value="pl.rank_genes_groups_dotplot">Marker genes: </option>!-->
300 <!--<option value="pl.rank_genes_groups_heatmap">Marker genes: </option>!--> 405 <!--<option value="pl.rank_genes_groups_heatmap">Marker genes: </option>!-->
301 <!--<option value="pl.rank_genes_groups_matrixplot">Marker genes: </option>!--> 406 <!--<option value="pl.rank_genes_groups_matrixplot">Marker genes: </option>!-->
302 <!--<option value="pl.rank_genes_groups_stacked_violin">Marker genes: </option>!--> 407 <!--<option value="pl.rank_genes_groups_stacked_violin">Marker genes: </option>!-->
303 <!--<option value="pl.rank_genes_groups_violin">Marker genes: </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>
304 <!--<option value="pl.phate">Misc: </option>!--> 409 <!--<option value="pl.phate">Misc: </option>!-->
305 <!--<option value="pl.matrix">Misc: </option>!--> 410 <!--<option value="pl.matrix">Misc: </option>!-->
306 <!--<option value="pl.paga_adjacency">Misc: </option>!--> 411 <!--<option value="pl.paga_adjacency">Misc: </option>!-->
307 <!--<option value="pl.timeseries">Misc: </option>!--> 412 <!--<option value="pl.timeseries">Misc: </option>!-->
308 <!--<option value="pl.timeseries_as_heatmap">Misc: </option>!--> 413 <!--<option value="pl.timeseries_as_heatmap">Misc: </option>!-->
315 <option value="basis">Using tool that computes coordinates</option> 420 <option value="basis">Using tool that computes coordinates</option>
316 </param> 421 </param>
317 <when value="xy"> 422 <when value="xy">
318 <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either `.obs` or `.var`"/> 423 <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either `.obs` or `.var`"/>
319 <param argument="y" type="text" value="" label="y 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`"/>
320 <param argument="layer_x" type="text" value="X" label="Layers for x coordinate" help="Use the `layers` attribute of `adata` if present"/> 425 <conditional name="layers">
321 <param argument="layer_y" type="text" value="X" label="Layers for y coordinate" help="Use the `layers` attribute of `adata` if present"/> 426 <param argument="use_layers" type="select" label="Use the layers attribute?">
322 <param argument="layer_color" type="text" value="X" label="Layers for color" help="Use the `layers` attribute of `adata` if present"/> 427 <option value="true">Yes</option>
428 <option value="false" selected="true">No</option>
429 </param>
430 <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"/>
432 <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"/>
434 </when>
435 <when value="false"/>
436 </conditional>
323 </when> 437 </when>
324 <when value="basis"> 438 <when value="basis">
325 <param argument="basis" type="select" label="Plotting tool that computes coordinates" help=""> 439 <param argument="basis" type="select" label="Plotting tool that computes coordinates" help="">
326 <option value="pca">pca (need to run on `tl.pca` output)</option> 440 <option value="pca">pca (need to run on `tl.pca` output)</option>
327 <option value="tsne">tsne (need to run on `tl.tsne` output)</option> 441 <option value="tsne">tsne (need to run on `tl.tsne` output)</option>
353 <expand macro="param_swap_axes"/> 467 <expand macro="param_swap_axes"/>
354 <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."/> 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."/>
355 <section name="matplotlib_pyplot_imshow" title="Parameters for matplotlib.pyplot.imshow"> 469 <section name="matplotlib_pyplot_imshow" title="Parameters for matplotlib.pyplot.imshow">
356 <expand macro="param_cmap"/> 470 <expand macro="param_cmap"/>
357 <param name="interpolation" type="select" label="Interpolation method" help=""> 471 <param name="interpolation" type="select" label="Interpolation method" help="">
358 <option value="none">none</option> 472 <option value="None">none</option>
359 <option value="nearest">nearest</option> 473 <option value="nearest">nearest</option>
360 <option value="bilinear">bilinear</option> 474 <option value="bilinear">bilinear</option>
361 <option value="bicubic">bicubic</option> 475 <option value="bicubic">bicubic</option>
362 <option value="spline16">spline16</option> 476 <option value="spline16">spline16</option>
363 <option value="spline36">spline36</option> 477 <option value="spline36">spline36</option>
394 <when value="pl.violin"> 508 <when value="pl.violin">
395 <conditional name="key_variables"> 509 <conditional name="key_variables">
396 <param name="type" type="select" label="Keys for accessing variables"> 510 <param name="type" type="select" label="Keys for accessing variables">
397 <option value="var_names">All variables in `.var_names`</option> 511 <option value="var_names">All variables in `.var_names`</option>
398 <option value="obs">All fields in `.obs`</option> 512 <option value="obs">All fields in `.obs`</option>
399 <option value="custom">Subset of variables in `adata.var_names` or fields of `.obs`"</option> 513 <option value="custom">Subset of variables in `adata.var_names` or fields of `.obs`</option>
400 </param> 514 </param>
401 <when value="var_names"/> 515 <when value="var_names"/>
402 <when value="obs"/> 516 <when value="obs"/>
403 <when value="custom"> 517 <when value="custom">
404 <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`"/> 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`"/>
405 </when> 519 </when>
406 </conditional> 520 </conditional>
407 <expand macro="param_groupby"/> 521 <expand macro="param_groupby"/>
408 <expand macro="param_log"/> 522 <expand macro="param_log"/>
409 <expand macro="param_use_raw"/> 523 <expand macro="param_use_raw"/>
410 <expand macro="section_violin_plots"/> 524 <section name="violin_plot" title="Violin plot attributes">
525 <expand macro="conditional_stripplot"/>
526 <conditional name="multi_panel">
527 <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>
529 <option value="False" selected="true">No</option>
530 </param>
531 <when value="True">
532 <param argument="width" type="integer" min="0" value="" optional="true" label="Width of the figure" help=""/>
533 <param argument="height" type="integer" min="0" value="" optional="true" label="Height of the figure" help=""/>
534 </when>
535 <when value="False"/>
536 </conditional>
537 <expand macro="param_scale"/>
538 </section>
411 <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."/> 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."/>
412 <param argument="rotation" type="float" value="" optional="true" label="Rotation of xtick labels" help=""/> 540 <param argument="rotation" type="float" value="" optional="true" label="Rotation of xtick labels" help=""/>
541 <expand macro="seaborn_violinplot"/>
542 </when>
543 <when value="pl.stacked_violin">
544 <expand macro="params_plots"/>
545 <expand macro="param_swap_axes"/>
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>
413 <expand macro="seaborn_violinplot"/> 559 <expand macro="seaborn_violinplot"/>
414 </when> 560 </when>
415 <when value="pl.matrixplot"> 561 <when value="pl.matrixplot">
416 <expand macro="params_plots"/> 562 <expand macro="params_plots"/>
417 <expand macro="param_swap_axes"/> 563 <expand macro="param_swap_axes"/>
425 <expand macro="param_alpha"/> 571 <expand macro="param_alpha"/>
426 <param argument="snap" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Snap the mesh to pixel boundaries?" help=""/> 572 <param argument="snap" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Snap the mesh to pixel boundaries?" help=""/>
427 </section> 573 </section>
428 </when> 574 </when>
429 <when value="pl.clustermap"> 575 <when value="pl.clustermap">
430 <param argument="obs_keys" type="text" value="" label="Categorical annotation to plot with a different color map" help="Currently, only a single key is supported."/> 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."/>
431 <expand macro="param_use_raw"/> 577 <expand macro="param_use_raw"/>
432 <section name="seaborn_clustermap" title="Parameters for seaborn.clustermap"> 578 <section name="seaborn_clustermap" title="Parameters for seaborn.clustermap">
433 <param name="method" type="select" label="Linkage method to use for calculating clusters" help="More details in https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html"> 579 <param name="method" type="select" label="Linkage method to use for calculating clusters" help="More details in https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html">
434 <option value="single">single: Nearest Point Algorithm</option> 580 <option value="single">single: Nearest Point Algorithm</option>
435 <option value="complete">complete: Farthest Point Algorithm or Voor Hees Algorithm</option> 581 <option value="complete">complete: Farthest Point Algorithm or Voor Hees Algorithm</option>
454 </param> 600 </param>
455 <param name="col_cluster" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cluster the columns?" help=""/> 601 <param name="col_cluster" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cluster the columns?" help=""/>
456 <param name="row_cluster" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cluster the rows?" help=""/> 602 <param name="row_cluster" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cluster the rows?" help=""/>
457 </section> 603 </section>
458 </when> 604 </when>
605 <when value="pl.highly_variable_genes">
606 <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?"/>
608 </when>
459 <when value="pl.highest_expr_genes"> 609 <when value="pl.highest_expr_genes">
460 <param argument="n_top" type="integer" min="0" value="30" label="Number of top genes" help=""/> 610 <param argument="n_top" type="integer" min="0" value="30" label="Number of top genes" help=""/>
461 <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`."/> 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`."/>
462 <section name="setseaborn_boxplot" title="Plot settings" expanded="false"> 612 <section name="setseaborn_boxplot" title="Plot settings" expanded="false">
463 <param argument="color" type="text" value="" optional="true" label="Color for all of the elements, or seed for a gradient palette" help=""/> 613 <param argument="color" type="text" value="" optional="true" label="Color for all of the elements, or seed for a gradient palette" help=""/>
511 <expand macro="section_matplotlib_pyplot_scatter"/> 661 <expand macro="section_matplotlib_pyplot_scatter"/>
512 </when> 662 </when>
513 <when value="pl.diffmap"> 663 <when value="pl.diffmap">
514 <expand macro="param_color"/> 664 <expand macro="param_color"/>
515 <expand macro="param_use_raw"/> 665 <expand macro="param_use_raw"/>
666 <expand macro="param_sort_order"/>
667 <expand macro="pl_groups"/>
668 <expand macro="pl_attribute_section"/>
669 <expand macro="section_matplotlib_pyplot_scatter"/>
670 </when>
671 <when value="pl.draw_graph">
672 <expand macro="param_color"/>
673 <expand macro="gene_symbols"/>
674 <expand macro="param_use_raw"/>
675 <param argument="layout" type="select" optional="true" label="Plotting layout" help="">
676 <expand macro="options_layout"/>
677 </param>
678 <expand macro="pl_edges"/>
679 <expand macro="param_arrows"/>
516 <expand macro="param_sort_order"/> 680 <expand macro="param_sort_order"/>
517 <expand macro="pl_groups"/> 681 <expand macro="pl_groups"/>
518 <expand macro="pl_attribute_section"/> 682 <expand macro="pl_attribute_section"/>
519 <expand macro="section_matplotlib_pyplot_scatter"/> 683 <expand macro="section_matplotlib_pyplot_scatter"/>
520 </when> 684 </when>
534 </conditional> 698 </conditional>
535 </when> 699 </when>
536 <when value="pl.paga"> 700 <when value="pl.paga">
537 <expand macro="inputs_paga"/> 701 <expand macro="inputs_paga"/>
538 </when> 702 </when>
703 <when value="pl.paga_compare">
704 <expand macro="inputs_paga"/>
705 </when>
706 <when value="pl.paga_path">
707 <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"/>
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`"/>
710 <expand macro="param_use_raw"/>
711 <param argument="annotations" type="text" value="" optional="true" label="Key to plot" help="Keys for obs, comma-separated"/>
712 <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"/>
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"/>
715 <param argument="as_heatmap" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot the timeseries as heatmap?" help="If not, annotations have no effect."/>
716 <param argument="show_node_names" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot the node names on the nodes bar?"/>
717 <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?"/>
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?"/>
720 </when>
721 <when value="pl.rank_genes_groups">
722 <expand macro="pl_groups"/>
723 <expand macro="n_genes"/>
724 <expand macro="gene_symbols"/>
725 <param argument="fontsize" type="integer" min="0" value="8" label="Font size for gene names"/>
726 <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"/>
728 </when>
729 <when value="pl.rank_genes_groups_violin">
730 <expand macro="pl_groups"/>
731 <conditional name="genes">
732 <param argument="select" type="select" label="Which genes to plot?" help="">
733 <option value="n_genes">A number of genes</option>
734 <option value="gene_names">A custom list of genes</option>
735 </param>
736 <when value="n_genes">
737 <expand macro="n_genes"/>
738 </when>
739 <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"/>
741 </when>
742 </conditional>
743 <expand macro="gene_symbols"/>
744 <expand macro="param_use_raw"/>
745 <param argument="split" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Split the violins?"/>
746 <section name="violin_plot" title="Violin plot attributes">
747 <expand macro="conditional_stripplot"/>
748 <expand macro="param_scale"/>
749 </section>
750 </when>
539 </conditional> 751 </conditional>
540 </inputs> 752 </inputs>
541 <outputs> 753 <outputs>
542 <data name="out_png" format="png" from_work_dir="*.png" label="${tool.name} on ${on_string}"> 754 <data name="out_png" format="png" from_work_dir="*.png" label="${tool.name} (${method.method}) on ${on_string}">
543 <filter>format == 'png'</filter> 755 <filter>format == 'png' and method['method'] != 'pl.rank_genes_groups_violin'</filter>
544 </data> 756 </data>
545 <data name="out_pdf" format="pdf" from_work_dir="*.pdf" label="${tool.name} on ${on_string}"> 757 <collection name="collection_png" type="list" label="${tool.name} (${method.method}) on ${on_string}">
546 <filter>format == 'pdf'</filter> 758 <discover_datasets pattern="rank_genes_groups_cell_type_(?P&lt;designation&gt;.*).png" format="png"/>
759 <filter>format == 'png' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
760 </collection>
761 <data name="out_pdf" format="pdf" from_work_dir="*.pdf" label="${tool.name} (${method.method}) on ${on_string}">
762 <filter>format == 'pdf' and method['method'] != pl.rank_genes_groups_violin</filter>
547 </data> 763 </data>
548 <data name="out_svg" format="svg" from_work_dir="*.svg" label="${tool.name} on ${on_string}"> 764 <collection name="collection_pdf" type="list" label="${tool.name} (${method.method}) on ${on_string}">
549 <filter>format == 'svg'</filter> 765 <discover_datasets pattern="rank_genes_groups_cell_type_(?P&lt;designation&gt;.*).pdf" format="pdf"/>
766 <filter>format == 'pdf' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
767 </collection>
768 <data name="out_svg" format="svg" from_work_dir="*.svg" label="${tool.name} (${method.method}) on ${on_string}">
769 <filter>format == 'svg' and method['method'] != pl.rank_genes_groups_violin</filter>
550 </data> 770 </data>
771 <collection name="collection_svg" type="list" label="${tool.name} (${method.method}) on ${on_string}">
772 <discover_datasets pattern="rank_genes_groups_cell_type_(?P&lt;designation&gt;.*).svg" format="svg"/>
773 <filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
774 </collection>
551 </outputs> 775 </outputs>
552 <tests> 776 <tests>
553 <test> 777 <test>
554 <!-- Test pl.scatter !--> 778 <!-- test 1: pl.scatter !-->
555 <conditional name="input"> 779 <param name="adata" value="pbmc68k_reduced.h5ad" />
556 <param name="format" value="h5ad" />
557 <param name="adata" value="pp.pca.krumsiek11.h5ad" />
558 </conditional>
559 <param name="format" value="png"/> 780 <param name="format" value="png"/>
560 <conditional name="method"> 781 <conditional name="method">
561 <param name="method" value="pl.scatter"/> 782 <param name="method" value="pl.scatter"/>
562 <conditional name="type"> 783 <conditional name="type">
563 <param name="type" value="basis"/> 784 <param name="type" value="basis"/>
564 <param name="basis" value="pca"/> 785 <param name="basis" value="umap"/>
565 <param name="color" value="EgrNab, Gata2"/> 786 <param name="color" value="HES4"/>
566 </conditional> 787 </conditional>
567 <param name="use_raw" value="False"/> 788 <param name="use_raw" value="True"/>
568 <param name="sort_order" value="True"/> 789 <param name="sort_order" value="True"/>
569 <section name="plot"> 790 <section name="plot">
570 <param name="projection" value="2d"/> 791 <param name="projection" value="2d"/>
571 <param name="legend_loc" value="right margin"/> 792 <param name="legend_loc" value="right margin"/>
572 <param name="legend_fontsize" value="1"/> 793 <param name="legend_fontsize" value="1"/>
577 <param name="size" value="1"/> 798 <param name="size" value="1"/>
578 </section> 799 </section>
579 </conditional> 800 </conditional>
580 <assert_stdout> 801 <assert_stdout>
581 <has_text_matching expression="sc.pl.scatter"/> 802 <has_text_matching expression="sc.pl.scatter"/>
582 <has_text_matching expression="basis='pca'" /> 803 <has_text_matching expression="basis='umap'" />
583 <has_text_matching expression="color=\['EgrNab', 'Gata2'\]"/> 804 <has_text_matching expression="color=\['HES4'\]"/>
584 <has_text_matching expression="use_raw=False"/> 805 <has_text_matching expression="use_raw=True"/>
585 <has_text_matching expression="sort_order=True"/> 806 <has_text_matching expression="sort_order=True"/>
586 <has_text_matching expression="groups=None"/>
587 <has_text_matching expression="components=None"/>
588 <has_text_matching expression="projection='2d'"/> 807 <has_text_matching expression="projection='2d'"/>
589 <has_text_matching expression="legend_loc='right margin'"/> 808 <has_text_matching expression="legend_loc='right margin'"/>
590 <has_text_matching expression="legend_fontsize=1"/> 809 <has_text_matching expression="legend_fontsize=1"/>
591 <has_text_matching expression="legend_fontweight='normal'"/> 810 <has_text_matching expression="legend_fontweight='normal'"/>
592 <has_text_matching expression="color_map='inferno'"/> 811 <has_text_matching expression="color_map='inferno'"/>
593 <has_text_matching expression="palette='inferno'"/> 812 <has_text_matching expression="palette='inferno'"/>
594 <has_text_matching expression="frameon=True"/> 813 <has_text_matching expression="frameon=True"/>
595 <has_text_matching expression="size=1.0"/> 814 <has_text_matching expression="size=1.0"/>
596 </assert_stdout> 815 </assert_stdout>
597 <output name="out_png" file="pl.scatter.pca.krumsiek11.png" ftype="png" compare="sim_size"/> 816 <output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="sim_size"/>
598 </test> 817 </test>
599 <test> 818 <test>
600 <!-- Test pl.scatter !--> 819 <!-- test 2: pl.scatter !-->
601 <conditional name="input"> 820 <param name="adata" value="krumsiek11.h5ad" />
602 <param name="format" value="h5ad" />
603 <param name="adata" value="krumsiek11.h5ad" />
604 </conditional>
605 <param name="format" value="png"/> 821 <param name="format" value="png"/>
606 <conditional name="method"> 822 <conditional name="method">
607 <param name="method" value="pl.scatter"/> 823 <param name="method" value="pl.scatter"/>
608 <conditional name="type"> 824 <conditional name="type">
609 <param name="type" value="xy"/> 825 <param name="type" value="xy"/>
610 <param name="x" value="EKLF"/> 826 <param name="x" value="EKLF"/>
611 <param name="y" value="Cebpa"/> 827 <param name="y" value="Cebpa"/>
612 <param name="layer_x" value="X"/> 828 <conditional name="layers">
613 <param name="layer_y" value="X"/> 829 <param name="use_layers" value="false"/>
614 <param name="layer_color" value="X"/> 830 </conditional>
615 </conditional> 831 </conditional>
616 <param name="use_raw" value="False"/> 832 <param name="use_raw" value="False"/>
617 <param name="sort_order" value="True"/> 833 <param name="sort_order" value="True"/>
618 <section name="plot"> 834 <section name="plot">
619 <param name="projection" value="2d"/> 835 <param name="projection" value="2d"/>
628 </conditional> 844 </conditional>
629 <assert_stdout> 845 <assert_stdout>
630 <has_text_matching expression="sc.pl.scatter"/> 846 <has_text_matching expression="sc.pl.scatter"/>
631 <has_text_matching expression="x='EKLF'" /> 847 <has_text_matching expression="x='EKLF'" />
632 <has_text_matching expression="y='Cebpa'"/> 848 <has_text_matching expression="y='Cebpa'"/>
633 <has_text_matching expression="layers=\('X', 'X', 'X'\)"/>
634 <has_text_matching expression="use_raw=False"/> 849 <has_text_matching expression="use_raw=False"/>
635 <has_text_matching expression="sort_order=True"/> 850 <has_text_matching expression="sort_order=True"/>
636 <has_text_matching expression="groups=None,"/>
637 <has_text_matching expression="components=None,"/>
638 <has_text_matching expression="projection='2d'"/> 851 <has_text_matching expression="projection='2d'"/>
639 <has_text_matching expression="legend_loc='right margin'"/> 852 <has_text_matching expression="legend_loc='right margin'"/>
640 <has_text_matching expression="legend_fontsize=1"/> 853 <has_text_matching expression="legend_fontsize=1"/>
641 <has_text_matching expression="legend_fontweight='normal'"/> 854 <has_text_matching expression="legend_fontweight='normal'"/>
642 <has_text_matching expression="color_map='viridis'"/> 855 <has_text_matching expression="color_map='viridis'"/>
646 <has_text_matching expression="title='A title'"/> 859 <has_text_matching expression="title='A title'"/>
647 </assert_stdout> 860 </assert_stdout>
648 <output name="out_png" file="pl.scatter.krumsiek11.png" ftype="png" compare="sim_size"/> 861 <output name="out_png" file="pl.scatter.krumsiek11.png" ftype="png" compare="sim_size"/>
649 </test> 862 </test>
650 <test> 863 <test>
651 <!-- test pl.heatmap !--> 864 <!-- test 3: pl.heatmap !-->
652 <conditional name="input"> 865 <param name="adata" value="krumsiek11.h5ad" />
653 <param name="format" value="h5ad" />
654 <param name="adata" value="krumsiek11.h5ad" />
655 </conditional>
656 <param name="format" value="png"/> 866 <param name="format" value="png"/>
657 <conditional name="method"> 867 <conditional name="method">
658 <param name="method" value="pl.heatmap"/> 868 <param name="method" value="pl.heatmap"/>
659 <conditional name="var_names"> 869 <conditional name="var_names">
660 <param name="type" value="all"/> 870 <param name="type" value="all"/>
671 <param name="dendrogram" value="True"/> 881 <param name="dendrogram" value="True"/>
672 <param name="swap_axes" value="True"/> 882 <param name="swap_axes" value="True"/>
673 <param name="show_gene_labels" value="False"/> 883 <param name="show_gene_labels" value="False"/>
674 <section name="matplotlib_pyplot_imshow"> 884 <section name="matplotlib_pyplot_imshow">
675 <param name="cmap" value="YlGnBu"/> 885 <param name="cmap" value="YlGnBu"/>
676 <param name="interpolation" value="none"/> 886 <param name="interpolation" value="None"/>
677 <param name="origin" value="upper"/> 887 <param name="origin" value="upper"/>
678 </section> 888 </section>
679 </conditional> 889 </conditional>
680 <assert_stdout> 890 <assert_stdout>
681 <has_text_matching expression="sc.pl.heatmap"/> 891 <has_text_matching expression="sc.pl.heatmap"/>
683 <has_text_matching expression="groupby='cell_type'"/> 893 <has_text_matching expression="groupby='cell_type'"/>
684 <has_text_matching expression="log=False"/> 894 <has_text_matching expression="log=False"/>
685 <has_text_matching expression="use_raw=False"/> 895 <has_text_matching expression="use_raw=False"/>
686 <has_text_matching expression="num_categories=7"/> 896 <has_text_matching expression="num_categories=7"/>
687 <has_text_matching expression="dendrogram=True"/> 897 <has_text_matching expression="dendrogram=True"/>
688 <has_text_matching expression="var_group_positions=None"/>
689 <has_text_matching expression="var_group_labels=None"/>
690 <has_text_matching expression="figsize=\(10, 3\)"/> 898 <has_text_matching expression="figsize=\(10, 3\)"/>
691 <has_text_matching expression="swap_axes=True"/> 899 <has_text_matching expression="swap_axes=True"/>
692 <has_text_matching expression="show_gene_labels=False"/> 900 <has_text_matching expression="show_gene_labels=False"/>
693 <has_text_matching expression="interpolation='none'"/>
694 <has_text_matching expression="cmap='YlGnBu'"/> 901 <has_text_matching expression="cmap='YlGnBu'"/>
695 <has_text_matching expression="origin='upper'"/> 902 <has_text_matching expression="origin='upper'"/>
696 </assert_stdout> 903 </assert_stdout>
697 <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="sim_size"/> 904 <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="sim_size"/>
698 </test> 905 </test>
699 <test> 906 <test>
700 <!-- test pl.dotplot !--> 907 <!-- test 4: pl.dotplot !-->
701 <conditional name="input"> 908 <param name="adata" value="pbmc68k_reduced.h5ad" />
702 <param name="format" value="h5ad" />
703 <param name="adata" value="pbmc68k_reduced.h5ad" />
704 </conditional>
705 <param name="format" value="png"/> 909 <param name="format" value="png"/>
706 <conditional name="method"> 910 <conditional name="method">
707 <param name="method" value="pl.dotplot"/> 911 <param name="method" value="pl.dotplot"/>
708 <conditional name="var_names"> 912 <conditional name="var_names">
709 <param name="type" value="custom"/> 913 <param name="type" value="custom"/>
712 <param name="groupby" value="louvain"/> 916 <param name="groupby" value="louvain"/>
713 <param name="log" value="False"/> 917 <param name="log" value="False"/>
714 <param name="use_raw" value="False"/> 918 <param name="use_raw" value="False"/>
715 <param name="num_categories" value="7"/> 919 <param name="num_categories" value="7"/>
716 <param name="dendrogram" value="True"/> 920 <param name="dendrogram" value="True"/>
717 <conditional name="figsize">
718 <param name="test" value="no"/>
719 </conditional>
720 <param name="dendrogram" value="False"/>
721 <repeat name="var_group_positions"> 921 <repeat name="var_group_positions">
722 <param name="start" value="0"/> 922 <param name="start" value="0"/>
723 <param name="end" value="1"/> 923 <param name="end" value="1"/>
724 <param name="label" value="B cells"/> 924 <param name="label" value="B cells"/>
725 </repeat> 925 </repeat>
726 <repeat name="var_group_positions"> 926 <repeat name="var_group_positions">
727 <param name="start" value="11"/> 927 <param name="start" value="11"/>
728 <param name="end" value="12"/> 928 <param name="end" value="12"/>
729 <param name="label" value="dendritic"/> 929 <param name="label" value="dendritic"/>
730 </repeat> 930 </repeat>
931 <conditional name="figsize">
932 <param name="test" value="no"/>
933 </conditional>
731 <param name="color_map" value="hot"/> 934 <param name="color_map" value="hot"/>
732 <param name="dot_max" value="0.7"/> 935 <param name="dot_max" value="0.7"/>
733 <param name="dot_min" value="0.1"/> 936 <param name="dot_min" value="0.1"/>
734 <section name="matplotlib_pyplot_scatter"> 937 <section name="matplotlib_pyplot_scatter">
735 <param name="linewidths" value="0" /> 938 <param name="linewidths" value="0" />
741 <has_text_matching expression="var_names=\['CD79A', 'MS4A1', 'CD8A', 'CD8B', 'LYZ', 'GNLY', 'NKG7', 'RP3-467N11.1', 'FCGR3A', 'FCER1A', 'CST3', 'POU2AF1', 'LINC00402'\]" /> 944 <has_text_matching expression="var_names=\['CD79A', 'MS4A1', 'CD8A', 'CD8B', 'LYZ', 'GNLY', 'NKG7', 'RP3-467N11.1', 'FCGR3A', 'FCER1A', 'CST3', 'POU2AF1', 'LINC00402'\]" />
742 <has_text_matching expression="groupby='louvain'"/> 945 <has_text_matching expression="groupby='louvain'"/>
743 <has_text_matching expression="log=False"/> 946 <has_text_matching expression="log=False"/>
744 <has_text_matching expression="use_raw=False"/> 947 <has_text_matching expression="use_raw=False"/>
745 <has_text_matching expression="num_categories=7"/> 948 <has_text_matching expression="num_categories=7"/>
746 <has_text_matching expression="dendrogram=False"/> 949 <has_text_matching expression="dendrogram=True"/>
747 <has_text_matching expression="var_group_positions=\[\(0, 1\), \(11, 12\)\]"/> 950 <has_text_matching expression="var_group_positions=\[\(0, 1\), \(11, 12\)\]"/>
748 <has_text_matching expression="var_group_labels=\['B cells', 'dendritic'\]"/> 951 <has_text_matching expression="var_group_labels=\['B cells', 'dendritic'\]"/>
749 <has_text_matching expression="color_map='hot'"/> 952 <has_text_matching expression="color_map='hot'"/>
750 <has_text_matching expression="dot_max=0.7"/> 953 <has_text_matching expression="dot_max=0.7"/>
751 <has_text_matching expression="dot_min=0.1"/> 954 <has_text_matching expression="dot_min=0.1"/>
753 <has_text_matching expression="edgecolors='face'"/> 956 <has_text_matching expression="edgecolors='face'"/>
754 </assert_stdout> 957 </assert_stdout>
755 <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="sim_size"/> 958 <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="sim_size"/>
756 </test> 959 </test>
757 <test> 960 <test>
758 <!-- test pl.violin !--> 961 <!-- test 5: pl.violin !-->
759 <conditional name="input"> 962 <param name="adata" value="pbmc68k_reduced.h5ad" />
760 <param name="format" value="h5ad" />
761 <param name="adata" value="pbmc68k_reduced.h5ad" />
762 </conditional>
763 <param name="format" value="png"/> 963 <param name="format" value="png"/>
764 <conditional name="method"> 964 <conditional name="method">
765 <param name="method" value="pl.violin"/> 965 <param name="method" value="pl.violin"/>
766 <conditional name="key_variables"> 966 <conditional name="key_variables">
767 <param name="type" value="custom"/> 967 <param name="type" value="custom"/>
793 <assert_stdout> 993 <assert_stdout>
794 <has_text_matching expression="sc.pl.violin"/> 994 <has_text_matching expression="sc.pl.violin"/>
795 <has_text_matching expression="keys=\['n_genes', 'percent_mito', 'n_counts'\]" /> 995 <has_text_matching expression="keys=\['n_genes', 'percent_mito', 'n_counts'\]" />
796 <has_text_matching expression="log=False"/> 996 <has_text_matching expression="log=False"/>
797 <has_text_matching expression="use_raw=False"/> 997 <has_text_matching expression="use_raw=False"/>
798 <has_text_matching expression="sstripplot=True"/> 998 <has_text_matching expression="stripplot=True"/>
799 <has_text_matching expression="jitter=True"/> 999 <has_text_matching expression="jitter=True"/>
800 <has_text_matching expression="size=1"/> 1000 <has_text_matching expression="size=1"/>
801 <has_text_matching expression="multi_panel=True"/> 1001 <has_text_matching expression="multi_panel=True"/>
1002 <has_text_matching expression="figsize=\(20, 20\)"/>
802 <has_text_matching expression="scale='width'"/> 1003 <has_text_matching expression="scale='width'"/>
803 <has_text_matching expression="bw='scott'"/> 1004 <has_text_matching expression="bw='scott'"/>
804 <has_text_matching expression="scale='width'"/> 1005 <has_text_matching expression="scale='width'"/>
805 <has_text_matching expression="linewidth=0.0"/> 1006 <has_text_matching expression="linewidth=0.0"/>
806 <has_text_matching expression="color='AliceBlue'"/> 1007 <has_text_matching expression="color='AliceBlue'"/>
808 <has_text_matching expression="saturation=0.75"/> 1009 <has_text_matching expression="saturation=0.75"/>
809 </assert_stdout> 1010 </assert_stdout>
810 <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="sim_size"/> 1011 <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="sim_size"/>
811 </test> 1012 </test>
812 <test> 1013 <test>
813 <!-- test pl.matrixplot !--> 1014 <!-- test 6: pl.stacked_violin !-->
814 <conditional name="input"> 1015 <param name="adata" value="krumsiek11.h5ad" />
815 <param name="format" value="h5ad" /> 1016 <param name="format" value="png"/>
816 <param name="adata" value="krumsiek11.h5ad" /> 1017 <conditional name="method">
817 </conditional> 1018 <param name="method" value="pl.stacked_violin"/>
818 <param name="format" value="png"/>
819 <conditional name="method">
820 <param name="method" value="pl.matrixplot"/>
821 <conditional name="var_names"> 1019 <conditional name="var_names">
822 <param name="type" value="all"/> 1020 <param name="type" value="all"/>
823 </conditional> 1021 </conditional>
824 <param name="groupby" value="cell_type"/> 1022 <param name="groupby" value="cell_type"/>
825 <param name="log" value="False"/> 1023 <param name="log" value="False"/>
828 <param name="dendrogram" value="True"/> 1026 <param name="dendrogram" value="True"/>
829 <conditional name="figsize"> 1027 <conditional name="figsize">
830 <param name="test" value="no"/> 1028 <param name="test" value="no"/>
831 </conditional> 1029 </conditional>
832 <param name="swap_axes" value="True"/> 1030 <param name="swap_axes" value="True"/>
1031 <section name="violin_plot">
1032 <conditional name="stripplot">
1033 <param name="stripplot" value="True"/>
1034 <param name="jitter" value="True"/>
1035 <param name="size" value="1"/>
1036 </conditional>
1037 <param name="scale" value="width"/>
1038 </section>
1039 <param name="row_palette" value="muted"/>
1040 <param name="standard_scale" value="None"/>
1041 <section name="seaborn_violinplot">
1042 <param name="bw" value="scott"/>
1043 <param name="linewidth" value="0"/>
1044 <param name="color" value="AliceBlue"/>
1045 <param name="palette" value="viridis"/>
1046 <param name="saturation" value="0.75"/>
1047 </section>
1048 </conditional>
1049 <assert_stdout>
1050 <has_text_matching expression="sc.pl.stacked_violin"/>
1051 <has_text_matching expression="groupby='cell_type'"/>
1052 <has_text_matching expression="log=False"/>
1053 <has_text_matching expression="use_raw=False"/>
1054 <has_text_matching expression="num_categories=7"/>
1055 <has_text_matching expression="dendrogram=True"/>
1056 <has_text_matching expression="swap_axes=True"/>
1057 <has_text_matching expression="stripplot=True"/>
1058 <has_text_matching expression="jitter=True"/>
1059 <has_text_matching expression="size=1"/>
1060 <has_text_matching expression="scale='width'"/>
1061 <has_text_matching expression="bw='scott'"/>
1062 <has_text_matching expression="scale='width'"/>
1063 <has_text_matching expression="linewidth=0.0"/>
1064 <has_text_matching expression="color='AliceBlue'"/>
1065 <has_text_matching expression="palette='viridis'"/>
1066 <has_text_matching expression="saturation=0.75"/>
1067 </assert_stdout>
1068 <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="sim_size"/>
1069 </test>
1070 <test>
1071 <!-- test 7: pl.matrixplot !-->
1072 <param name="adata" value="krumsiek11.h5ad" />
1073 <param name="format" value="png"/>
1074 <conditional name="method">
1075 <param name="method" value="pl.matrixplot"/>
1076 <conditional name="var_names">
1077 <param name="type" value="all"/>
1078 </conditional>
1079 <param name="groupby" value="cell_type"/>
1080 <param name="log" value="False"/>
1081 <param name="use_raw" value="False"/>
1082 <param name="num_categories" value="7"/>
1083 <param name="dendrogram" value="True"/>
1084 <conditional name="figsize">
1085 <param name="test" value="no"/>
1086 </conditional>
1087 <param name="swap_axes" value="True"/>
833 <section name="matplotlib_pyplot_pcolor"> 1088 <section name="matplotlib_pyplot_pcolor">
834 <param name="cmap" value="viridis"/> 1089 <param name="cmap" value="viridis"/>
835 <param name="edgecolors" value="face"/> 1090 <param name="edgecolors" value="face"/>
836 <param name="snap" value="False"/> 1091 <param name="snap" value="False"/>
837 </section> 1092 </section>
842 <has_text_matching expression="groupby='cell_type'"/> 1097 <has_text_matching expression="groupby='cell_type'"/>
843 <has_text_matching expression="log=False"/> 1098 <has_text_matching expression="log=False"/>
844 <has_text_matching expression="use_raw=False"/> 1099 <has_text_matching expression="use_raw=False"/>
845 <has_text_matching expression="num_categories=7"/> 1100 <has_text_matching expression="num_categories=7"/>
846 <has_text_matching expression="dendrogram=True"/> 1101 <has_text_matching expression="dendrogram=True"/>
847 <has_text_matching expression="var_group_positions=None"/>
848 <has_text_matching expression="var_group_labels=None"/>
849 <has_text_matching expression="swap_axes=True"/> 1102 <has_text_matching expression="swap_axes=True"/>
850 <has_text_matching expression="cmap='viridis'"/> 1103 <has_text_matching expression="cmap='viridis'"/>
851 <has_text_matching expression="edgecolors='face'"/> 1104 <has_text_matching expression="edgecolors='face'"/>
852 <has_text_matching expression="snap=False"/> 1105 <has_text_matching expression="snap=False"/>
853 </assert_stdout> 1106 </assert_stdout>
854 <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="sim_size"/> 1107 <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="sim_size"/>
855 </test> 1108 </test>
856 <test> 1109 <test>
857 <!-- test pl.clustermap !--> 1110 <!-- test 8: pl.clustermap !-->
858 <conditional name="input"> 1111 <param name="adata" value="krumsiek11.h5ad" />
859 <param name="format" value="h5ad" />
860 <param name="adata" value="krumsiek11.h5ad" />
861 </conditional>
862 <param name="format" value="png"/> 1112 <param name="format" value="png"/>
863 <conditional name="method"> 1113 <conditional name="method">
864 <param name="method" value="pl.clustermap"/> 1114 <param name="method" value="pl.clustermap"/>
865 <param name="obs_keys" value="cell_type"/>
866 <param name="use_raw" value="False"/> 1115 <param name="use_raw" value="False"/>
867 <section name="seaborn_clustermap"> 1116 <section name="seaborn_clustermap">
868 <param name="method" value="single"/> 1117 <param name="method" value="single"/>
869 <param name="metric" value="braycurtis"/> 1118 <param name="metric" value="euclidean"/>
870 <param name="z_score" value="None"/> 1119 <param name="z_score" value="None"/>
871 <param name="standard_scale" value="None"/> 1120 <param name="standard_scale" value="None"/>
872 <param name="col_cluster" value="False"/> 1121 <param name="col_cluster" value="False"/>
873 <param name="row_cluster" value="False"/> 1122 <param name="row_cluster" value="False"/>
874 </section> 1123 </section>
875 </conditional> 1124 </conditional>
876 <assert_stdout> 1125 <assert_stdout>
877 <has_text_matching expression="sc.pl.clustermap"/> 1126 <has_text_matching expression="sc.pl.clustermap"/>
878 <has_text_matching expression="adata=adata" /> 1127 <has_text_matching expression="adata=adata" />
879 <has_text_matching expression="obs_keys='cell_type'" />
880 <has_text_matching expression="use_raw=False"/> 1128 <has_text_matching expression="use_raw=False"/>
881 <has_text_matching expression="method='single'"/> 1129 <has_text_matching expression="method='single'"/>
882 <has_text_matching expression="metric='braycurtis'"/> 1130 <has_text_matching expression="metric='euclidean'"/>
883 <has_text_matching expression="z_score=None"/>
884 <has_text_matching expression="standard_scale=None"/>
885 <has_text_matching expression="col_cluster=False"/> 1131 <has_text_matching expression="col_cluster=False"/>
886 <has_text_matching expression="row_cluster=False"/> 1132 <has_text_matching expression="row_cluster=False"/>
887 </assert_stdout> 1133 </assert_stdout>
888 <output name="out_png" file="pl.clustermap.krumsiek11.png" ftype="png" compare="sim_size"/> 1134 <output name="out_png" file="pl.clustermap.krumsiek11.png" ftype="png" compare="sim_size"/>
889 </test> 1135 </test>
890 <test> 1136 <test>
891 <!-- test pl.highest_expr_genes !--> 1137 <!-- test 9: pl.highest_expr_genes !-->
892 <conditional name="input"> 1138 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
893 <param name="format" value="h5ad" />
894 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
895 </conditional>
896 <param name="format" value="png"/> 1139 <param name="format" value="png"/>
897 <conditional name="method"> 1140 <conditional name="method">
898 <param name="method" value="pl.highest_expr_genes"/> 1141 <param name="method" value="pl.highest_expr_genes"/>
899 <param name="n_top" value="30"/> 1142 <param name="n_top" value="30"/>
900 <param name="gene_symbols" value="means"/> 1143 <param name="gene_symbols" value="means"/>
911 <has_text_matching expression="saturation=0.5"/> 1154 <has_text_matching expression="saturation=0.5"/>
912 </assert_stdout> 1155 </assert_stdout>
913 <output name="out_png" file="pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png" ftype="png" compare="sim_size"/> 1156 <output name="out_png" file="pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png" ftype="png" compare="sim_size"/>
914 </test> 1157 </test>
915 <test> 1158 <test>
916 <!-- test pl.pca !--> 1159 <!-- test 10: pl.highly_variable_genes !-->
917 <conditional name="input"> 1160 <param name="adata" value="pp.highly_variable_genes.seurat.blobs.h5ad" />
918 <param name="format" value="h5ad" /> 1161 <param name="format" value="png"/>
919 <param name="adata" value="pbmc68k_reduced.h5ad" /> 1162 <conditional name="method">
920 </conditional> 1163 <param name="method" value="pl.highly_variable_genes"/>
1164 <param name="log" value="false"/>
1165 <param name="highly_variable_genes" value="true"/>
1166 </conditional>
1167 <assert_stdout>
1168 <has_text_matching expression="sc.pl.highly_variable_genes"/>
1169 <has_text_matching expression="adata_or_result=adata" />
1170 <has_text_matching expression="log=False" />
1171 <has_text_matching expression="highly_variable_genes=True"/>
1172 </assert_stdout>
1173 <output name="out_png" file="pl.highly_variable_genes.seurat.blobs.png" ftype="png" compare="sim_size"/>
1174 </test>
1175 <test>
1176 <!-- test 11: pl.pca !-->
1177 <param name="adata" value="pbmc68k_reduced.h5ad" />
921 <param name="format" value="pdf"/> 1178 <param name="format" value="pdf"/>
922 <conditional name="method"> 1179 <conditional name="method">
923 <param name="method" value="pl.pca"/> 1180 <param name="method" value="pl.pca"/>
924 <param name="color" value="CD3D,CD79A"/> 1181 <param name="color" value="CD3D,CD79A"/>
925 <param name="use_raw" value="False"/> 1182 <param name="use_raw" value="False"/>
953 <has_text_matching expression="sc.pl.pca"/> 1210 <has_text_matching expression="sc.pl.pca"/>
954 <has_text_matching expression="save='.pdf'" /> 1211 <has_text_matching expression="save='.pdf'" />
955 <has_text_matching expression="color=\['CD3D', 'CD79A'\]" /> 1212 <has_text_matching expression="color=\['CD3D', 'CD79A'\]" />
956 <has_text_matching expression="use_raw=False" /> 1213 <has_text_matching expression="use_raw=False" />
957 <has_text_matching expression="sort_order=True" /> 1214 <has_text_matching expression="sort_order=True" />
958 <has_text_matching expression="groups=None" />
959 <has_text_matching expression="components=\['1,2', '1,3'\]" /> 1215 <has_text_matching expression="components=\['1,2', '1,3'\]" />
960 <has_text_matching expression="projection='2d'" /> 1216 <has_text_matching expression="projection='2d'" />
961 <has_text_matching expression="legend_loc='right margin'" /> 1217 <has_text_matching expression="legend_loc='right margin'" />
962 <has_text_matching expression="legend_fontsize=1" /> 1218 <has_text_matching expression="legend_fontsize=1" />
963 <has_text_matching expression="legend_fontweight='normal'" /> 1219 <has_text_matching expression="legend_fontweight='normal'" />
971 <has_text_matching expression="edgecolors='face" /> 1227 <has_text_matching expression="edgecolors='face" />
972 </assert_stdout> 1228 </assert_stdout>
973 <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/> 1229 <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/>
974 </test> 1230 </test>
975 <test> 1231 <test>
976 <!-- test pl.pca_loadings !--> 1232 <!-- test 12: pl.pca_loadings !-->
977 <conditional name="input"> 1233 <param name="adata" value="pp.pca.krumsiek11.h5ad" />
978 <param name="format" value="h5ad" />
979 <param name="adata" value="pp.pca.krumsiek11.h5ad" />
980 </conditional>
981 <param name="format" value="png"/> 1234 <param name="format" value="png"/>
982 <conditional name="method"> 1235 <conditional name="method">
983 <param name="method" value="pl.pca_loadings"/> 1236 <param name="method" value="pl.pca_loadings"/>
984 <param name="components" value="1,2,3"/> 1237 <param name="components" value="1,2,3"/>
985 </conditional> 1238 </conditional>
986 <assert_stdout> 1239 <assert_stdout>
987 <has_text_matching expression="sc.pl.pca_loadings"/> 1240 <has_text_matching expression="sc.pl.pca_loadings"/>
988 <has_text_matching expression="components=\[1, 2, 3\]" /> 1241 <has_text_matching expression="components=\[1, 2, 3\]" />
989 </assert_stdout> 1242 </assert_stdout>
990 <output name="out_png" file="pl.pca_loadings.pp.pca.krumsiek11.png"/> 1243 <output name="out_png" file="pl.pca_loadings.pp.pca.krumsiek11.png" compare="sim_size"/>
991 </test> 1244 </test>
992 <test> 1245 <test>
993 <!-- test pl.pca_variance_ratio !--> 1246 <!-- test 13: pl.pca_variance_ratio !-->
994 <conditional name="input"> 1247 <param name="adata" value="pp.pca.krumsiek11.h5ad" />
995 <param name="format" value="h5ad" />
996 <param name="adata" value="pp.pca.krumsiek11.h5ad" />
997 </conditional>
998 <param name="format" value="png"/> 1248 <param name="format" value="png"/>
999 <conditional name="method"> 1249 <conditional name="method">
1000 <param name="method" value="pl.pca_variance_ratio"/> 1250 <param name="method" value="pl.pca_variance_ratio"/>
1001 <param name="n_pcs" value="5"/> 1251 <param name="n_pcs" value="5"/>
1002 <param name="log" value="False"/> 1252 <param name="log" value="False"/>
1004 <assert_stdout> 1254 <assert_stdout>
1005 <has_text_matching expression="sc.pl.pca_variance_ratio"/> 1255 <has_text_matching expression="sc.pl.pca_variance_ratio"/>
1006 <has_text_matching expression="n_pcs=5" /> 1256 <has_text_matching expression="n_pcs=5" />
1007 <has_text_matching expression="log=False" /> 1257 <has_text_matching expression="log=False" />
1008 </assert_stdout> 1258 </assert_stdout>
1009 <output name="out_png" file="pl.pca_variance_ratio.pp.pca.krumsiek11.png"/> 1259 <output name="out_png" file="pl.pca_variance_ratio.pp.pca.krumsiek11.png" compare="sim_size"/>
1010 </test> 1260 </test>
1011 <test> 1261 <test>
1012 <!-- test pl.pca_overview !--> 1262 <!-- test 14: pl.pca_overview !-->
1013 <conditional name="input"> 1263 <param name="adata" value="pp.pca.krumsiek11.h5ad" />
1014 <param name="format" value="h5ad" />
1015 <param name="adata" value="pp.pca.krumsiek11.h5ad" />
1016 </conditional>
1017 <param name="format" value="png"/> 1264 <param name="format" value="png"/>
1018 <conditional name="method"> 1265 <conditional name="method">
1019 <param name="method" value="pl.pca_overview"/> 1266 <param name="method" value="pl.pca_overview"/>
1020 <param name="color" value="cell_type"/>
1021 <param name="use_raw" value="False"/> 1267 <param name="use_raw" value="False"/>
1022 <param name="sort_order" value="True"/> 1268 <param name="sort_order" value="True"/>
1023 <section name="plot"> 1269 <section name="plot">
1024 <param name="projection" value="3d"/> 1270 <param name="projection" value="2d"/>
1025 <param name="legend_loc" value="right margin"/> 1271 <param name="legend_loc" value="right margin"/>
1026 <param name="legend_fontsize" value="1"/> 1272 <param name="legend_fontsize" value="1"/>
1027 <param name="legend_fontweight" value="normal"/> 1273 <param name="legend_fontweight" value="normal"/>
1028 <param name="size" value="1"/> 1274 <param name="size" value="1"/>
1029 <param name="palette" value="viridis"/> 1275 <param name="palette" value="viridis"/>
1030 <param name="frameon" value="True"/> 1276 <param name="frameon" value="True"/>
1031 <param name="ncols" value="4"/> 1277 <param name="ncols" value="4"/>
1032 <param name="wspace" value="0.1"/> 1278 <param name="wspace" value="0.1"/>
1033 <param name="hspace" value="0.25"/> 1279 <param name="hspace" value="0.25"/>
1034 </section> 1280 </section>
1035 <section name="matplotlib_pyplot_scatter">
1036 <param name="linewidths" value="0"/>
1037 <param name="edgecolors" value="face"/>
1038 <param name="vmin" value="-5"/>
1039 <param name="vmax" value="5"/>
1040 <param name="edgecolors" value="face"/>
1041 </section>
1042 </conditional> 1281 </conditional>
1043 <assert_stdout> 1282 <assert_stdout>
1044 <has_text_matching expression="sc.pl.pca_overview"/> 1283 <has_text_matching expression="sc.pl.pca_overview"/>
1045 <has_text_matching expression="color=\['cell_type'\]"/>
1046 <has_text_matching expression="use_raw=False"/> 1284 <has_text_matching expression="use_raw=False"/>
1047 <has_text_matching expression="sort_order=True"/> 1285 <has_text_matching expression="sort_order=True"/>
1048 <has_text_matching expression="groups=None"/> 1286 <has_text_matching expression="projection='2d'"/>
1049 <has_text_matching expression="components=None"/>
1050 <has_text_matching expression="projection='3d'"/>
1051 <has_text_matching expression="legend_loc='right margin'"/> 1287 <has_text_matching expression="legend_loc='right margin'"/>
1052 <has_text_matching expression="legend_fontsize=1"/> 1288 <has_text_matching expression="legend_fontsize=1"/>
1053 <has_text_matching expression="legend_fontweight='normal'"/> 1289 <has_text_matching expression="legend_fontweight='normal'"/>
1054 <has_text_matching expression="size=1.0"/> 1290 <has_text_matching expression="size=1.0"/>
1055 <has_text_matching expression="palette='viridis'"/> 1291 <has_text_matching expression="palette='viridis'"/>
1056 <has_text_matching expression="frameon=True"/> 1292 <has_text_matching expression="frameon=True"/>
1057 <has_text_matching expression="ncols=4"/> 1293 <has_text_matching expression="ncols=4"/>
1058 <has_text_matching expression="wspace=0.1"/> 1294 <has_text_matching expression="wspace=0.1"/>
1059 <has_text_matching expression="hspace=0.25"/> 1295 <has_text_matching expression="hspace=0.25"/>
1060 <has_text_matching expression="vmin=-5.0"/>
1061 <has_text_matching expression="vmax=5.0"/>
1062 <has_text_matching expression="linewidths=0.0"/>
1063 <has_text_matching expression="edgecolors='face'"/>
1064 </assert_stdout> 1296 </assert_stdout>
1065 <output name="out_png" file="pl.pca_overview.pp.pca.krumsiek11.png" compare="sim_size"/> 1297 <output name="out_png" file="pl.pca_overview.pp.pca.krumsiek11.png" compare="sim_size"/>
1066 </test> 1298 </test>
1067 <test> 1299 <test>
1068 <!-- test pl.tsne !--> 1300 <!-- test 15: pl.tsne !-->
1069 <conditional name="input"> 1301 <param name="adata" value="tl.tsne.krumsiek11.h5ad" />
1070 <param name="format" value="h5ad" />
1071 <param name="adata" value="tl.tsne.krumsiek11.h5ad" />
1072 </conditional>
1073 <param name="format" value="png"/> 1302 <param name="format" value="png"/>
1074 <conditional name="method"> 1303 <conditional name="method">
1075 <param name="method" value="pl.tsne"/> 1304 <param name="method" value="pl.tsne"/>
1076 <param name="use_raw" value="False"/> 1305 <param name="use_raw" value="False"/>
1077 <conditional name="edges"> 1306 <conditional name="edges">
1096 <param name="edgecolors" value="face"/> 1325 <param name="edgecolors" value="face"/>
1097 </section> 1326 </section>
1098 </conditional> 1327 </conditional>
1099 <assert_stdout> 1328 <assert_stdout>
1100 <has_text_matching expression="sc.pl.tsne"/> 1329 <has_text_matching expression="sc.pl.tsne"/>
1101 <has_text_matching expression="color=None"/>
1102 <has_text_matching expression="use_raw=False"/> 1330 <has_text_matching expression="use_raw=False"/>
1103 <has_text_matching expression="edges=False"/> 1331 <has_text_matching expression="edges=False"/>
1104 <has_text_matching expression="arrows=False"/> 1332 <has_text_matching expression="arrows=False"/>
1105 <has_text_matching expression="sort_order=True"/> 1333 <has_text_matching expression="sort_order=True"/>
1106 <has_text_matching expression="groups=None"/>
1107 <has_text_matching expression="components=None"/>
1108 <has_text_matching expression="projection='2d'"/> 1334 <has_text_matching expression="projection='2d'"/>
1109 <has_text_matching expression="legend_loc='right margin'"/> 1335 <has_text_matching expression="legend_loc='right margin'"/>
1110 <has_text_matching expression="legend_fontsize=1"/> 1336 <has_text_matching expression="legend_fontsize=1"/>
1111 <has_text_matching expression="legend_fontweight='normal'"/> 1337 <has_text_matching expression="legend_fontweight='normal'"/>
1112 <has_text_matching expression="size=1.0"/> 1338 <has_text_matching expression="size=1.0"/>
1119 <has_text_matching expression="edgecolors='face'"/> 1345 <has_text_matching expression="edgecolors='face'"/>
1120 </assert_stdout> 1346 </assert_stdout>
1121 <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="sim_size"/> 1347 <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="sim_size"/>
1122 </test> 1348 </test>
1123 <test> 1349 <test>
1124 <!-- test pl.umap !--> 1350 <!-- test 16: pl.umap !-->
1125 <conditional name="input"> 1351 <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
1126 <param name="format" value="h5ad" />
1127 <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
1128 </conditional>
1129 <param name="format" value="png"/> 1352 <param name="format" value="png"/>
1130 <conditional name="method"> 1353 <conditional name="method">
1131 <param name="method" value="pl.umap"/> 1354 <param name="method" value="pl.umap"/>
1132 <param name="color" value="paul15_clusters"/> 1355 <param name="color" value="paul15_clusters"/>
1133 <param name="use_raw" value="False"/> 1356 <param name="use_raw" value="False"/>
1161 <has_text_matching expression="edges=True"/> 1384 <has_text_matching expression="edges=True"/>
1162 <has_text_matching expression="edges_width=0.1"/> 1385 <has_text_matching expression="edges_width=0.1"/>
1163 <has_text_matching expression="edges_color='AliceBlue'"/> 1386 <has_text_matching expression="edges_color='AliceBlue'"/>
1164 <has_text_matching expression="arrows=False"/> 1387 <has_text_matching expression="arrows=False"/>
1165 <has_text_matching expression="sort_order=True"/> 1388 <has_text_matching expression="sort_order=True"/>
1166 <has_text_matching expression="groups=None"/>
1167 <has_text_matching expression="components=None"/>
1168 <has_text_matching expression="projection='2d'"/> 1389 <has_text_matching expression="projection='2d'"/>
1169 <has_text_matching expression="legend_loc='right margin'"/> 1390 <has_text_matching expression="legend_loc='right margin'"/>
1170 <has_text_matching expression="legend_fontsize=1"/> 1391 <has_text_matching expression="legend_fontsize=1"/>
1171 <has_text_matching expression="legend_fontweight='normal'"/> 1392 <has_text_matching expression="legend_fontweight='normal'"/>
1172 <has_text_matching expression="size=1.0"/> 1393 <has_text_matching expression="size=1.0"/>
1179 <has_text_matching expression="edgecolors='face'"/> 1400 <has_text_matching expression="edgecolors='face'"/>
1180 </assert_stdout> 1401 </assert_stdout>
1181 <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/> 1402 <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
1182 </test> 1403 </test>
1183 <test> 1404 <test>
1184 <!-- test pl.diffmap !--> 1405 <!-- test 17: pl.diffmap !-->
1185 <conditional name="input"> 1406 <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
1186 <param name="format" value="h5ad" />
1187 <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
1188 </conditional>
1189 <param name="format" value="png"/> 1407 <param name="format" value="png"/>
1190 <conditional name="method"> 1408 <conditional name="method">
1191 <param name="method" value="pl.diffmap"/> 1409 <param name="method" value="pl.diffmap"/>
1192 <param name="color" value="paul15_clusters"/> 1410 <param name="color" value="paul15_clusters"/>
1193 <param name="use_raw" value="False"/> 1411 <param name="use_raw" value="False"/>
1212 <assert_stdout> 1430 <assert_stdout>
1213 <has_text_matching expression="sc.pl.diffmap"/> 1431 <has_text_matching expression="sc.pl.diffmap"/>
1214 <has_text_matching expression="color=\['paul15_clusters'\]"/> 1432 <has_text_matching expression="color=\['paul15_clusters'\]"/>
1215 <has_text_matching expression="use_raw=False"/> 1433 <has_text_matching expression="use_raw=False"/>
1216 <has_text_matching expression="sort_order=True"/> 1434 <has_text_matching expression="sort_order=True"/>
1217 <has_text_matching expression="groups=None"/>
1218 <has_text_matching expression="components=None"/>
1219 <has_text_matching expression="projection='2d'"/> 1435 <has_text_matching expression="projection='2d'"/>
1220 <has_text_matching expression="legend_loc='right margin'"/> 1436 <has_text_matching expression="legend_loc='right margin'"/>
1221 <has_text_matching expression="legend_fontsize=1"/> 1437 <has_text_matching expression="legend_fontsize=1"/>
1222 <has_text_matching expression="legend_fontweight='normal'"/> 1438 <has_text_matching expression="legend_fontweight='normal'"/>
1223 <has_text_matching expression="size=1.0"/> 1439 <has_text_matching expression="size=1.0"/>
1229 <has_text_matching expression="linewidths=0.0"/> 1445 <has_text_matching expression="linewidths=0.0"/>
1230 <has_text_matching expression="edgecolors='face'"/> 1446 <has_text_matching expression="edgecolors='face'"/>
1231 </assert_stdout> 1447 </assert_stdout>
1232 <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/> 1448 <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
1233 </test> 1449 </test>
1450 <test>
1451 <!-- test 18: pl.draw_graph !-->
1452 <param name="adata" value="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
1453 <param name="format" value="png"/>
1454 <conditional name="method">
1455 <param name="method" value="pl.draw_graph"/>
1456 <param name="use_raw" value="false"/>
1457 <conditional name="edges">
1458 <param name="edges" value="True"/>
1459 <param name="edges_width" value="0.1"/>
1460 <param name="edges_color" value="Crimson"/>
1461 </conditional>
1462 <param name="arrows" value="false"/>
1463 <param name="sort_order" value="false"/>
1464 <section name="plot">
1465 <param name="projection" value="2d"/>
1466 <param name="legend_loc" value="right margin"/>
1467 <param name="legend_fontweight" value="normal"/>
1468 <param name="palette" value="viridis"/>
1469 <param name="frameon" value="True"/>
1470 <param name="ncols" value="4"/>
1471 <param name="wspace" value="0.1"/>
1472 <param name="hspace" value="0.25"/>
1473 </section>
1474 <section name="matplotlib_pyplot_scatter">
1475 <param name="linewidths" value="0"/>
1476 <param name="edgecolors" value="face"/>
1477 </section>
1478 </conditional>
1479 <assert_stdout>
1480 <has_text_matching expression="sc.pl.draw_graph"/>
1481 <has_text_matching expression="use_raw=False"/>
1482 <has_text_matching expression="edges=True"/>
1483 <has_text_matching expression="edges_width=0.1"/>
1484 <has_text_matching expression="edges_color='Crimson'"/>
1485 <has_text_matching expression="arrows=False"/>
1486 <has_text_matching expression="sort_order=False"/>
1487 <has_text_matching expression="projection='2d'"/>
1488 <has_text_matching expression="legend_loc='right margin'"/>
1489 <has_text_matching expression="legend_fontweight='normal'"/>
1490 <has_text_matching expression="palette='viridis'"/>
1491 <has_text_matching expression="frameon=True"/>
1492 <has_text_matching expression="ncols=4"/>
1493 <has_text_matching expression="wspace=0.1"/>
1494 <has_text_matching expression="hspace=0.25"/>
1495 <has_text_matching expression="linewidths=0.0"/>
1496 <has_text_matching expression="edgecolors='face"/>
1497 </assert_stdout>
1498 <output name="out_png" file="pl.draw_graph.png" ftype="png" compare="sim_size"/>
1499 </test>
1234 <!--<test> 1500 <!--<test>
1235 < test pl.dpt_groups_pseudotime > 1501 < test pl.dpt_groups_pseudotime >
1236 <conditional name="input"> 1502 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
1237 <param name="format" value="h5ad" />
1238 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
1239 </conditional>
1240 <param name="format" value="png"/> 1503 <param name="format" value="png"/>
1241 <conditional name="method"> 1504 <conditional name="method">
1242 <param name="method" value="pl.dpt_groups_pseudotime"/> 1505 <param name="method" value="pl.dpt_groups_pseudotime"/>
1243 <param name="color_map" value="viridis"/> 1506 <param name="color_map" value="viridis"/>
1244 </conditional> 1507 </conditional>
1247 <has_text_matching expression="color_map='viridis'"/> 1510 <has_text_matching expression="color_map='viridis'"/>
1248 </assert_stdout> 1511 </assert_stdout>
1249 <output name="out_png" file="pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/> 1512 <output name="out_png" file="pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
1250 </test>!--> 1513 </test>!-->
1251 <test> 1514 <test>
1252 <!-- test pl.dpt_timeseries !--> 1515 <!-- test 19: pl.dpt_timeseries !-->
1253 <conditional name="input"> 1516 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
1254 <param name="format" value="h5ad" />
1255 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
1256 </conditional>
1257 <param name="format" value="png"/> 1517 <param name="format" value="png"/>
1258 <conditional name="method"> 1518 <conditional name="method">
1259 <param name="method" value="pl.dpt_timeseries"/> 1519 <param name="method" value="pl.dpt_timeseries"/>
1260 <conditional name="heatmap"> 1520 <conditional name="heatmap">
1261 <param name="as_heatmap" value="True"/> 1521 <param name="as_heatmap" value="True"/>
1269 </assert_stdout> 1529 </assert_stdout>
1270 <output name="out_png" file="pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/> 1530 <output name="out_png" file="pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
1271 </test> 1531 </test>
1272 <!--<test> 1532 <!--<test>
1273 test pl.paga 1533 test pl.paga
1274 <conditional name="input"> 1534 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad" />
1275 <param name="format" value="h5ad" />
1276 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad" />
1277 </conditional>
1278 <param name="format" value="png"/> 1535 <param name="format" value="png"/>
1279 <conditional name="method"> 1536 <conditional name="method">
1280 <param name="method" value="pl.paga"/> 1537 <param name="method" value="pl.paga"/>
1281 <param name="threshold" value="0.01"/> 1538 <param name="threshold" value="0.01"/>
1282 <param name="color" value="paul15_clusters"/> 1539 <param name="color" value="paul15_clusters"/>
1294 <param name="cmap" value="viridis"/> 1551 <param name="cmap" value="viridis"/>
1295 <param name="frameon" value="True"/> 1552 <param name="frameon" value="True"/>
1296 </conditional> 1553 </conditional>
1297 <output name="out_png" file="pl.paga.paul15_gauss_braycurtis.png" ftype="png" compare="sim_size"/> 1554 <output name="out_png" file="pl.paga.paul15_gauss_braycurtis.png" ftype="png" compare="sim_size"/>
1298 </test>!--> 1555 </test>!-->
1556 <!--<test>
1557 test pl.paga_compare
1558 </test>!-->
1559 <!--<test>
1560 test pl.paga_path
1561 </test>!-->
1562 <test>
1563 <!-- test 20: pl.rank_genes_groups !-->
1564 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
1565 <param name="format" value="png"/>
1566 <conditional name="method">
1567 <param name="method" value="pl.rank_genes_groups"/>
1568 <param name="n_genes" value="10"/>
1569 <param name="fontsize" value="8"/>
1570 <param name="ncols" value="4"/>
1571 <param name="sharey" value="true"/>
1572 </conditional>
1573 <assert_stdout>
1574 <has_text_matching expression="sc.pl.rank_genes_groups"/>
1575 <has_text_matching expression="n_genes=10"/>
1576 <has_text_matching expression="fontsize=8"/>
1577 <has_text_matching expression="ncols=4"/>
1578 <has_text_matching expression="sharey=True"/>
1579 </assert_stdout>
1580 <output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
1581 </test>
1582 <test>
1583 <!-- test 21: pl.rank_genes_groups_violin !-->
1584 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
1585 <param name="format" value="png"/>
1586 <conditional name="method">
1587 <param name="method" value="pl.rank_genes_groups_violin"/>
1588 <conditional name="genes">
1589 <param name="select" value="n_genes"/>
1590 <param name="n_genes" value="10"/>
1591 </conditional>
1592 <param name="use_raw" value="false"/>
1593 <param name="split" value="true"/>
1594 <section name="violin_plot">
1595 <conditional name="stripplot">
1596 <param name="stripplot" value="True"/>
1597 <param name="jitter" value="True"/>
1598 <param name="size" value="1"/>
1599 </conditional>
1600 <param name="scale" value="width"/>
1601 </section>
1602 </conditional>
1603 <assert_stdout>
1604 <has_text_matching expression="sc.pl.rank_genes_groups_violin"/>
1605 <has_text_matching expression="n_genes=10"/>
1606 <has_text_matching expression="use_raw=False"/>
1607 <has_text_matching expression="split=True"/>
1608 <has_text_matching expression="strip=True"/>
1609 <has_text_matching expression="jitter=True"/>
1610 <has_text_matching expression="size=1"/>
1611 <has_text_matching expression="scale='width'"/>
1612 </assert_stdout>
1613 <output_collection name="collection_png">
1614 <element name="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"/>
1616 <element name="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"/>
1618 <element name="progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="sim_size"/>
1619 </output_collection>
1620 </test>
1299 </tests> 1621 </tests>
1300 <help><![CDATA[ 1622 <help><![CDATA[
1301 Generic: Scatter plot along observations or variables axes (`pl.scatter`) 1623 Generic: Scatter plot along observations or variables axes (`pl.scatter`)
1302 ========================================================================= 1624 =========================================================================
1303 1625
1340 ================================== 1662 ==================================
1341 1663
1342 Wraps `seaborn.violinplot` for `anndata.AnnData`. 1664 Wraps `seaborn.violinplot` for `anndata.AnnData`.
1343 1665
1344 More details on the `scanpy documentation 1666 More details on the `scanpy documentation
1667 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.violin.html>`__
1668
1669 Generic: Stacked violin plots (`pl.stacked_violin`)
1670 ===================================================
1671
1672 Makes a compact image composed of individual violin plots (from `seaborn.violinplot`)
1673 stacked on top of each other. Useful to visualize gene expression per cluster.
1674
1675 More details on the `scanpy documentation
1345 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.stacked_violin.html>`__ 1676 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.stacked_violin.html>`__
1346 1677
1347 Generic: Heatmap of the mean expression values per cluster (`pl.matrixplot`) 1678 Generic: Heatmap of the mean expression values per cluster (`pl.matrixplot`)
1348 ============================================================================ 1679 ============================================================================
1349 1680
1351 1682
1352 If groupby is not given, the matrixplot assumes that all data belongs to a single 1683 If groupby is not given, the matrixplot assumes that all data belongs to a single
1353 category. 1684 category.
1354 1685
1355 More details on the `scanpy documentation 1686 More details on the `scanpy documentation
1356 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.matrixplot.html>`__ 1687 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.matrixplot.html>`__
1357 1688
1358 Generic: Hierarchically-clustered heatmap (`pl.clustermap`) 1689 Generic: Hierarchically-clustered heatmap (`pl.clustermap`)
1359 =========================================================== 1690 ===========================================================
1360 1691
1361 Wraps `seaborn.clustermap 1692 Wraps `seaborn.clustermap
1369 clustergrid.dendrogram_row.reordered_ind 1700 clustergrid.dendrogram_row.reordered_ind
1370 1701
1371 Column indices, use: clustergrid.dendrogram_col.reordered_ind 1702 Column indices, use: clustergrid.dendrogram_col.reordered_ind
1372 1703
1373 More details on the `scanpy documentation 1704 More details on the `scanpy documentation
1374 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.clustermap.html>`__ 1705 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.clustermap.html>`__
1375 1706
1376 Preprocessing: Plot the fraction of counts assigned to each gene over all cells (`pl.highest_expr_genes`) 1707 Preprocessing: Plot the fraction of counts assigned to each gene over all cells (`pl.highest_expr_genes`)
1377 ========================================================================================================= 1708 =========================================================================================================
1378 1709
1379 Computes, for each gene, the fraction of counts assigned to that gene within 1710 Computes, for each gene, the fraction of counts assigned to that gene within
1380 a cell. The `n_top` genes with the highest mean fraction over all cells are 1711 a cell. The `n_top` genes with the highest mean fraction over all cells are
1381 plotted as boxplots. 1712 plotted as boxplots.
1382 1713
1383 This plot is similar to the `scater` package function `plotHighestExprs(type= "highest-expression")`, see `here 1714 This plot is similar to the `scater` package function `plotHighestExprs(type= "highest-expression")`
1384 <https://bioconductor.org/packages/devel/bioc/vignettes/scater/inst/doc/vignette-qc.html>`__. 1715
1385 -- Davis McCarthy and Aaron Lun 1716 More details on the `scanpy documentation
1386 1717 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.highest_expr_genes.html>`__
1387 More details on the `scanpy documentation 1718
1388 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.highest_expr_genes.html>`__ 1719 Preprocessing: Plot dispersions versus means for genes (`pl.highly_variable_genes`)
1720 ===================================================================================
1721
1722 It produces Supp. Fig. 5c of Zheng et al. (2017) and MeanVarPlot() of Seurat.
1723
1724 More details on the `scanpy documentation
1725 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.highly_variable_genes.html>`__
1389 1726
1390 PCA: Scatter plot in PCA coordinates (`pl.pca`) 1727 PCA: Scatter plot in PCA coordinates (`pl.pca`)
1391 =============================================== 1728 ===============================================
1392 1729
1393 More details on the `scanpy documentation 1730 More details on the `scanpy documentation
1394 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.pca.html>`__ 1731 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca.html>`__
1395 1732
1396 PCA: Rank genes according to contributions to PCs (`pl.pca_loadings`) 1733 PCA: Rank genes according to contributions to PCs (`pl.pca_loadings`)
1397 ===================================================================== 1734 =====================================================================
1398 1735
1399 More details on the `scanpy documentation 1736 More details on the `scanpy documentation
1400 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.pca_loadings.html>`__ 1737 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca_loadings.html>`__
1401 1738
1402 PCA: Plot the variance ratio (`pl.pca_variance_ratio`) 1739 PCA: Plot the variance ratio (`pl.pca_variance_ratio`)
1403 ====================================================== 1740 ======================================================
1404 1741
1405 More details on the `scanpy documentation 1742 More details on the `scanpy documentation
1406 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.pca_variance_ratio.html>`__ 1743 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca_variance_ratio.html>`__
1407 1744
1408 PCA: Plot PCA results (`pl.pca_overview`) 1745 PCA: Plot PCA results (`pl.pca_overview`)
1409 ========================================= 1746 =========================================
1410 1747
1411 The parameters are the ones of the scatter plot. Call pca_ranking separately 1748 The parameters are the ones of the scatter plot. Call pca_ranking separately
1412 if you want to change the default settings. 1749 if you want to change the default settings.
1413 1750
1414 More details on the `scanpy documentation 1751 More details on the `scanpy documentation
1415 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.pca_overview.html>`__ 1752 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca_overview.html>`__
1416 1753
1417 Embedding: Scatter plot in tSNE basis (`pl.tsne`) 1754 Embedding: Scatter plot in tSNE basis (`pl.tsne`)
1418 ================================================= 1755 =================================================
1419 1756
1420 More details on the `scanpy documentation 1757 More details on the `scanpy documentation
1421 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.tsne.html>`__ 1758 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.tsne.html>`__
1422 1759
1423 Embeddings: Scatter plot in UMAP basis (`pl.umap`) 1760 Embeddings: Scatter plot in UMAP basis (`pl.umap`)
1424 ================================================== 1761 ==================================================
1425 1762
1426 More details on the `scanpy documentation 1763 More details on the `scanpy documentation
1427 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.umap.html>`__ 1764 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.umap.html>`__
1428 1765
1429 Embeddings: Scatter plot in Diffusion Map basis (`pl.diffmap`) 1766 Embeddings: Scatter plot in Diffusion Map basis (`pl.diffmap`)
1430 ============================================================== 1767 ==============================================================
1431 1768
1432 More details on the `scanpy documentation 1769 More details on the `scanpy documentation
1433 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.diffmap.html>`__ 1770 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.diffmap.html>`__
1434 1771
1435 Branching trajectories and pseudotime, clustering: Plot groups and pseudotime (`pl.dpt_groups_pseudotime`) 1772 Branching trajectories and pseudotime, clustering: Plot groups and pseudotime (`pl.dpt_groups_pseudotime`)
1436 =========================================================================================================== 1773 ===========================================================================================================
1437 1774
1438 More details on the `scanpy documentation 1775 More details on the `scanpy documentation
1439 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.dpt_groups_pseudotime.html>`__ 1776 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.dpt_groups_pseudotime.html>`__
1440 1777
1441 Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series (`pl.dpt_timeseries`) 1778 Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series (`pl.dpt_timeseries`)
1442 ===================================================================================================== 1779 =====================================================================================================
1443 1780
1444 More details on the `scanpy documentation 1781 More details on the `scanpy documentation
1445 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.dpt_timeseries.html>`__ 1782 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.dpt_timeseries.html>`__
1446 1783
1447 1784
1448 Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges (`pl.paga`) 1785 Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges (`pl.paga`)
1449 ==================================================================================================================================== 1786 ====================================================================================================================================
1450 1787
1453 When initializing the positions, note that - for some reason - igraph 1790 When initializing the positions, note that - for some reason - igraph
1454 mirrors coordinates along the x axis... that is, you should increase the 1791 mirrors coordinates along the x axis... that is, you should increase the
1455 `maxiter` parameter by 1 if the layout is flipped. 1792 `maxiter` parameter by 1 if the layout is flipped.
1456 1793
1457 More details on the `scanpy documentation 1794 More details on the `scanpy documentation
1458 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.paga.html>`__ 1795 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.paga.html>`__
1459 1796
1460 1797
1798 Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side (`pl.paga_compare`)
1799 ==========================================================================================================
1800
1801 More details on the `scanpy documentation
1802 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.paga_compare.html>`__
1803
1804 Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths (`pl.paga_path`)
1805 ======================================================================================================================
1806
1807 More details on the `scanpy documentation
1808 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.paga_path.html>`__
1809
1810 Marker genes: Plot ranking of genes using dotplot plot (`pl.rank_genes_groups`)
1811 ===============================================================================
1812
1813 More details on the `scanpy documentation
1814 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups.html>`__
1815
1816 Marker genes: Plot ranking of genes for all tested comparisons (`pl.rank_genes_groups_violin`)
1817 ==============================================================================================
1818
1819 More details on the `scanpy documentation
1820 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_violin.html>`__
1461 ]]></help> 1821 ]]></help>
1462 <expand macro="citations"/> 1822 <expand macro="citations"/>
1463 </tool> 1823 </tool>