scanpy_plot: plot.xml comparison

comparison plot.xml @ 11:95777145cb92 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d

author	iuc
date	Wed, 08 Nov 2023 14:47:20 +0000
parents	aa0c474463c2
children	9b0cdb8cf6be

comparison

equal deleted inserted replaced

-:aa0c474463c2
+:95777145cb92
-<tool id="scanpy_plot" name="Plot" version="1.7.1+galaxy1" profile="@profile@">
+<tool id="scanpy_plot" name="Plot" version="@galaxy_version@" profile="@profile@">
 <description> with scanpy</description>
-<expand macro="bio_tools"/>
 <macros>
 <import>macros.xml</import>
 </macros>
+<expand macro="bio_tools"/>
 <expand macro="requirements"/>
 <stdio>
 <regex match="... storing" source="stderr" level="warning"/>
 </stdio>
 <expand macro="version_command"/>
 sc.settings.figdir = '.'
 #if $method.method == 'pl.scatter'
+#if $method.type.type == 'xy':
+x_field='$method.type.x'
+y_field='$method.type.y'
+#if $method.type.log:
+if x_field in adata.obs or x_field in adata.var:
+if x_field in adata.obs:
+adata.obs[f"log_{x_field}"] = np.log10(adata.obs[x_field])
+elif x_field in adata.var:
+adata.var[f"log_{x_field}"] = np.log10(adata.var[x_field])
+x_field=f"log_{x_field}"
+if y_field in adata.obs or y_field in adata.var:
+if y_field in adata.obs:
+adata.obs[f"log_{y_field}"] = np.log10(adata.obs[y_field])
+elif y_field in adata.var:
+adata.var[f"log_{y_field}"] = np.log10(adata.var[y_field])
+y_field=f"log_{y_field}"
+#end if
+#end if
 sc.pl.scatter(
 @CMD_param_plot_inputs@
-#if $method.type.type == 'xy'
+#if $method.type.type == 'xy':
-x='$method.type.x',
+x=x_field,
-y='$method.type.y',
+y=y_field,
 #if str($method.type.color) != ''
 color='$method.type.color',
 	  #end if
 #if str('$method.type.layers.use_layers') == 'true'
 layers=('$method.type.layers.layer_x', '$method.type.layers.layer_y', '$method.type.layers.layer_color'),
 @CMD_params_groups@
 @CMD_params_pl_components@
 @CMD_pl_attribute_section@
 @CMD_params_matplotlib_pyplot_scatter@)
+#else if $method.method == 'pl.embedding_density'
+sc.pl.embedding_density(
+@CMD_param_plot_inputs@
+basis='$method.basis',
+#if str($method.key) != ''
+key='$method.key',
+#end if
+#if str($method.groupby) != ''
+groupby='$method.groupby',
+#end if
+#if str($method.group) != ''
+#set $group = ([x.strip() for x in str($method.group).split(',')])
+group=$group,
+#end if
+#if str($method.color_map) != ''
+color_map='$method.color_map',
+#end if
+bg_dotsize=$method.bg_dotsize,
+fg_dotsize=$method.fg_dotsize,
+ncols=$method.ncols,
+wspace=$method.wspace,
+hspace=$method.hspace)
 #else if $method.method == 'pl.dpt_groups_pseudotime'
 sc.pl.dpt_groups_pseudotime(
 @CMD_param_plot_inputs@
 #if str($method.color_map) != ''
 color_map='$method.color_map'
 use_raw=$method.use_raw,
 #if str($method.annotations) != ''
 #set $annotations=([x.strip() for x in str($method.annotations).split(',')])
 annotations=$annotations,
 #end if
-#if str($method.color_map) != ''
+#if str($method.color_map) != 'None'
 color_map='$method.color_map',
 #end if
 n_avg=$method.n_avg,
 #if str($method.annotations) != ''
 groups_key='$method.groups_key',
 #else if $method.method == 'pl.rank_genes_groups_dotplot'
 sc.pl.rank_genes_groups_dotplot(
 @CMD_param_plot_inputs@
 @CMD_pl_rank_genes_groups_ext@
+#if str($method.gene_symbols) != ''
+gene_symbols='$method.gene_symbols',
+#end if
 @CMD_params_plots@
 @CMD_pl_dotplot@)
 #else if $method.method == 'pl.rank_genes_groups_heatmap'
 sc.pl.rank_genes_groups_heatmap(
 @CMD_param_plot_inputs@
 @CMD_pl_rank_genes_groups_ext@
 @CMD_params_plots@
+#if str($method.gene_symbols) != ''
+gene_symbols='$method.gene_symbols',
+#end if
 @CMD_pl_heatmap@)
 #else if $method.method == 'pl.rank_genes_groups_matrixplot'
 sc.pl.rank_genes_groups_matrixplot(
 @CMD_param_plot_inputs@
 @CMD_pl_rank_genes_groups_ext@
 @CMD_params_plots@
+#if str($method.gene_symbols) != ''
+gene_symbols='$method.gene_symbols',
+#end if
 @CMD_pl_matrixplot@)
 #else if $method.method == 'pl.rank_genes_groups_stacked_violin'
 sc.pl.rank_genes_groups_stacked_violin(
 @CMD_param_plot_inputs@
 @CMD_pl_rank_genes_groups_ext@
 @CMD_params_plots@
+#if str($method.gene_symbols) != ''
+gene_symbols='$method.gene_symbols',
+#end if
 @CMD_pl_stacked_violin@)
 #end if
 ]]></configfile>
 </configfiles>
 <option value="pl.dotplot">Generic: Makes a dot plot of the expression values, using 'pl.dotplot'</option>
 <option value="pl.violin">Generic: Violin plot, using 'pl.violin'</option>
 <option value="pl.stacked_violin">Generic: Stacked violin plots, using 'pl.stacked_violin'</option>
 <option value="pl.matrixplot">Generic: Heatmap of the mean expression values per cluster, using 'pl.matrixplot'</option>
 <option value="pl.clustermap">Generic: Hierarchically-clustered heatmap, using 'pl.clustermap'</option>
-<!--<option value="pl.ranking">Generic: </option>!-->
 <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>
 <!--<option value="pl.filter_genes_dispersion">Preprocessing: Plot dispersions versus means for genes, using 'pl.filter_genes_dispersion'</option>-->
 <option value="pl.highly_variable_genes">Preprocessing: Plot dispersions versus means for genes, using 'pl.highly_variable_genes'</option>
 <option value="pl.pca">PCA: Scatter plot in PCA coordinates, using 'pl.pca'</option>
 <option value="pl.pca_loadings">PCA: Rank genes according to contributions to PCs, using 'pl.pca_loadings'</option>
 <option value="pl.pca_overview">PCA: Plot PCA results, using 'pl.pca_overview'</option>
 <option value="pl.tsne">Embeddings: Scatter plot in tSNE basis, using 'pl.tsne'</option>
 <option value="pl.umap">Embeddings: Scatter plot in UMAP basis, using 'pl.umap'</option>
 <option value="pl.diffmap">Embeddings: Scatter plot in Diffusion Map basis, using 'pl.diffmap'</option>
 <option value="pl.draw_graph">Embeddings: Scatter plot in graph-drawing basis, using 'pl.draw_graph'</option>
+<option value="pl.embedding_density">Embeddings: Plot the density of cells in an embedding (per condition), using 'pl.embedding_density'</option>
 <option value="pl.dpt_groups_pseudotime">Branching trajectories and pseudotime, clustering: Plot groups and pseudotime, using 'pl.dpt_groups_pseudotime'</option>
 <option value="pl.dpt_timeseries">Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series, using 'pl.dpt_timeseries'</option>
 <option value="pl.paga">Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges, using 'pl.paga'</option>
 <option value="pl.paga_compare">Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side, using 'pl.paga_compare'</option>
 <option value="pl.paga_path">Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths, using 'pl.paga_path'</option>
 <option value="pl.rank_genes_groups">Marker genes: Plot ranking of genes using dotplot plot, using 'pl.rank_genes_groups'</option>
-<!-- doesn't currenty work: https://github.com/galaxyproject/tools-iuc/pull/3485#issuecomment-800055967
 <option value="pl.rank_genes_groups_violin">Marker genes: Plot ranking of genes as violin plot, using 'pl.rank_genes_groups_violin'</option>
--->
 <option value="pl.rank_genes_groups_dotplot">Marker genes: Plot ranking of genes as dotplot plot, using 'pl.rank_genes_groups_dotplot'</option>
 <option value="pl.rank_genes_groups_heatmap">Marker genes: Plot ranking of genes as heatmap plot, using 'pl.rank_genes_groups_heatmap'</option>
 <option value="pl.rank_genes_groups_matrixplot">Marker genes: Plot ranking of genes as matrixplot plot, using 'pl.rank_genes_groups_matrixplot'</option>
 <option value="pl.rank_genes_groups_stacked_violin">Marker genes: Plot ranking of genes as stacked violin plot, using 'pl.rank_genes_groups_stacked_violin'</option>
 </param>
 <expand macro="sanitize_query" />
 </param>
 <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either '.obs' or '.var'">
 <expand macro="sanitize_query" />
 </param>
+<expand macro="param_log"/>
 <param argument="color" type="text" value="" label="Color by" help="Color points by single variable in `.obs` or `.var`">
 <expand macro="sanitize_query" />
 </param>
 <conditional name="layers">
 <param argument="use_layers" type="select" label="Use the layers attribute?">
 <expand macro="param_sort_order"/>
 <expand macro="param_groups"/>
 <expand macro="pl_attribute_section"/>
 <expand macro="section_matplotlib_pyplot_scatter"/>
 </when>
+<when value="pl.embedding_density">
+<param argument="basis" type="text" value="umap" label="The embedding over which the density was calculated." help="This embedded representation should be found in adata.obsm['X_[basis]']">
+<expand macro="sanitize_query" />
+</param>
+<param argument="key" type="text" optional="true" value="" label="Name of the .obs covariate that contains the density estimates" help="Alternatively, pass _groupby_.">
+<expand macro="sanitize_query" />
+</param>
+<param argument="groupby" type="text" optional="true" value="" label="Name of the condition used in tl.embedding_density" help="Alternatively, pass _key_.">
+<expand macro="sanitize_query" />
+</param>
+<param argument="group" type="text" optional="all" value="" label="The category in the categorical observation annotation to be plotted"
+help="For example, 'G1' in the cell cycle 'phase' covariate. If multiple categories want to be plotted use a comma separated list">
+<expand macro="sanitize_query" />
+</param>
+<expand macro="param_color_map"/>
+<param argument="bg_dotsize" type="integer" min="0" value="80" label="Dot size for background data points not in the group"/>
+<param argument="fg_dotsize" type="integer" min="0" value="180" label="Dot size for foreground data points in the group"/>
+<expand macro="param_ncols"/>
+<expand macro="param_wspace"/>
+<expand macro="param_hspace"/>
+</when>
 <when value="pl.dpt_groups_pseudotime">
 <expand macro="param_color_map"/>
 </when>
 <when value="pl.dpt_timeseries">
 <conditional name="heatmap">
 <when value="n_genes">
 <expand macro="param_n_genes"/>
 </when>
 <when value="gene_names">
 <param argument="gene_names" type="text" value="" label="List of genes to plot" help="A list of comma-separated names">
 <expand macro="sanitize_query" />
 </param>
 </when>
 </conditional>
 <expand macro="gene_symbols"/>
 <expand macro="param_use_raw"/>
 </section>
 </when>
 <when value="pl.rank_genes_groups_dotplot">
 <expand macro="pl_rank_genes_groups_ext"/>
 <expand macro="params_plots"/>
+<expand macro="gene_symbols"/>
 <expand macro="pl_dotplot"/>
 </when>
 <when value="pl.rank_genes_groups_heatmap">
 <expand macro="pl_rank_genes_groups_ext"/>
 <expand macro="params_plots"/>
+<expand macro="gene_symbols"/>
 <expand macro="pl_heatmap"/>
 </when>
 <when value="pl.rank_genes_groups_matrixplot">
 <expand macro="pl_rank_genes_groups_ext"/>
 <expand macro="params_plots"/>
+<expand macro="gene_symbols"/>
 <expand macro="pl_matrixplot"/>
 </when>
 <when value="pl.rank_genes_groups_stacked_violin">
 <expand macro="pl_rank_genes_groups_ext"/>
 <expand macro="params_plots"/>
+<expand macro="gene_symbols"/>
 <expand macro="pl_stacked_violin"/>
 </when>
 </conditional>
 <expand macro="inputs_common_advanced"/>
 </inputs>
 <outputs>
-<data name="out_png" format="png" from_work_dir="*.png" label="${tool.name} (${method.method}) on ${on_string}">
+<data name="out_png" format="png" from_work_dir="*.png" label="PNG plot from ${tool.name} (${method.method}) on ${on_string}">
 <filter>format == 'png' and method['method'] != 'pl.rank_genes_groups_violin'</filter>
 </data>
-<collection name="collection_png" type="list" label="${tool.name} (${method.method}) on ${on_string}">
+<collection name="collection_png" type="list" label="PNG plots from ${tool.name} (${method.method}) on ${on_string}">
 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).png" format="png"/>
 <filter>format == 'png' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
 </collection>
-<data name="out_pdf" format="pdf" from_work_dir="*.pdf" label="${tool.name} (${method.method}) on ${on_string}">
+<data name="out_pdf" format="pdf" from_work_dir="*.pdf" label="PDF plot from ${tool.name} (${method.method}) on ${on_string}">
-<filter>format == 'pdf' and method['method'] != pl.rank_genes_groups_violin</filter>
+<filter>format == 'pdf' and method['method'] != 'pl.rank_genes_groups_violin'</filter>
 </data>
-<collection name="collection_pdf" type="list" label="${tool.name} (${method.method}) on ${on_string}">
+<collection name="collection_pdf" type="list" label="PDF plots from ${tool.name} (${method.method}) on ${on_string}">
 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).pdf" format="pdf"/>
 <filter>format == 'pdf' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
 </collection>
-<data name="out_svg" format="svg" from_work_dir="*.svg" label="${tool.name} (${method.method}) on ${on_string}">
+<data name="out_svg" format="svg" from_work_dir="*.svg" label="SVG plot from ${tool.name} (${method.method}) on ${on_string}">
 <filter>format == 'svg' and method['method'] != pl.rank_genes_groups_violin</filter>
 </data>
-<collection name="collection_svg" type="list" label="${tool.name} (${method.method}) on ${on_string}">
+<collection name="collection_svg" type="list" label="SVG plots from ${tool.name} (${method.method}) on ${on_string}">
 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).svg" format="svg"/>
 <filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
 </collection>
 <data name="hidden_output" format="txt" label="Log file" hidden="true" >
 <filter>advanced_common['show_log']</filter>
 </data>
 </outputs>
 <tests>
-<test>
+<test expect_num_outputs="2">
-<!-- test 0: pl.scatter !-->
+<!-- test 1: pl.scatter -->
 <param name="adata" value="pbmc68k_reduced.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.scatter"/>
 <conditional name="type">
 <has_text_matching expression="size=1.0"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 1: pl.scatter !-->
+<!-- test 2: pl.scatter -->
 <param name="adata" value="krumsiek11.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.scatter"/>
 <conditional name="type">
 <param name="show_log" value="true" />
 </section>
 <output name="hidden_output">
 <assert_contents>
 <has_text_matching expression="sc.pl.scatter"/>
-<has_text_matching expression="x='EKLF'" />
+<has_text_matching expression="x_field='EKLF'" />
-<has_text_matching expression="y='Cebpa'"/>
+<has_text_matching expression="y_field='Cebpa'"/>
 <has_text_matching expression="use_raw=False"/>
 <has_text_matching expression="sort_order=True"/>
 <has_text_matching expression="projection='2d'"/>
 <has_text_matching expression="legend_loc='right margin'"/>
 <has_text_matching expression="legend_fontsize=1"/>
 <has_text_matching expression="title='A title'"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.scatter.krumsiek11.png" ftype="png" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 2: pl.heatmap !-->
+<!-- test 3: pl.heatmap -->
 <param name="adata" value="krumsiek11.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.heatmap"/>
 <conditional name="var_names">
 <has_text_matching expression="origin='upper'"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 2.1: pl.heatmap with symbols !-->
+<!-- test 4: pl.heatmap with symbols -->
 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.heatmap"/>
 <conditional name="var_names">
 <has_text_matching expression="cmap='YlGnBu'"/>
 <has_text_matching expression="origin='upper'"/>
 </assert_contents>
 </output>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 3: pl.dotplot !-->
+<!-- test 5: pl.dotplot -->
 <param name="adata" value="pbmc68k_reduced.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.dotplot"/>
 <conditional name="var_names">
 <has_text_matching expression="edgecolors='face'"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 3.1: pl.dotplot with symbols !-->
+<!-- test 6: pl.dotplot with symbols -->
 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.dotplot"/>
 <conditional name="var_names">
 <has_text_matching expression="num_categories=7"/>
 <has_text_matching expression="dendrogram=True"/>
 </assert_contents>
 </output>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 4: pl.violin !-->
+<!-- test 7: pl.violin -->
 <param name="adata" value="pbmc68k_reduced.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.violin"/>
 <conditional name="key_variables">
 <has_text_matching expression="saturation=0.75"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 5: pl.stacked_violin !-->
+<!-- test 8: pl.stacked_violin -->
 <param name="adata" value="krumsiek11.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.stacked_violin"/>
 <conditional name="var_names">
 <has_text_matching expression="saturation=0.75"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 5.1: pl.stacked_violin with symbols !-->
+<!-- test 9: pl.stacked_violin with symbols -->
 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.stacked_violin"/>
 <conditional name="var_names">
 <has_text_matching expression="dendrogram=True"/>
 <has_text_matching expression="swap_axes=True"/>
 </assert_contents>
 </output>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 6: pl.matrixplot !-->
+<!-- test 10: pl.matrixplot -->
 <param name="adata" value="krumsiek11.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.matrixplot"/>
 <conditional name="var_names">
 <has_text_matching expression="snap=False"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 6.1: pl.matrixplot with symbols !-->
+<!-- test 11: pl.matrixplot with symbols -->
 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.matrixplot"/>
 <conditional name="var_names">
 <has_text_matching expression="dendrogram=True"/>
 <has_text_matching expression="swap_axes=False"/>
 </assert_contents>
 </output>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 7: pl.clustermap !-->
+<!-- test 12: pl.clustermap -->
 <param name="adata" value="krumsiek11.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.clustermap"/>
 <param name="use_raw" value="False"/>
 <has_text_matching expression="row_cluster=False"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.clustermap.krumsiek11.png" ftype="png" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 8: pl.highest_expr_genes !-->
+<!-- test 13: pl.highest_expr_genes -->
 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.highest_expr_genes"/>
 <param name="n_top" value="30"/>
 <has_text_matching expression="saturation=0.5"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png" ftype="png" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 9: pl.highly_variable_genes !-->
+<!-- test 14: pl.highly_variable_genes -->
 <param name="adata" value="pp.highly_variable_genes.seurat.blobs.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.highly_variable_genes"/>
 <param name="log" value="false"/>
 <has_text_matching expression="highly_variable_genes=True"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.highly_variable_genes.seurat.blobs.png" ftype="png" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 10: pl.pca !-->
+<!-- test 15: pl.pca -->
 <param name="adata" value="pbmc68k_reduced.h5ad" />
 <param name="format" value="pdf"/>
 <conditional name="method">
 <param name="method" value="pl.pca"/>
 <param name="color" value="CD3D,CD79A"/>
 <has_text_matching expression="frameon=True" />
 <has_text_matching expression="ncols=2" />
 <has_text_matching expression="wspace=0.1" />
 <has_text_matching expression="hspace=0.25" />
 <has_text_matching expression="linewidths=0.0" />
-<has_text_matching expression="edgecolors='face" />
+<has_text_matching expression="edgecolors='face'" />
 </assert_contents>
 </output>
 <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 11: pl.pca_loadings !-->
+<!-- test 16: pl.pca_loadings -->
 <param name="adata" value="pp.pca.krumsiek11.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.pca_loadings"/>
 <param name="components" value="1,2,3"/>
 <has_text_matching expression="components=\[1, 2, 3\]" />
 </assert_contents>
 </output>
 <output name="out_png" file="pl.pca_loadings.pp.pca.krumsiek11.png" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 12: pl.pca_variance_ratio !-->
+<!-- test 17: pl.pca_variance_ratio -->
 <param name="adata" value="pp.pca.krumsiek11.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.pca_variance_ratio"/>
 <param name="n_pcs" value="5"/>
 <has_text_matching expression="log=False" />
 </assert_contents>
 </output>
 <output name="out_png" file="pl.pca_variance_ratio.pp.pca.krumsiek11.png" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 13: pl.pca_overview !-->
+<!-- test 18: pl.pca_overview -->
 <param name="adata" value="pp.pca.krumsiek11.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.pca_overview"/>
 <param name="use_raw" value="False"/>
 <has_text_matching expression="hspace=0.25"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.pca_overview.pp.pca.krumsiek11.png" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 14: pl.tsne !-->
+<!-- test 19: pl.tsne -->
 <param name="adata" value="tl.tsne.krumsiek11.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.tsne"/>
 <param name="use_raw" value="False"/>
 <has_text_matching expression="edgecolors='face'"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 15: pl.umap !-->
+<!-- test 20: pl.umap -->
 <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.umap"/>
 <param name="color" value="paul15_clusters"/>
 <has_text_matching expression="edgecolors='face'"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 16: pl.diffmap !-->
+<!-- test 21: pl.diffmap -->
 <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.diffmap"/>
 <param name="color" value="paul15_clusters"/>
 <has_text_matching expression="edgecolors='face'"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 17: pl.draw_graph !-->
+<!-- test 22: pl.draw_graph -->
 <param name="adata" value="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.draw_graph"/>
 <param name="use_raw" value="false"/>
 <has_text_matching expression="edgecolors='face"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.draw_graph.png" ftype="png" compare="sim_size"/>
 </test>
-<!--<test>
+<test expect_num_outputs="2">
-< test pl.dpt_groups_pseudotime >
+<!-- test 23: pl.embedding_density -->
+<param name="adata" value="tl.embedding_density.umap.pbmc68k_reduced.h5ad" />
+<param name="format" value="png"/>
+<conditional name="method">
+<param name="method" value="pl.embedding_density"/>
+<param name="basis" value="umap"/>
+<param name="key" value="umap_density_bulk_labels"/>
+</conditional>
+<section name="advanced_common">
+<param name="show_log" value="true" />
+</section>
+<output name="hidden_output">
+<assert_contents>
+<has_text_matching expression="sc.pl.embedding_density"/>
+<has_text_matching expression="basis='umap'" />
+<has_text_matching expression="key='umap_density_bulk_labels'"/>
+</assert_contents>
+</output>
+<output name="out_png" file="pl.embedding_density.pbmc68k_reduced.png" ftype="png" compare="sim_size"/>
+</test>
+<test expect_num_outputs="2">
+<!-- test 24: pl.dpt_groups_pseudotime -->
 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.dpt_groups_pseudotime"/>
 <param name="color_map" value="viridis"/>
 </conditional>
-<assert_stdout>
+<section name="advanced_common">
-<has_text_matching expression="sc.pl.dpt_groups_pseudotime"/>
+<param name="show_log" value="true" />
-<has_text_matching expression="color_map='viridis'"/>
+</section>
-</assert_stdout>
+<output name="hidden_output">
+<assert_contents>
+<has_text_matching expression="sc.pl.dpt_groups_pseudotime"/>
+<has_text_matching expression="color_map='viridis'"/>
+</assert_contents>
+</output>
 <output name="out_png" file="pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
-</test>!-->
+</test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 18: pl.dpt_timeseries !-->
+<!-- test 25: pl.dpt_timeseries -->
 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.dpt_timeseries"/>
 <conditional name="heatmap">
 <has_text_matching expression="as_heatmap=True"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
 </test>
-<!--<test>
+<test expect_num_outputs="1">
-test pl.paga
+<!-- test 26: pl.paga -->
 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.paga"/>
 <param name="threshold" value="0.01"/>
-<param name="color" value="paul15_clusters"/>
+<param name="color" value="louvain"/>
-<param name="labels" value="label" />
 <param name="layout" value="fr"/>
 <param name="random_state" value="0"/>
 <param name="solid_edges" value="connectivities"/>
 <param name="single_component" value="False"/>
 <param name="fontsize" value="1"/>
 <param name="normalize_to_color" value="False"/>
 <param name="cmap" value="viridis"/>
 <param name="frameon" value="True"/>
 </conditional>
 <output name="out_png" file="pl.paga.paul15_gauss_braycurtis.png" ftype="png" compare="sim_size"/>
-</test>!-->
+</test>
-<!--<test>
+<test expect_num_outputs="1">
-test pl.paga_compare
+<!-- test 27: pl.paga_compare -->
-</test>!-->
+<param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad" />
-<!--<test>
+<param name="format" value="png"/>
+<conditional name="method">
+<param name="method" value="pl.paga_compare"/>
+<param name="threshold" value="0.01"/>
+<param name="color" value="louvain"/>
+<param name="layout" value="fr"/>
+<param name="random_state" value="0"/>
+<param name="solid_edges" value="connectivities"/>
+<param name="single_component" value="False"/>
+<param name="fontsize" value="1"/>
+<param name="node_size_scale" value="1.0"/>
+<param name="node_size_power" value="0.5"/>
+<param name="edge_width_scale" value="5"/>
+<param name="arrowsize" value="30"/>
+<param name="normalize_to_color" value="False"/>
+<param name="cmap" value="viridis"/>
+<param name="frameon" value="True"/>
+</conditional>
+<output name="out_png" file="pl.paga_compare.paul15_gauss_braycurtis.png" ftype="png" compare="sim_size"/>
+</test>
+<!--<test expect_num_outputs="2">
 test pl.paga_path
-</test>!-->
+</test>-->
-<test>
+<test expect_num_outputs="2">
-<!-- test 19: pl.rank_genes_groups !-->
+<!-- test 28: pl.rank_genes_groups -->
 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.rank_genes_groups"/>
+<param name="gene_symbols" value="symbol"/>
 <param name="n_genes" value="10"/>
 <param name="fontsize" value="8"/>
 <param name="ncols" value="4"/>
 <param name="sharey" value="true"/>
 </conditional>
 <has_text_matching expression="sharey=True"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
 </test>
-<!-- test 20: pl.rank_genes_groups_violin, currently broken
+<test expect_num_outputs="2">
-<test>
+<!-- test 29: pl.rank_genes_groups_violin -->
 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.rank_genes_groups_violin"/>
 <conditional name="genes">
 <element name="cell_type_Mo" file="pl.rank_genes_groups_violin.Mo.png" ftype="png" compare="sim_size"/>
 <element name="cell_type_Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="sim_size"/>
 <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="sim_size"/>
 </output_collection>
 </test>
--->
+<test expect_num_outputs="2">
-<test>
+<!-- test 30: pl.rank_genes_groups_dotplot -->
-<!-- test 21: pl.rank_genes_groups_dotplot !-->
 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.rank_genes_groups_dotplot"/>
+<param name="gene_symbols" value="symbol"/>
 <param name="n_genes" value="10"/>
 <param name="log" value="False"/>
 <param name="use_raw" value="False"/>
 <param name="dendrogram" value="False"/>
 <param name="color_map" value="viridis"/>
 <has_text_matching expression="edgecolors='face'"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 22: pl.rank_genes_groups_heatmap !-->
+<!-- test 31: pl.rank_genes_groups_heatmap -->
 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.rank_genes_groups_heatmap"/>
+<param name="gene_symbols" value="symbol"/>
 <param name="n_genes" value="10"/>
 <param name="log" value="False"/>
 <param name="use_raw" value="False"/>
 <param name="dendrogram" value="False"/>
 <param name="swap_axes" value="False"/>
 <has_text_matching expression="origin='upper'"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 23: pl.rank_genes_groups_matrixplot !-->
+<!-- test 32: pl.rank_genes_groups_matrixplot -->
 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.rank_genes_groups_matrixplot"/>
+<param name="gene_symbols" value="symbol"/>
 <param name="n_genes" value="10"/>
 <param name="log" value="False"/>
 <param name="use_raw" value="False"/>
 <param name="dendrogram" value="False"/>
 <param name="swap_axes" value="False"/>
 <has_text_matching expression="snap=False"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
 </test>
-<test>
+<test expect_num_outputs="2">
-<!-- test 24: pl.rank_genes_groups_stacked_violin !-->
+<!-- test 33: pl.rank_genes_groups_stacked_violin -->
 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.rank_genes_groups_stacked_violin"/>
+<param name="gene_symbols" value="symbol"/>
 <param name="n_genes" value="10"/>
 <param name="log" value="False"/>
 <param name="use_raw" value="False"/>
 <param name="dendrogram" value="True"/>
 <param name="swap_axes" value="True"/>
 <has_text_matching expression="saturation=0.75"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
 </test>
+<test expect_num_outputs="2">
+<!-- test 34: pl.scatter log !-->
+<param name="adata" value="pbmc68k_reduced.h5ad" />
+<param name="format" value="png"/>
+<conditional name="method">
+<param name="method" value="pl.scatter"/>
+<conditional name="type">
+<param name="type" value="xy"/>
+<param name="x" value="n_genes"/>
+<param name="y" value="n_counts"/>
+<param name="log" value="True"/>
+<conditional name="layers">
+<param name="use_layers" value="false"/>
+</conditional>
+</conditional>
+<param name="use_raw" value="False"/>
+<param name="sort_order" value="True"/>
+<section name="plot">
+<param name="projection" value="2d"/>
+<param name="legend_loc" value="right margin"/>
+<param name="legend_fontsize" value="1"/>
+<param name="legend_fontweight" value="normal"/>
+<param name="palette" value="bwr"/>
+<param name="frameon" value="False"/>
+<param name="size" value="1"/>
+<param name="title" value="A title"/>
+</section>
+</conditional>
+<section name="advanced_common">
+<param name="show_log" value="true" />
+</section>
+<output name="hidden_output">
+<assert_contents>
+<has_text_matching expression="sc.pl.scatter"/>
+<has_text_matching expression="use_raw=False"/>
+<has_text_matching expression="sort_order=True"/>
+<has_text_matching expression="projection='2d'"/>
+<has_text_matching expression="legend_loc='right margin'"/>
+<has_text_matching expression="legend_fontsize=1"/>
+<has_text_matching expression="legend_fontweight='normal'"/>
+<has_text_matching expression="frameon=False"/>
+<has_text_matching expression="size=1.0"/>
+<has_text_matching expression="title='A title'"/>
+</assert_contents>
+</output>
+<output name="out_png" file="pl.scatter.pbmc68k_reduced.png" ftype="png" compare="sim_size"/>
+</test>
 </tests>
 <help><![CDATA[
 Generic: Scatter plot along observations or variables axes (`pl.scatter`)
 =========================================================================
 Color the plot using annotations of observations (`.obs`), variables
 (`.var`) or expression of genes (`.var_names`).
 More details on the `scanpy documentation
-<https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.scatter.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.scatter.html>`__
 Generic: Heatmap of the expression values of set of genes (`pl.heatmap`)
 ========================================================================
 If `groupby` is given, the heatmap is ordered by the respective group. For
 the `groupby` observation annotation is not categorical the observation
 annotation is turned into a categorical by binning the data into the number
 specified in `num_categories`.
 More details on the `scanpy documentation
-<https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.heatmap.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.heatmap.html>`__
 Generic: Makes a dot plot of the expression values (`pl.dotplot`)
 =================================================================
 For each var_name and each `groupby` category a dot is plotted. Each dot
 For instance, for each marker gene, the mean value and the percentage of cells
 expressing the gene can be visualized for each cluster.
 More details on the `scanpy documentation
-<https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.dotplot.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.dotplot.html>`__
 Generic: Violin plot (`pl.violin`)
 ==================================
 Wraps `seaborn.violinplot` for `anndata.AnnData`.
 More details on the `scanpy documentation
-<https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.violin.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.violin.html>`__
 Generic: Stacked violin plots (`pl.stacked_violin`)
 ===================================================
 Makes a compact image composed of individual violin plots (from `seaborn.violinplot`)
 stacked on top of each other. Useful to visualize gene expression per cluster.
 More details on the `scanpy documentation
-<https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.stacked_violin.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.stacked_violin.html>`__
 Generic: Heatmap of the mean expression values per cluster (`pl.matrixplot`)
 ============================================================================
 Creates a heatmap of the mean expression values per cluster of each var_names
 If groupby is not given, the matrixplot assumes that all data belongs to a single
 category.
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.matrixplot.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.matrixplot.html>`__
 Generic: Hierarchically-clustered heatmap (`pl.clustermap`)
 ===========================================================
 Wraps `seaborn.clustermap
 clustergrid.dendrogram_row.reordered_ind
 Column indices, use: clustergrid.dendrogram_col.reordered_ind
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.clustermap.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.clustermap.html>`__
 Preprocessing: Plot the fraction of counts assigned to each gene over all cells (`pl.highest_expr_genes`)
 =========================================================================================================
 Computes, for each gene, the fraction of counts assigned to that gene within
 plotted as boxplots.
 This plot is similar to the `scater` package function `plotHighestExprs(type= "highest-expression")`
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.highest_expr_genes.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.highest_expr_genes.html>`__
 Preprocessing: Plot dispersions versus means for genes (`pl.highly_variable_genes`)
 ===================================================================================
 It produces Supp. Fig. 5c of Zheng et al. (2017) and MeanVarPlot() of Seurat.
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.highly_variable_genes.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.highly_variable_genes.html>`__
 PCA: Scatter plot in PCA coordinates (`pl.pca`)
 ===============================================
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.pca.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca.html>`__
 PCA: Rank genes according to contributions to PCs (`pl.pca_loadings`)
 =====================================================================
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.pca_loadings.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca_loadings.html>`__
 PCA: Plot the variance ratio (`pl.pca_variance_ratio`)
 ======================================================
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.pca_variance_ratio.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca_variance_ratio.html>`__
 PCA: Plot PCA results (`pl.pca_overview`)
 =========================================
 The parameters are the ones of the scatter plot. Call pca_ranking separately
 if you want to change the default settings.
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.pca_overview.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca_overview.html>`__
 Embedding: Scatter plot in tSNE basis (`pl.tsne`)
 =================================================
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.tsne.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.tsne.html>`__
 Embeddings: Scatter plot in UMAP basis (`pl.umap`)
 ==================================================
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.umap.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.umap.html>`__
 Embeddings: Scatter plot in Diffusion Map basis (`pl.diffmap`)
 ==============================================================
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.diffmap.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.diffmap.html>`__
 Branching trajectories and pseudotime, clustering: Plot groups and pseudotime (`pl.dpt_groups_pseudotime`)
 ===========================================================================================================
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.dpt_groups_pseudotime.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.dpt_groups_pseudotime.html>`__
 Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series (`pl.dpt_timeseries`)
 =====================================================================================================
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.dpt_timeseries.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.dpt_timeseries.html>`__
 Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges (`pl.paga`)
 ====================================================================================================================================
 When initializing the positions, note that - for some reason - igraph
 mirrors coordinates along the x axis... that is, you should increase the
 `maxiter` parameter by 1 if the layout is flipped.
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.paga.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.paga.html>`__
 Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side (`pl.paga_compare`)
 ==========================================================================================================
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.paga_compare.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.paga_compare.html>`__
 Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths (`pl.paga_path`)
 ======================================================================================================================
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.paga_path.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.paga_path.html>`__
 Marker genes: Plot ranking of genes using dotplot plot (`pl.rank_genes_groups`)
 ===============================================================================
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.rank_genes_groups.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups.html>`__
 Marker genes: Plot ranking of genes as violin plot (`pl.rank_genes_groups_violin`)
 ==================================================================================
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.rank_genes_groups_violin.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_violin.html>`__
 Marker genes: Plot ranking of genes as dotplot plot (`pl.rank_genes_groups_dotplot`)
 ====================================================================================
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.rank_genes_groups_dotplot.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_dotplot.html>`__
 Marker genes: Plot ranking of genes as heatmap plot (`pl.rank_genes_groups_heatmap`)
 ====================================================================================
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.rank_genes_groups_heatmap.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_heatmap.html>`__
 Marker genes: Plot ranking of genes as matrixplot plot (`pl.rank_genes_groups_matrixplot`)
 ==========================================================================================
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.rank_genes_groups_matrixplot.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_matrixplot.html>`__
 Marker genes: Plot ranking of genes as stacked violin plot (`pl.rank_genes_groups_stacked_violin`)
 ==================================================================================================
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.rank_genes_groups_stacked_violin.html>`__
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_stacked_violin.html>`__
 ]]></help>
 <expand macro="citations"/>
 </tool>

Mercurial > repos > iuc > scanpy_plot

comparison plot.xml @ 11:95777145cb92 draft