scanpy_plot: plot.xml comparison

comparison plot.xml @ 1:072b759d0fca draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"

author	iuc
date	Wed, 16 Oct 2019 06:21:53 -0400
parents	729198e3330c
children	791469a96577

comparison

equal deleted inserted replaced

-:729198e3330c
+:072b759d0fca
-<tool id="scanpy_plot" name="Plot with scanpy" version="@galaxy_version@">
+<tool id="scanpy_plot" name="Plot" version="@galaxy_version@">
-<description></description>
+<description> with scanpy</description>
 <macros>
 <import>macros.xml</import>
 </macros>
 <expand macro="requirements"/>
 <stdio>
 sc.pl.scatter(
 @CMD_param_plot_inputs@
 #if $method.type.type == 'xy'
 x='$method.type.x',
 y='$method.type.y',
-layers=('$method.type.layer_x', '$method.type.layer_y', '$method.type.layer_color'),
+#if str('$method.type.layers.use_layers') == 'true'
+layers=('$method.type.layers.layer_x', '$method.type.layers.layer_y', '$method.type.layers.layer_color'),
+#end if
 #else
 basis='$method.type.basis',
 #if str($method.type.color) != ''
 #set $color = ([x.strip() for x in str($method.type.color).split(',')])
 color=$color,
-#else
-color=None,
 #end if
 #end if
 use_raw=$method.use_raw,
 sort_order=$method.sort_order,
 @CMD_params_pl_groups@
 #if $method.plot.title
 title='$method.plot.title',
 #end if
 size=$method.plot.size)
-#elif $method.method == 'pl.heatmap'
+#else if $method.method == 'pl.heatmap'
 sc.pl.heatmap(
 @CMD_param_plot_inputs@
 @CMD_params_plots@
 swap_axes=$method.swap_axes,
 show_gene_labels=$method.show_gene_labels,
 cmap='$method.matplotlib_pyplot_imshow.cmap',
+#if str($method.matplotlib_pyplot_imshow.interpolation) != 'None'
 interpolation='$method.matplotlib_pyplot_imshow.interpolation',
+#end if
 #if $method.matplotlib_pyplot_imshow.alpha
 alpha=$method.matplotlib_pyplot_imshow.alpha,
 #end if
 #if $method.matplotlib_pyplot_imshow.vmin
 vmin=$method.matplotlib_pyplot_imshow.vmin,
 #if $method.matplotlib_pyplot_imshow.vmax
 vmax=$method.matplotlib_pyplot_imshow.vmax,
 #end if
 origin='$method.matplotlib_pyplot_imshow.origin')
-#elif $method.method == 'pl.dotplot'
+#else if $method.method == 'pl.dotplot'
 sc.pl.dotplot(
 @CMD_param_plot_inputs@
 @CMD_params_plots@
 color_map='$method.color_map',
 #if $method.dot_max
 #if $method.dot_min
 dot_min=$method.dot_min,
 #end if
 @CMD_params_matplotlib_pyplot_scatter@)
-#elif $method.method == 'pl.violin'
+#else if $method.method == 'pl.violin'
 sc.pl.violin(
 @CMD_param_plot_inputs@
 #if $method.key_variables.type == "var_names"
 #set $key_list = adata.var_names
-#elif $method.key_variables.type == "obs"
+#else if $method.key_variables.type == "obs"
 #set $key_list = adata.obs.select_dtypes(exclude=['category']).columns
-#elif $method.key_variables.type == "custom"
+#else if $method.key_variables.type == "custom"
 #set $key_list=([x.strip() for x in str($method.key_variables.keys).split(',')])
 #end if
 keys=$key_list,
 #if $method.groupby
 groupby='$method.groupby',
 #end if
 log=$method.log,
 use_raw=$method.use_raw,
-sstripplot=$method.violin_plot.stripplot.stripplot,
+@CMD_conditional_stripplot@
-#if $method.violin_plot.stripplot.stripplot == "True"
-jitter=$method.violin_plot.stripplot.jitter.jitter,
-#if $method.violin_plot.stripplot.jitter.jitter == "True"
-size=$method.violin_plot.stripplot.jitter.size,
-#end if
-#end if
 multi_panel=$method.violin_plot.multi_panel.multi_panel,
+#if $method.violin_plot.multi_panel.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != '' and str($method.violin_plot.multi_panel.height) != ''
+figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height),
+#end if
 scale='$method.violin_plot.scale',
 #if $method.xlabel
 xlabel='$method.xlabel',
 #end if
 #if $method.rotation
 rotation=$method.rotation,
 #end if
 @CMD_params_seaborn_violinplot@)
-#elif $method.method == 'pl.matrixplot'
+#else if $method.method == 'pl.stacked_violin'
+sc.pl.stacked_violin(
+@CMD_param_plot_inputs@
+@CMD_params_plots@
+swap_axes=$method.swap_axes,
+@CMD_conditional_stripplot@
+scale='$method.violin_plot.scale',
+row_palette='$method.row_palette',
+#if str($method.standard_scale) != 'None'
+standard_scale='$method.standard_scale',
+#end if
+@CMD_params_seaborn_violinplot@)
+#else if $method.method == 'pl.matrixplot'
 sc.pl.matrixplot(
 @CMD_param_plot_inputs@
 @CMD_params_plots@
 swap_axes=$method.swap_axes,
 cmap='$method.matplotlib_pyplot_pcolor.cmap',
 #if $method.matplotlib_pyplot_pcolor.alpha
 alpha=$method.matplotlib_pyplot_pcolor.alpha,
 #end if
 snap=$method.matplotlib_pyplot_pcolor.snap)
-#elif $method.method == 'pl.clustermap'
+#else if $method.method == 'pl.clustermap'
 sc.pl.clustermap(
 #if str($method.use_raw) == 'True'
 adata=adata.X,
 #else
 adata=adata,
 #end if
 show=False,
+#if str($method.obs_keys) != ''
 obs_keys='$method.obs_keys',
+#end if
 use_raw=$method.use_raw,
 method='$method.seaborn_clustermap.method',
 metric='$method.seaborn_clustermap.metric',
-#if str($method.seaborn_clustermap.z_score) == 'None'
+#if str($method.seaborn_clustermap.z_score) != 'None'
-z_score=None,
-#else
 z_score=$method.seaborn_clustermap.z_score,
 #end if
-#if str($method.seaborn_clustermap.standard_scale) == 'None'
+#if str($method.seaborn_clustermap.standard_scale) != 'None'
-standard_scale=None,
-#else
 standard_scale=$method.seaborn_clustermap.standard_scale,
 #end if
 col_cluster=$method.seaborn_clustermap.col_cluster,
 row_cluster=$method.seaborn_clustermap.row_cluster).savefig(fname="output.$format")
-#elif $method.method == 'pl.highest_expr_genes'
+#else if $method.method == 'pl.highest_expr_genes'
 sc.pl.highest_expr_genes(
 @CMD_param_plot_inputs@
 n_top=$method.n_top,
 #if str($method.gene_symbols) != ''
 gene_symbols='$method.gene_symbols',
 #if str($method.setseaborn_boxplot.palette) != 'None'
 palette='$method.setseaborn_boxplot.palette',
 #end if
 saturation=$method.setseaborn_boxplot.saturation)
-#elif $method.method == 'pl.pca'
+#else if $method.method == 'pl.highly_variable_genes'
+sc.pl.highly_variable_genes(
+adata_or_result=adata,
+log=$method.log,
+save='.$format',
+show=False,
+highly_variable_genes=$method.highly_variable_genes
+)
+#else if $method.method == 'pl.pca'
 sc.pl.pca(
 @CMD_param_plot_inputs@
 @CMD_param_color@
 use_raw=$method.use_raw,
 sort_order=$method.sort_order,
 @CMD_params_pl_groups@
 @CMD_params_pl_components@
 @CMD_pl_attribute_section@
 @CMD_params_matplotlib_pyplot_scatter@)
-#elif $method.method == 'pl.pca_loadings'
+#else if $method.method == 'pl.pca_loadings'
 sc.pl.pca_loadings(
 @CMD_param_plot_inputs@
 #set $components = ([int(x.strip()) for x in str($method.components).split(',')])
 components=$components)
-#elif $method.method == 'pl.pca_variance_ratio'
+#else if $method.method == 'pl.pca_variance_ratio'
 sc.pl.pca_variance_ratio(
 @CMD_param_plot_inputs@
 n_pcs=$method.n_pcs,
 log=$method.log)
-#elif $method.method == 'pl.pca_overview'
+#else if $method.method == 'pl.pca_overview'
 sc.pl.pca_overview(
 @CMD_param_plot_inputs@
 @CMD_param_color@
 use_raw=$method.use_raw,
 sort_order=$method.sort_order,
 @CMD_params_pl_groups@
 @CMD_params_pl_components@
 @CMD_pl_attribute_section@
 @CMD_params_matplotlib_pyplot_scatter@)
-#elif $method.method == 'pl.tsne'
+#else if $method.method == 'pl.tsne'
 sc.pl.tsne(
 @CMD_param_plot_inputs@
 @CMD_param_color@
 use_raw=$method.use_raw,
 @CMD_pl_edges@
 @CMD_params_pl_groups@
 @CMD_params_pl_components@
 @CMD_pl_attribute_section@
 @CMD_params_matplotlib_pyplot_scatter@)
-#elif $method.method == 'pl.umap'
+#else if $method.method == 'pl.umap'
 sc.pl.umap(
 @CMD_param_plot_inputs@
 @CMD_param_color@
 use_raw=$method.use_raw,
 @CMD_pl_edges@
 @CMD_params_pl_groups@
 @CMD_params_pl_components@
 @CMD_pl_attribute_section@
 @CMD_params_matplotlib_pyplot_scatter@)
-#elif $method.method == 'pl.diffmap'
+#else if $method.method == 'pl.diffmap'
 sc.pl.diffmap(
 @CMD_param_plot_inputs@
 @CMD_param_color@
 use_raw=$method.use_raw,
 sort_order=$method.sort_order,
 @CMD_params_pl_groups@
 @CMD_params_pl_components@
 @CMD_pl_attribute_section@
 @CMD_params_matplotlib_pyplot_scatter@)
-#elif $method.method == 'pl.dpt_groups_pseudotime'
+#else if $method.method == 'pl.draw_graph'
+sc.pl.draw_graph(
+@CMD_param_plot_inputs@
+@CMD_param_color@
+#if str($method.gene_symbols) != ''
+gene_symbols='$method.gene_symbols',
+#end if
+use_raw=$method.use_raw,
+#if str($method.layout) != 'None'
+layout='$method.layout',
+#end if
+edges=$method.edges.edges,
+#if str($method.edges.edges) == 'True'
+edges_width=$method.edges.edges_width,
+edges_color='$method.edges.edges_color',
+#end if
+arrows=$method.arrows,
+sort_order=$method.sort_order,
+@CMD_params_pl_groups@
+@CMD_params_pl_components@
+@CMD_pl_attribute_section@
+@CMD_params_matplotlib_pyplot_scatter@)
+#else if $method.method == 'pl.dpt_groups_pseudotime'
 sc.pl.dpt_groups_pseudotime(
 @CMD_param_plot_inputs@
 color_map='$method.color_map')
-#elif $method.method == 'pl.dpt_timeseries'
+#else if $method.method == 'pl.dpt_timeseries'
 sc.pl.dpt_timeseries(
 @CMD_param_plot_inputs@
 #if $method.heatmap.as_heatmap == "True"
 color_map='$method.heatmap.color_map',
 #end if
 as_heatmap=$method.heatmap.as_heatmap)
-#elif $method.method == 'pl.paga'
+#else if $method.method == 'pl.paga'
 sc.pl.paga(
 @CMD_param_plot_inputs@
 @CMD_params_pl_paga@)
+#else if $method.method == 'pl.paga_compare'
+sc.pl.paga_compare(
+@CMD_param_plot_inputs@
+@CMD_params_pl_paga@)
+#else if $method.method == 'pl.paga_path'
+sc.pl.paga_path(
+@CMD_param_plot_inputs@
+#set $nodes = ([int(x.strip()) for x in str($method.nodes).split(',')])
+nodes=$nodes,
+#set $keys=([x.strip() for x in str($method.keys).split(',')])
+keys=$keys,
+use_raw=$method.use_raw,
+#if str($method.annotations) != ''
+#set $annotations=([x.strip() for x in str($method.annotations).split(',')])
+annotations=$annotations,
+#end if
+color_map='$method.color_map',
+n_avg=$method.n_avg,
+#if str($method.annotations) != ''
+groups_key='$method.groups_key',
+#end if
+as_heatmap=$method.as_heatmap,
+show_node_names=$method.show_node_names,
+show_colorbar=$method.show_colorbar,
+show_yticks=$method.show_yticks,
+normalize_to_zero_one=$method.normalize_to_zero_one)
+#else if $method.method == 'pl.rank_genes_groups'
+sc.pl.rank_genes_groups(
+@CMD_param_plot_inputs@
+@CMD_params_pl_groups@
+n_genes=$method.n_genes,
+#if str($method.gene_symbols) != ''
+gene_symbols='$method.gene_symbols',
+#end if
+fontsize=$method.fontsize,
+ncols=$method.ncols,
+sharey=$method.sharey)
+#else if $method.method == 'pl.rank_genes_groups_violin'
+sc.pl.rank_genes_groups_violin(
+@CMD_param_plot_inputs@
+@CMD_params_pl_groups@
+#if $method.genes.select == 'n_genes'
+n_genes=$method.genes.n_genes,
+#else
+#set $gene_names = ([x.strip() for x in str($method.genes.gene_names).split(',')])
+gene_names=$gene_names,
+#end if
+gene_symbols='$method.gene_symbols',
+use_raw=$method.use_raw,
+split=$method.split,
+strip=$method.violin_plot.stripplot.stripplot,
+#if $method.violin_plot.stripplot.stripplot == "True"
+jitter=$method.violin_plot.stripplot.jitter.jitter,
+#if $method.violin_plot.stripplot.jitter.jitter == "True"
+size=$method.violin_plot.stripplot.jitter.size,
+#end if
+#end if
+scale='$method.violin_plot.scale')
 #end if
 ]]></configfile>
 </configfiles>
 <inputs>
 <expand macro="inputs_anndata"/>
 <param argument="method" type="select" label="Method used for plotting">
 <option value="pl.scatter">Generic: Scatter plot along observations or variables axes, using `pl.scatter`</option>
 <option value="pl.heatmap">Generic: Heatmap of the expression values of set of genes, using `pl.heatmap`</option>
 <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: </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: </option>!-->
+<option value="pl.highly_variable_genes">Preprocessing: Plot dispersions versus means for genes, using `pl.highly_variable_genes`</option>
 <!--<option value="pl.calculate_qc_metrics">Preprocessing: </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_variance_ratio">PCA: Scatter plot in PCA coordinates, using `pl.pca_variance_ratio`</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: </option>!-->
+<option value="pl.draw_graph">Embeddings: Scatter plot in graph-drawing basis, using `pl.draw_graph`</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: </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: </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_gene_groups">Marker genes: Plot ranking of genes using dotplot plot, using `pl.rank_gene_groups`</option>!-->
+<option value="pl.rank_genes_groups">Marker genes: Plot ranking of genes using dotplot plot, using `pl.rank_genes_groups`</option>
 <!--<option value="pl.rank_genes_groups_dotplot">Marker genes: </option>!-->
 <!--<option value="pl.rank_genes_groups_heatmap">Marker genes: </option>!-->
 <!--<option value="pl.rank_genes_groups_matrixplot">Marker genes: </option>!-->
 <!--<option value="pl.rank_genes_groups_stacked_violin">Marker genes: </option>!-->
-<!--<option value="pl.rank_genes_groups_violin">Marker genes: </option>!-->
+<option value="pl.rank_genes_groups_violin">Marker genes: Plot ranking of genes for all tested comparisons, using `pl.rank_genes_groups_violin`</option>
 <!--<option value="pl.phate">Misc: </option>!-->
 <!--<option value="pl.matrix">Misc: </option>!-->
 <!--<option value="pl.paga_adjacency">Misc: </option>!-->
 <!--<option value="pl.timeseries">Misc: </option>!-->
 <!--<option value="pl.timeseries_as_heatmap">Misc: </option>!-->
 <option value="basis">Using tool that computes coordinates</option>
 </param>
 <when value="xy">
 <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either `.obs` or `.var`"/>
 <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either `.obs` or `.var`"/>
-<param argument="layer_x" type="text" value="X" label="Layers for x coordinate" help="Use the `layers` attribute of `adata` if present"/>
+<conditional name="layers">
-<param argument="layer_y" type="text" value="X" label="Layers for y coordinate" help="Use the `layers` attribute of `adata` if present"/>
+<param argument="use_layers" type="select" label="Use the layers attribute?">
-<param argument="layer_color" type="text" value="X" label="Layers for color" help="Use the `layers` attribute of `adata` if present"/>
+<option value="true">Yes</option>
+<option value="false" selected="true">No</option>
+</param>
+<when value="true">
+<param argument="layer_x" type="text" value="" optional="true" label="Layers for x coordinate" help="Use the `layers` attribute of `adata` if present"/>
+<param argument="layer_y" type="text" value="" optional="true" label="Layers for y coordinate" help="Use the `layers` attribute of `adata` if present"/>
+<param argument="layer_color" type="text" value="" optional="true" label="Layers for color" help="Use the `layers` attribute of `adata` if present"/>
+</when>
+<when value="false"/>
+</conditional>
 </when>
 <when value="basis">
 <param argument="basis" type="select" label="Plotting tool that computes coordinates" help="">
 <option value="pca">pca (need to run on `tl.pca` output)</option>
 <option value="tsne">tsne (need to run on `tl.tsne` output)</option>
 <expand macro="param_swap_axes"/>
 <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."/>
 <section name="matplotlib_pyplot_imshow" title="Parameters for matplotlib.pyplot.imshow">
 <expand macro="param_cmap"/>
 <param name="interpolation" type="select" label="Interpolation method" help="">
-<option value="none">none</option>
+<option value="None">none</option>
 <option value="nearest">nearest</option>
 <option value="bilinear">bilinear</option>
 <option value="bicubic">bicubic</option>
 <option value="spline16">spline16</option>
 <option value="spline36">spline36</option>
 <when value="pl.violin">
 <conditional name="key_variables">
 <param name="type" type="select" label="Keys for accessing variables">
 <option value="var_names">All variables in `.var_names`</option>
 <option value="obs">All fields in `.obs`</option>
-<option value="custom">Subset of variables in `adata.var_names` or fields of `.obs`"</option>
+<option value="custom">Subset of variables in `adata.var_names` or fields of `.obs`</option>
 </param>
 <when value="var_names"/>
 <when value="obs"/>
 <when value="custom">
 <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`"/>
 </when>
 </conditional>
 <expand macro="param_groupby"/>
 <expand macro="param_log"/>
 <expand macro="param_use_raw"/>
-<expand macro="section_violin_plots"/>
+<section name="violin_plot" title="Violin plot attributes">
+<expand macro="conditional_stripplot"/>
+<conditional name="multi_panel">
+<param argument="multi_panel" type="select" label="Display keys in multiple panels" help="Also when `groupby is not provided">
+<option value="True">Yes</option>
+<option value="False" selected="true">No</option>
+</param>
+<when value="True">
+<param argument="width" type="integer" min="0" value="" optional="true" label="Width of the figure" help=""/>
+<param argument="height" type="integer" min="0" value="" optional="true" label="Height of the figure" help=""/>
+</when>
+<when value="False"/>
+</conditional>
+<expand macro="param_scale"/>
+</section>
 <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."/>
 <param argument="rotation" type="float" value="" optional="true" label="Rotation of xtick labels" help=""/>
+<expand macro="seaborn_violinplot"/>
+</when>
+<when value="pl.stacked_violin">
+<expand macro="params_plots"/>
+<expand macro="param_swap_axes"/>
+<section name="violin_plot" title="Violin plot attributes">
+<expand macro="conditional_stripplot"/>
+<expand macro="param_scale"/>
+</section>
+<param argument="row_palette" type="select" label="Colors to use in each of the stacked violin plots">
+<option value="muted">muted</option>
+<expand macro="seaborn_color_palette_options"/>
+</param>
+<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.">
+<option value="None">No standardization</option>
+<option value="var">Standardization on variable</option>
+<option value="obs">Standardization on observation</option>
+</param>
 <expand macro="seaborn_violinplot"/>
 </when>
 <when value="pl.matrixplot">
 <expand macro="params_plots"/>
 <expand macro="param_swap_axes"/>
 <expand macro="param_alpha"/>
 <param argument="snap" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Snap the mesh to pixel boundaries?" help=""/>
 </section>
 </when>
 <when value="pl.clustermap">
-<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."/>
+<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."/>
 <expand macro="param_use_raw"/>
 <section name="seaborn_clustermap" title="Parameters for seaborn.clustermap">
 <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">
 <option value="single">single: Nearest Point Algorithm</option>
 <option value="complete">complete: Farthest Point Algorithm or Voor Hees Algorithm</option>
 </param>
 <param name="col_cluster" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cluster the columns?" help=""/>
 <param name="row_cluster" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cluster the rows?" help=""/>
 </section>
 </when>
+<when value="pl.highly_variable_genes">
+<expand macro="param_log"/>
+<param argument="highly_variable_genes" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot highly variable genes or gene subset?"/>
+</when>
 <when value="pl.highest_expr_genes">
 <param argument="n_top" type="integer" min="0" value="30" label="Number of top genes" help=""/>
 <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`."/>
 <section name="setseaborn_boxplot" title="Plot settings" expanded="false">
 <param argument="color" type="text" value="" optional="true" label="Color for all of the elements, or seed for a gradient palette" help=""/>
 <expand macro="section_matplotlib_pyplot_scatter"/>
 </when>
 <when value="pl.diffmap">
 <expand macro="param_color"/>
 <expand macro="param_use_raw"/>
+<expand macro="param_sort_order"/>
+<expand macro="pl_groups"/>
+<expand macro="pl_attribute_section"/>
+<expand macro="section_matplotlib_pyplot_scatter"/>
+</when>
+<when value="pl.draw_graph">
+<expand macro="param_color"/>
+<expand macro="gene_symbols"/>
+<expand macro="param_use_raw"/>
+<param argument="layout" type="select" optional="true" label="Plotting layout" help="">
+<expand macro="options_layout"/>
+</param>
+<expand macro="pl_edges"/>
+<expand macro="param_arrows"/>
 <expand macro="param_sort_order"/>
 <expand macro="pl_groups"/>
 <expand macro="pl_attribute_section"/>
 <expand macro="section_matplotlib_pyplot_scatter"/>
 </when>
 </conditional>
 </when>
 <when value="pl.paga">
 <expand macro="inputs_paga"/>
 </when>
+<when value="pl.paga_compare">
+<expand macro="inputs_paga"/>
+</when>
+<when value="pl.paga_path">
+<param argument="nodes" type="text" value="" label="A path through nodes of the abstracted graph"
+help="Each node is represented by its indice (within .categories) for the groups that have been used to run PAGA. Comma-separated"/>
+<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`"/>
+<expand macro="param_use_raw"/>
+<param argument="annotations" type="text" value="" optional="true" label="Key to plot" help="Keys for obs, comma-separated"/>
+<expand macro="param_color_map"/>
+<param argument="n_avg" type="integer" value="1" label="Number of data points to include in computation of running average"/>
+<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"/>
+<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."/>
+<param argument="show_node_names" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot the node names on the nodes bar?"/>
+<param argument="show_colorbar" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the colorbar?"/>
+<param argument="show_yticks" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the y ticks?"/>
+<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?"/>
+</when>
+<when value="pl.rank_genes_groups">
+<expand macro="pl_groups"/>
+<expand macro="n_genes"/>
+<expand macro="gene_symbols"/>
+<param argument="fontsize" type="integer" min="0" value="8" label="Font size for gene names"/>
+<expand macro="param_ncols"/>
+<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"/>
+</when>
+<when value="pl.rank_genes_groups_violin">
+<expand macro="pl_groups"/>
+<conditional name="genes">
+<param argument="select" type="select" label="Which genes to plot?" help="">
+<option value="n_genes">A number of genes</option>
+<option value="gene_names">A custom list of genes</option>
+</param>
+<when value="n_genes">
+<expand macro="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"/>
+</when>
+</conditional>
+<expand macro="gene_symbols"/>
+<expand macro="param_use_raw"/>
+<param argument="split" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Split the violins?"/>
+<section name="violin_plot" title="Violin plot attributes">
+<expand macro="conditional_stripplot"/>
+<expand macro="param_scale"/>
+</section>
+</when>
 </conditional>
 </inputs>
 <outputs>
-<data name="out_png" format="png" from_work_dir="*.png" label="${tool.name} on ${on_string}">
+<data name="out_png" format="png" from_work_dir="*.png" label="${tool.name} (${method.method}) on ${on_string}">
-<filter>format == 'png'</filter>
+<filter>format == 'png' and method['method'] != 'pl.rank_genes_groups_violin'</filter>
 </data>
-<data name="out_pdf" format="pdf" from_work_dir="*.pdf" label="${tool.name} on ${on_string}">
+<collection name="collection_png" type="list" label="${tool.name} (${method.method}) on ${on_string}">
-<filter>format == 'pdf'</filter>
+<discover_datasets pattern="rank_genes_groups_cell_type_(?P&lt;designation&gt;.*).png" format="png"/>
+<filter>format == 'png' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
+</collection>
+<data name="out_pdf" format="pdf" from_work_dir="*.pdf" label="${tool.name} (${method.method}) on ${on_string}">
+<filter>format == 'pdf' and method['method'] != pl.rank_genes_groups_violin</filter>
 </data>
-<data name="out_svg" format="svg" from_work_dir="*.svg" label="${tool.name} on ${on_string}">
+<collection name="collection_pdf" type="list" label="${tool.name} (${method.method}) on ${on_string}">
-<filter>format == 'svg'</filter>
+<discover_datasets pattern="rank_genes_groups_cell_type_(?P&lt;designation&gt;.*).pdf" format="pdf"/>
+<filter>format == 'pdf' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
+</collection>
+<data name="out_svg" format="svg" from_work_dir="*.svg" label="${tool.name} (${method.method}) on ${on_string}">
+<filter>format == 'svg' and method['method'] != pl.rank_genes_groups_violin</filter>
 </data>
+<collection name="collection_svg" type="list" label="${tool.name} (${method.method}) on ${on_string}">
+<discover_datasets pattern="rank_genes_groups_cell_type_(?P&lt;designation&gt;.*).svg" format="svg"/>
+<filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
+</collection>
 </outputs>
 <tests>
 <test>
-<!-- Test pl.scatter !-->
+<!-- test 1: pl.scatter !-->
-<conditional name="input">
+<param name="adata" value="pbmc68k_reduced.h5ad" />
-<param name="format" value="h5ad" />
-<param name="adata" value="pp.pca.krumsiek11.h5ad" />
-</conditional>
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.scatter"/>
 <conditional name="type">
 <param name="type" value="basis"/>
-<param name="basis" value="pca"/>
+<param name="basis" value="umap"/>
-<param name="color" value="EgrNab, Gata2"/>
+<param name="color" value="HES4"/>
 </conditional>
-<param name="use_raw" value="False"/>
+<param name="use_raw" value="True"/>
 <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="size" value="1"/>
 </section>
 </conditional>
 <assert_stdout>
 <has_text_matching expression="sc.pl.scatter"/>
-<has_text_matching expression="basis='pca'" />
+<has_text_matching expression="basis='umap'" />
-<has_text_matching expression="color=\['EgrNab', 'Gata2'\]"/>
+<has_text_matching expression="color=\['HES4'\]"/>
-<has_text_matching expression="use_raw=False"/>
+<has_text_matching expression="use_raw=True"/>
 <has_text_matching expression="sort_order=True"/>
-<has_text_matching expression="groups=None"/>
-<has_text_matching expression="components=None"/>
 <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="color_map='inferno'"/>
 <has_text_matching expression="palette='inferno'"/>
 <has_text_matching expression="frameon=True"/>
 <has_text_matching expression="size=1.0"/>
 </assert_stdout>
-<output name="out_png" file="pl.scatter.pca.krumsiek11.png" ftype="png" compare="sim_size"/>
+<output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="sim_size"/>
 </test>
 <test>
-<!-- Test pl.scatter !-->
+<!-- test 2: pl.scatter !-->
-<conditional name="input">
+<param name="adata" value="krumsiek11.h5ad" />
-<param name="format" value="h5ad" />
-<param name="adata" value="krumsiek11.h5ad" />
-</conditional>
 <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="EKLF"/>
 <param name="y" value="Cebpa"/>
-<param name="layer_x" value="X"/>
+<conditional name="layers">
-<param name="layer_y" value="X"/>
+<param name="use_layers" value="false"/>
-<param name="layer_color" value="X"/>
+</conditional>
 </conditional>
 <param name="use_raw" value="False"/>
 <param name="sort_order" value="True"/>
 <section name="plot">
 <param name="projection" value="2d"/>
 </conditional>
 <assert_stdout>
 <has_text_matching expression="sc.pl.scatter"/>
 <has_text_matching expression="x='EKLF'" />
 <has_text_matching expression="y='Cebpa'"/>
-<has_text_matching expression="layers=\('X', 'X', 'X'\)"/>
 <has_text_matching expression="use_raw=False"/>
 <has_text_matching expression="sort_order=True"/>
-<has_text_matching expression="groups=None,"/>
-<has_text_matching expression="components=None,"/>
 <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="color_map='viridis'"/>
 <has_text_matching expression="title='A title'"/>
 </assert_stdout>
 <output name="out_png" file="pl.scatter.krumsiek11.png" ftype="png" compare="sim_size"/>
 </test>
 <test>
-<!-- test pl.heatmap !-->
+<!-- test 3: pl.heatmap !-->
-<conditional name="input">
+<param name="adata" value="krumsiek11.h5ad" />
-<param name="format" value="h5ad" />
-<param name="adata" value="krumsiek11.h5ad" />
-</conditional>
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.heatmap"/>
 <conditional name="var_names">
 <param name="type" value="all"/>
 <param name="dendrogram" value="True"/>
 <param name="swap_axes" value="True"/>
 <param name="show_gene_labels" value="False"/>
 <section name="matplotlib_pyplot_imshow">
 <param name="cmap" value="YlGnBu"/>
-<param name="interpolation" value="none"/>
+<param name="interpolation" value="None"/>
 <param name="origin" value="upper"/>
 </section>
 </conditional>
 <assert_stdout>
 <has_text_matching expression="sc.pl.heatmap"/>
 <has_text_matching expression="groupby='cell_type'"/>
 <has_text_matching expression="log=False"/>
 <has_text_matching expression="use_raw=False"/>
 <has_text_matching expression="num_categories=7"/>
 <has_text_matching expression="dendrogram=True"/>
-<has_text_matching expression="var_group_positions=None"/>
-<has_text_matching expression="var_group_labels=None"/>
 <has_text_matching expression="figsize=\(10, 3\)"/>
 <has_text_matching expression="swap_axes=True"/>
 <has_text_matching expression="show_gene_labels=False"/>
-<has_text_matching expression="interpolation='none'"/>
 <has_text_matching expression="cmap='YlGnBu'"/>
 <has_text_matching expression="origin='upper'"/>
 </assert_stdout>
 <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="sim_size"/>
 </test>
 <test>
-<!-- test pl.dotplot !-->
+<!-- test 4: pl.dotplot !-->
-<conditional name="input">
+<param name="adata" value="pbmc68k_reduced.h5ad" />
-<param name="format" value="h5ad" />
-<param name="adata" value="pbmc68k_reduced.h5ad" />
-</conditional>
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.dotplot"/>
 <conditional name="var_names">
 <param name="type" value="custom"/>
 <param name="groupby" value="louvain"/>
 <param name="log" value="False"/>
 <param name="use_raw" value="False"/>
 <param name="num_categories" value="7"/>
 <param name="dendrogram" value="True"/>
-<conditional name="figsize">
-<param name="test" value="no"/>
-</conditional>
-<param name="dendrogram" value="False"/>
 <repeat name="var_group_positions">
 <param name="start" value="0"/>
 <param name="end" value="1"/>
 <param name="label" value="B cells"/>
 </repeat>
 <repeat name="var_group_positions">
 <param name="start" value="11"/>
 <param name="end" value="12"/>
 <param name="label" value="dendritic"/>
 </repeat>
+<conditional name="figsize">
+<param name="test" value="no"/>
+</conditional>
 <param name="color_map" value="hot"/>
 <param name="dot_max" value="0.7"/>
 <param name="dot_min" value="0.1"/>
 <section name="matplotlib_pyplot_scatter">
 <param name="linewidths" value="0" />
 <has_text_matching expression="var_names=\['CD79A', 'MS4A1', 'CD8A', 'CD8B', 'LYZ', 'GNLY', 'NKG7', 'RP3-467N11.1', 'FCGR3A', 'FCER1A', 'CST3', 'POU2AF1', 'LINC00402'\]" />
 <has_text_matching expression="groupby='louvain'"/>
 <has_text_matching expression="log=False"/>
 <has_text_matching expression="use_raw=False"/>
 <has_text_matching expression="num_categories=7"/>
-<has_text_matching expression="dendrogram=False"/>
+<has_text_matching expression="dendrogram=True"/>
 <has_text_matching expression="var_group_positions=\[\(0, 1\), \(11, 12\)\]"/>
 <has_text_matching expression="var_group_labels=\['B cells', 'dendritic'\]"/>
 <has_text_matching expression="color_map='hot'"/>
 <has_text_matching expression="dot_max=0.7"/>
 <has_text_matching expression="dot_min=0.1"/>
 <has_text_matching expression="edgecolors='face'"/>
 </assert_stdout>
 <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="sim_size"/>
 </test>
 <test>
-<!-- test pl.violin !-->
+<!-- test 5: pl.violin !-->
-<conditional name="input">
+<param name="adata" value="pbmc68k_reduced.h5ad" />
-<param name="format" value="h5ad" />
-<param name="adata" value="pbmc68k_reduced.h5ad" />
-</conditional>
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.violin"/>
 <conditional name="key_variables">
 <param name="type" value="custom"/>
 <assert_stdout>
 <has_text_matching expression="sc.pl.violin"/>
 <has_text_matching expression="keys=\['n_genes', 'percent_mito', 'n_counts'\]" />
 <has_text_matching expression="log=False"/>
 <has_text_matching expression="use_raw=False"/>
-<has_text_matching expression="sstripplot=True"/>
+<has_text_matching expression="stripplot=True"/>
 <has_text_matching expression="jitter=True"/>
 <has_text_matching expression="size=1"/>
 <has_text_matching expression="multi_panel=True"/>
+<has_text_matching expression="figsize=\(20, 20\)"/>
 <has_text_matching expression="scale='width'"/>
 <has_text_matching expression="bw='scott'"/>
 <has_text_matching expression="scale='width'"/>
 <has_text_matching expression="linewidth=0.0"/>
 <has_text_matching expression="color='AliceBlue'"/>
 <has_text_matching expression="saturation=0.75"/>
 </assert_stdout>
 <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="sim_size"/>
 </test>
 <test>
-<!-- test pl.matrixplot !-->
+<!-- test 6: pl.stacked_violin !-->
-<conditional name="input">
+<param name="adata" value="krumsiek11.h5ad" />
-<param name="format" value="h5ad" />
+<param name="format" value="png"/>
-<param name="adata" value="krumsiek11.h5ad" />
+<conditional name="method">
-</conditional>
+<param name="method" value="pl.stacked_violin"/>
-<param name="format" value="png"/>
-<conditional name="method">
-<param name="method" value="pl.matrixplot"/>
 <conditional name="var_names">
 <param name="type" value="all"/>
 </conditional>
 <param name="groupby" value="cell_type"/>
 <param name="log" value="False"/>
 <param name="dendrogram" value="True"/>
 <conditional name="figsize">
 <param name="test" value="no"/>
 </conditional>
 <param name="swap_axes" value="True"/>
+<section name="violin_plot">
+<conditional name="stripplot">
+<param name="stripplot" value="True"/>
+<param name="jitter" value="True"/>
+<param name="size" value="1"/>
+</conditional>
+<param name="scale" value="width"/>
+</section>
+<param name="row_palette" value="muted"/>
+<param name="standard_scale" value="None"/>
+<section name="seaborn_violinplot">
+<param name="bw" value="scott"/>
+<param name="linewidth" value="0"/>
+<param name="color" value="AliceBlue"/>
+<param name="palette" value="viridis"/>
+<param name="saturation" value="0.75"/>
+</section>
+</conditional>
+<assert_stdout>
+<has_text_matching expression="sc.pl.stacked_violin"/>
+<has_text_matching expression="groupby='cell_type'"/>
+<has_text_matching expression="log=False"/>
+<has_text_matching expression="use_raw=False"/>
+<has_text_matching expression="num_categories=7"/>
+<has_text_matching expression="dendrogram=True"/>
+<has_text_matching expression="swap_axes=True"/>
+<has_text_matching expression="stripplot=True"/>
+<has_text_matching expression="jitter=True"/>
+<has_text_matching expression="size=1"/>
+<has_text_matching expression="scale='width'"/>
+<has_text_matching expression="bw='scott'"/>
+<has_text_matching expression="scale='width'"/>
+<has_text_matching expression="linewidth=0.0"/>
+<has_text_matching expression="color='AliceBlue'"/>
+<has_text_matching expression="palette='viridis'"/>
+<has_text_matching expression="saturation=0.75"/>
+</assert_stdout>
+<output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="sim_size"/>
+</test>
+<test>
+<!-- test 7: 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">
+<param name="type" value="all"/>
+</conditional>
+<param name="groupby" value="cell_type"/>
+<param name="log" value="False"/>
+<param name="use_raw" value="False"/>
+<param name="num_categories" value="7"/>
+<param name="dendrogram" value="True"/>
+<conditional name="figsize">
+<param name="test" value="no"/>
+</conditional>
+<param name="swap_axes" value="True"/>
 <section name="matplotlib_pyplot_pcolor">
 <param name="cmap" value="viridis"/>
 <param name="edgecolors" value="face"/>
 <param name="snap" value="False"/>
 </section>
 <has_text_matching expression="groupby='cell_type'"/>
 <has_text_matching expression="log=False"/>
 <has_text_matching expression="use_raw=False"/>
 <has_text_matching expression="num_categories=7"/>
 <has_text_matching expression="dendrogram=True"/>
-<has_text_matching expression="var_group_positions=None"/>
-<has_text_matching expression="var_group_labels=None"/>
 <has_text_matching expression="swap_axes=True"/>
 <has_text_matching expression="cmap='viridis'"/>
 <has_text_matching expression="edgecolors='face'"/>
 <has_text_matching expression="snap=False"/>
 </assert_stdout>
 <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="sim_size"/>
 </test>
 <test>
-<!-- test pl.clustermap !-->
+<!-- test 8: pl.clustermap !-->
-<conditional name="input">
+<param name="adata" value="krumsiek11.h5ad" />
-<param name="format" value="h5ad" />
-<param name="adata" value="krumsiek11.h5ad" />
-</conditional>
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.clustermap"/>
-<param name="obs_keys" value="cell_type"/>
 <param name="use_raw" value="False"/>
 <section name="seaborn_clustermap">
 <param name="method" value="single"/>
-<param name="metric" value="braycurtis"/>
+<param name="metric" value="euclidean"/>
 <param name="z_score" value="None"/>
 <param name="standard_scale" value="None"/>
 <param name="col_cluster" value="False"/>
 <param name="row_cluster" value="False"/>
 </section>
 </conditional>
 <assert_stdout>
 <has_text_matching expression="sc.pl.clustermap"/>
 <has_text_matching expression="adata=adata" />
-<has_text_matching expression="obs_keys='cell_type'" />
 <has_text_matching expression="use_raw=False"/>
 <has_text_matching expression="method='single'"/>
-<has_text_matching expression="metric='braycurtis'"/>
+<has_text_matching expression="metric='euclidean'"/>
-<has_text_matching expression="z_score=None"/>
-<has_text_matching expression="standard_scale=None"/>
 <has_text_matching expression="col_cluster=False"/>
 <has_text_matching expression="row_cluster=False"/>
 </assert_stdout>
 <output name="out_png" file="pl.clustermap.krumsiek11.png" ftype="png" compare="sim_size"/>
 </test>
 <test>
-<!-- test pl.highest_expr_genes !-->
+<!-- test 9: pl.highest_expr_genes !-->
-<conditional name="input">
+<param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
-<param name="format" value="h5ad" />
-<param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
-</conditional>
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.highest_expr_genes"/>
 <param name="n_top" value="30"/>
 <param name="gene_symbols" value="means"/>
 <has_text_matching expression="saturation=0.5"/>
 </assert_stdout>
 <output name="out_png" file="pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png" ftype="png" compare="sim_size"/>
 </test>
 <test>
-<!-- test pl.pca !-->
+<!-- test 10: pl.highly_variable_genes !-->
-<conditional name="input">
+<param name="adata" value="pp.highly_variable_genes.seurat.blobs.h5ad" />
-<param name="format" value="h5ad" />
+<param name="format" value="png"/>
-<param name="adata" value="pbmc68k_reduced.h5ad" />
+<conditional name="method">
-</conditional>
+<param name="method" value="pl.highly_variable_genes"/>
+<param name="log" value="false"/>
+<param name="highly_variable_genes" value="true"/>
+</conditional>
+<assert_stdout>
+<has_text_matching expression="sc.pl.highly_variable_genes"/>
+<has_text_matching expression="adata_or_result=adata" />
+<has_text_matching expression="log=False" />
+<has_text_matching expression="highly_variable_genes=True"/>
+</assert_stdout>
+<output name="out_png" file="pl.highly_variable_genes.seurat.blobs.png" ftype="png" compare="sim_size"/>
+</test>
+<test>
+<!-- test 11: 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"/>
 <param name="use_raw" value="False"/>
 <has_text_matching expression="sc.pl.pca"/>
 <has_text_matching expression="save='.pdf'" />
 <has_text_matching expression="color=\['CD3D', 'CD79A'\]" />
 <has_text_matching expression="use_raw=False" />
 <has_text_matching expression="sort_order=True" />
-<has_text_matching expression="groups=None" />
 <has_text_matching expression="components=\['1,2', '1,3'\]" />
 <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="edgecolors='face" />
 </assert_stdout>
 <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/>
 </test>
 <test>
-<!-- test pl.pca_loadings !-->
+<!-- test 12: pl.pca_loadings !-->
-<conditional name="input">
+<param name="adata" value="pp.pca.krumsiek11.h5ad" />
-<param name="format" value="h5ad" />
-<param name="adata" value="pp.pca.krumsiek11.h5ad" />
-</conditional>
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.pca_loadings"/>
 <param name="components" value="1,2,3"/>
 </conditional>
 <assert_stdout>
 <has_text_matching expression="sc.pl.pca_loadings"/>
 <has_text_matching expression="components=\[1, 2, 3\]" />
 </assert_stdout>
-<output name="out_png" file="pl.pca_loadings.pp.pca.krumsiek11.png"/>
+<output name="out_png" file="pl.pca_loadings.pp.pca.krumsiek11.png" compare="sim_size"/>
 </test>
 <test>
-<!-- test pl.pca_variance_ratio !-->
+<!-- test 13: pl.pca_variance_ratio !-->
-<conditional name="input">
+<param name="adata" value="pp.pca.krumsiek11.h5ad" />
-<param name="format" value="h5ad" />
-<param name="adata" value="pp.pca.krumsiek11.h5ad" />
-</conditional>
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.pca_variance_ratio"/>
 <param name="n_pcs" value="5"/>
 <param name="log" value="False"/>
 <assert_stdout>
 <has_text_matching expression="sc.pl.pca_variance_ratio"/>
 <has_text_matching expression="n_pcs=5" />
 <has_text_matching expression="log=False" />
 </assert_stdout>
-<output name="out_png" file="pl.pca_variance_ratio.pp.pca.krumsiek11.png"/>
+<output name="out_png" file="pl.pca_variance_ratio.pp.pca.krumsiek11.png" compare="sim_size"/>
 </test>
 <test>
-<!-- test pl.pca_overview !-->
+<!-- test 14: pl.pca_overview !-->
-<conditional name="input">
+<param name="adata" value="pp.pca.krumsiek11.h5ad" />
-<param name="format" value="h5ad" />
-<param name="adata" value="pp.pca.krumsiek11.h5ad" />
-</conditional>
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.pca_overview"/>
-<param name="color" value="cell_type"/>
 <param name="use_raw" value="False"/>
 <param name="sort_order" value="True"/>
 <section name="plot">
-<param name="projection" value="3d"/>
+<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="size" value="1"/>
 <param name="palette" value="viridis"/>
 <param name="frameon" value="True"/>
 <param name="ncols" value="4"/>
 <param name="wspace" value="0.1"/>
 <param name="hspace" value="0.25"/>
 </section>
-<section name="matplotlib_pyplot_scatter">
-<param name="linewidths" value="0"/>
-<param name="edgecolors" value="face"/>
-<param name="vmin" value="-5"/>
-<param name="vmax" value="5"/>
-<param name="edgecolors" value="face"/>
-</section>
 </conditional>
 <assert_stdout>
 <has_text_matching expression="sc.pl.pca_overview"/>
-<has_text_matching expression="color=\['cell_type'\]"/>
 <has_text_matching expression="use_raw=False"/>
 <has_text_matching expression="sort_order=True"/>
-<has_text_matching expression="groups=None"/>
+<has_text_matching expression="projection='2d'"/>
-<has_text_matching expression="components=None"/>
-<has_text_matching expression="projection='3d'"/>
 <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="size=1.0"/>
 <has_text_matching expression="palette='viridis'"/>
 <has_text_matching expression="frameon=True"/>
 <has_text_matching expression="ncols=4"/>
 <has_text_matching expression="wspace=0.1"/>
 <has_text_matching expression="hspace=0.25"/>
-<has_text_matching expression="vmin=-5.0"/>
-<has_text_matching expression="vmax=5.0"/>
-<has_text_matching expression="linewidths=0.0"/>
-<has_text_matching expression="edgecolors='face'"/>
 </assert_stdout>
 <output name="out_png" file="pl.pca_overview.pp.pca.krumsiek11.png" compare="sim_size"/>
 </test>
 <test>
-<!-- test pl.tsne !-->
+<!-- test 15: pl.tsne !-->
-<conditional name="input">
+<param name="adata" value="tl.tsne.krumsiek11.h5ad" />
-<param name="format" value="h5ad" />
-<param name="adata" value="tl.tsne.krumsiek11.h5ad" />
-</conditional>
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.tsne"/>
 <param name="use_raw" value="False"/>
 <conditional name="edges">
 <param name="edgecolors" value="face"/>
 </section>
 </conditional>
 <assert_stdout>
 <has_text_matching expression="sc.pl.tsne"/>
-<has_text_matching expression="color=None"/>
 <has_text_matching expression="use_raw=False"/>
 <has_text_matching expression="edges=False"/>
 <has_text_matching expression="arrows=False"/>
 <has_text_matching expression="sort_order=True"/>
-<has_text_matching expression="groups=None"/>
-<has_text_matching expression="components=None"/>
 <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="size=1.0"/>
 <has_text_matching expression="edgecolors='face'"/>
 </assert_stdout>
 <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="sim_size"/>
 </test>
 <test>
-<!-- test pl.umap !-->
+<!-- test 16: pl.umap !-->
-<conditional name="input">
+<param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
-<param name="format" value="h5ad" />
-<param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
-</conditional>
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.umap"/>
 <param name="color" value="paul15_clusters"/>
 <param name="use_raw" value="False"/>
 <has_text_matching expression="edges=True"/>
 <has_text_matching expression="edges_width=0.1"/>
 <has_text_matching expression="edges_color='AliceBlue'"/>
 <has_text_matching expression="arrows=False"/>
 <has_text_matching expression="sort_order=True"/>
-<has_text_matching expression="groups=None"/>
-<has_text_matching expression="components=None"/>
 <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="size=1.0"/>
 <has_text_matching expression="edgecolors='face'"/>
 </assert_stdout>
 <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
 </test>
 <test>
-<!-- test pl.diffmap !-->
+<!-- test 17: pl.diffmap !-->
-<conditional name="input">
+<param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
-<param name="format" value="h5ad" />
-<param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
-</conditional>
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.diffmap"/>
 <param name="color" value="paul15_clusters"/>
 <param name="use_raw" value="False"/>
 <assert_stdout>
 <has_text_matching expression="sc.pl.diffmap"/>
 <has_text_matching expression="color=\['paul15_clusters'\]"/>
 <has_text_matching expression="use_raw=False"/>
 <has_text_matching expression="sort_order=True"/>
-<has_text_matching expression="groups=None"/>
-<has_text_matching expression="components=None"/>
 <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="size=1.0"/>
 <has_text_matching expression="linewidths=0.0"/>
 <has_text_matching expression="edgecolors='face'"/>
 </assert_stdout>
 <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
 </test>
+<test>
+<!-- test 18: 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"/>
+<conditional name="edges">
+<param name="edges" value="True"/>
+<param name="edges_width" value="0.1"/>
+<param name="edges_color" value="Crimson"/>
+</conditional>
+<param name="arrows" value="false"/>
+<param name="sort_order" value="false"/>
+<section name="plot">
+<param name="projection" value="2d"/>
+<param name="legend_loc" value="right margin"/>
+<param name="legend_fontweight" value="normal"/>
+<param name="palette" value="viridis"/>
+<param name="frameon" value="True"/>
+<param name="ncols" value="4"/>
+<param name="wspace" value="0.1"/>
+<param name="hspace" value="0.25"/>
+</section>
+<section name="matplotlib_pyplot_scatter">
+<param name="linewidths" value="0"/>
+<param name="edgecolors" value="face"/>
+</section>
+</conditional>
+<assert_stdout>
+<has_text_matching expression="sc.pl.draw_graph"/>
+<has_text_matching expression="use_raw=False"/>
+<has_text_matching expression="edges=True"/>
+<has_text_matching expression="edges_width=0.1"/>
+<has_text_matching expression="edges_color='Crimson'"/>
+<has_text_matching expression="arrows=False"/>
+<has_text_matching expression="sort_order=False"/>
+<has_text_matching expression="projection='2d'"/>
+<has_text_matching expression="legend_loc='right margin'"/>
+<has_text_matching expression="legend_fontweight='normal'"/>
+<has_text_matching expression="palette='viridis'"/>
+<has_text_matching expression="frameon=True"/>
+<has_text_matching expression="ncols=4"/>
+<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"/>
+</assert_stdout>
+<output name="out_png" file="pl.draw_graph.png" ftype="png" compare="sim_size"/>
+</test>
 <!--<test>
 < test pl.dpt_groups_pseudotime >
-<conditional name="input">
+<param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
-<param name="format" value="h5ad" />
-<param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
-</conditional>
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.dpt_groups_pseudotime"/>
 <param name="color_map" value="viridis"/>
 </conditional>
 <has_text_matching expression="color_map='viridis'"/>
 </assert_stdout>
 <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 pl.dpt_timeseries !-->
+<!-- test 19: pl.dpt_timeseries !-->
-<conditional name="input">
+<param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
-<param name="format" value="h5ad" />
-<param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
-</conditional>
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.dpt_timeseries"/>
 <conditional name="heatmap">
 <param name="as_heatmap" value="True"/>
 </assert_stdout>
 <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 pl.paga
-<conditional name="input">
+<param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad" />
-<param name="format" value="h5ad" />
-<param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad" />
-</conditional>
 <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="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 pl.paga_compare
+</test>!-->
+<!--<test>
+test pl.paga_path
+</test>!-->
+<test>
+<!-- test 20: 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="n_genes" value="10"/>
+<param name="fontsize" value="8"/>
+<param name="ncols" value="4"/>
+<param name="sharey" value="true"/>
+</conditional>
+<assert_stdout>
+<has_text_matching expression="sc.pl.rank_genes_groups"/>
+<has_text_matching expression="n_genes=10"/>
+<has_text_matching expression="fontsize=8"/>
+<has_text_matching expression="ncols=4"/>
+<has_text_matching expression="sharey=True"/>
+</assert_stdout>
+<output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
+</test>
+<test>
+<!-- test 21: 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">
+<param name="select" value="n_genes"/>
+<param name="n_genes" value="10"/>
+</conditional>
+<param name="use_raw" value="false"/>
+<param name="split" value="true"/>
+<section name="violin_plot">
+<conditional name="stripplot">
+<param name="stripplot" value="True"/>
+<param name="jitter" value="True"/>
+<param name="size" value="1"/>
+</conditional>
+<param name="scale" value="width"/>
+</section>
+</conditional>
+<assert_stdout>
+<has_text_matching expression="sc.pl.rank_genes_groups_violin"/>
+<has_text_matching expression="n_genes=10"/>
+<has_text_matching expression="use_raw=False"/>
+<has_text_matching expression="split=True"/>
+<has_text_matching expression="strip=True"/>
+<has_text_matching expression="jitter=True"/>
+<has_text_matching expression="size=1"/>
+<has_text_matching expression="scale='width'"/>
+</assert_stdout>
+<output_collection name="collection_png">
+<element name="Ery" file="pl.rank_genes_groups_violin.Ery.png" ftype="png" compare="sim_size"/>
+<element name="Mk" file="pl.rank_genes_groups_violin.Mk.png" ftype="png" compare="sim_size"/>
+<element name="Mo" file="pl.rank_genes_groups_violin.Mo.png" ftype="png" compare="sim_size"/>
+<element name="Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="sim_size"/>
+<element name="progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="sim_size"/>
+</output_collection>
+</test>
 </tests>
 <help><![CDATA[
 Generic: Scatter plot along observations or variables axes (`pl.scatter`)
 =========================================================================
 ==================================
 Wraps `seaborn.violinplot` for `anndata.AnnData`.
 More details on the `scanpy documentation
+<https://scanpy.readthedocs.io/en/latest/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>`__
 Generic: Heatmap of the mean expression values per cluster (`pl.matrixplot`)
 ============================================================================
 If groupby is not given, the matrixplot assumes that all data belongs to a single
 category.
 More details on the `scanpy documentation
-<https://scanpy.readthedocs.io/en/latest/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://scanpy.readthedocs.io/en/latest/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
 a cell. The `n_top` genes with the highest mean fraction over all cells are
 plotted as boxplots.
-This plot is similar to the `scater` package function `plotHighestExprs(type= "highest-expression")`, see `here
+This plot is similar to the `scater` package function `plotHighestExprs(type= "highest-expression")`
-<https://bioconductor.org/packages/devel/bioc/vignettes/scater/inst/doc/vignette-qc.html>`__.
--- Davis McCarthy and Aaron Lun
+More details on the `scanpy documentation
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.highest_expr_genes.html>`__
-More details on the `scanpy documentation
-<https://scanpy.readthedocs.io/en/latest/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/stable/api/scanpy.pl.highly_variable_genes.html>`__
 PCA: Scatter plot in PCA coordinates (`pl.pca`)
 ===============================================
 More details on the `scanpy documentation
-<https://scanpy.readthedocs.io/en/latest/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://scanpy.readthedocs.io/en/latest/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://scanpy.readthedocs.io/en/latest/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://scanpy.readthedocs.io/en/latest/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://scanpy.readthedocs.io/en/latest/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://scanpy.readthedocs.io/en/latest/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://scanpy.readthedocs.io/en/latest/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://scanpy.readthedocs.io/en/latest/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://scanpy.readthedocs.io/en/latest/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://scanpy.readthedocs.io/en/latest/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/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/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/stable/api/scanpy.pl.rank_genes_groups.html>`__
+Marker genes: Plot ranking of genes for all tested comparisons (`pl.rank_genes_groups_violin`)
+==============================================================================================
+More details on the `scanpy documentation
+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_violin.html>`__
 ]]></help>
 <expand macro="citations"/>
 </tool>

Mercurial > repos > iuc > scanpy_plot

comparison plot.xml @ 1:072b759d0fca draft