Mercurial > repos > iuc > scanpy_plot
changeset 11:95777145cb92 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
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--- a/macros.xml Wed Sep 22 21:13:39 2021 +0000 +++ b/macros.xml Wed Nov 08 14:47:20 2023 +0000 @@ -1,12 +1,16 @@ <macros> - <token name="@version@">1.7.1</token> - <token name="@profile@">19.01</token> + <token name="@version@">1.9.6</token> + <token name="@profile@">22.05</token> <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token> <xml name="requirements"> <requirements> <requirement type="package" version="@version@">scanpy</requirement> - <requirement type="package" version="2.0.17">loompy</requirement> - <requirement type="package" version="0.8.3">leidenalg</requirement> + <requirement type="package" version="3.0.6">loompy</requirement> + <requirement type="package" version="0.10.1">leidenalg</requirement> + <requirement type="package" version="0.8.1">louvain</requirement> + <requirement type="package" version="1.5.3">pandas</requirement> + <requirement type="package" version="3.7">matplotlib</requirement> + <requirement type="package" version="0.12.2">seaborn</requirement> <yield /> </requirements> </xml> @@ -15,9 +19,15 @@ <xref type="bio.tools">scanpy</xref> </xrefs> </xml> + <xml name="creators"> + <creator> + <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" /> + </creator> + </xml> <xml name="citations"> <citations> <citation type="doi">10.1186/s13059-017-1382-0</citation> + <citation type="doi">10.1093/gigascience/giaa102</citation> </citations> </xml> <xml name="version_command"> @@ -56,7 +66,7 @@ <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/> </xml> <token name="@CMD_read_inputs@"><![CDATA[ -adata = sc.read('anndata.h5ad') +adata = sc.read_h5ad('anndata.h5ad') ]]> </token> <xml name="inputs_common_advanced"> @@ -66,12 +76,12 @@ </xml> <xml name="anndata_outputs"> <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/> - <data name="hidden_output" format="txt" label="Log file" > + <data name="hidden_output" format="txt" label="Log file" > <filter>advanced_common['show_log']</filter> </data> </xml> <token name="@CMD_anndata_write_outputs@"><![CDATA[ -adata.write('anndata.h5ad') +adata.write_h5ad('anndata.h5ad') with open('anndata_info.txt','w', encoding='utf-8') as ainfo: print(adata, file=ainfo) ]]> @@ -875,7 +885,7 @@ </xml> <xml name="param_color_map"> <param argument="color_map" type="select" label="Color map to use for continous variables" help=""> - <option value="None">Default</option> + <option value="" >Default</option> <expand macro="matplotlib_pyplot_colormap"/> </param> </xml> @@ -979,7 +989,7 @@ @CMD_param_legend_fontsize@ legend_fontweight='$method.plot.legend_fontweight', @CMD_param_size@ - #if str($method.plot.color_map) != 'None' + #if str($method.plot.color_map) != '' color_map='$method.plot.color_map', #end if #if str($method.plot.palette) != ''
--- a/plot.xml Wed Sep 22 21:13:39 2021 +0000 +++ b/plot.xml Wed Nov 08 14:47:20 2023 +0000 @@ -1,9 +1,9 @@ -<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"/> @@ -21,11 +21,32 @@ #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 $method.type.type == 'xy' - x='$method.type.x', - y='$method.type.y', + #if $method.type.type == 'xy': + x=x_field, + y=y_field, #if str($method.type.color) != '' color='$method.type.color', #end if @@ -265,6 +286,29 @@ @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@ @@ -305,7 +349,7 @@ #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=$method.n_avg, @@ -358,6 +402,9 @@ sc.pl.rank_genes_groups_dotplot( @CMD_param_plot_inputs@ @CMD_pl_rank_genes_groups_ext@ + #if str($method.gene_symbols) != '' + gene_symbols='$method.gene_symbols', + #end if @CMD_params_plots@ @CMD_pl_dotplot@) @@ -366,6 +413,9 @@ @CMD_param_plot_inputs@ @CMD_pl_rank_genes_groups_ext@ @CMD_params_plots@ + #if str($method.gene_symbols) != '' + gene_symbols='$method.gene_symbols', + #end if @CMD_pl_heatmap@) #else if $method.method == 'pl.rank_genes_groups_matrixplot' @@ -373,6 +423,9 @@ @CMD_param_plot_inputs@ @CMD_pl_rank_genes_groups_ext@ @CMD_params_plots@ + #if str($method.gene_symbols) != '' + gene_symbols='$method.gene_symbols', + #end if @CMD_pl_matrixplot@) #else if $method.method == 'pl.rank_genes_groups_stacked_violin' @@ -380,6 +433,9 @@ @CMD_param_plot_inputs@ @CMD_pl_rank_genes_groups_ext@ @CMD_params_plots@ + #if str($method.gene_symbols) != '' + gene_symbols='$method.gene_symbols', + #end if @CMD_pl_stacked_violin@) #end if @@ -397,7 +453,6 @@ <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> @@ -409,15 +464,14 @@ <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> @@ -436,6 +490,7 @@ <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> @@ -666,6 +721,27 @@ <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> @@ -730,7 +806,7 @@ </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" /> + <expand macro="sanitize_query" /> </param> </when> </conditional> @@ -745,45 +821,49 @@ <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 ${on_string}"> <discover_datasets pattern="rank_genes_groups_(?P<designation>.*).png" format="png"/> <filter>format == 'png' and method['method'] == 'pl.rank_genes_groups_violin'</filter> </collection> - <data name="out_pdf" format="pdf" from_work_dir="*.pdf" label="${tool.name} (${method.method}) on ${on_string}"> - <filter>format == 'pdf' and method['method'] != pl.rank_genes_groups_violin</filter> + <data name="out_pdf" format="pdf" from_work_dir="*.pdf" label="PDF plot from ${tool.name} (${method.method}) on ${on_string}"> + <filter>format == 'pdf' and method['method'] != 'pl.rank_genes_groups_violin'</filter> </data> - <collection name="collection_pdf" type="list" label="${tool.name} (${method.method}) on ${on_string}"> + <collection name="collection_pdf" type="list" label="PDF plots from ${tool.name} (${method.method}) on ${on_string}"> <discover_datasets pattern="rank_genes_groups_(?P<designation>.*).pdf" format="pdf"/> <filter>format == 'pdf' and method['method'] == 'pl.rank_genes_groups_violin'</filter> </collection> - <data name="out_svg" format="svg" from_work_dir="*.svg" label="${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<designation>.*).svg" format="svg"/> <filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter> </collection> @@ -792,8 +872,8 @@ </data> </outputs> <tests> - <test> - <!-- test 0: pl.scatter !--> + <test expect_num_outputs="2"> + <!-- test 1: pl.scatter --> <param name="adata" value="pbmc68k_reduced.h5ad" /> <param name="format" value="png"/> <conditional name="method"> @@ -837,8 +917,8 @@ </output> <output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="sim_size"/> </test> - <test> - <!-- test 1: pl.scatter !--> + <test expect_num_outputs="2"> + <!-- test 2: pl.scatter --> <param name="adata" value="krumsiek11.h5ad" /> <param name="format" value="png"/> <conditional name="method"> @@ -870,8 +950,8 @@ <output name="hidden_output"> <assert_contents> <has_text_matching expression="sc.pl.scatter"/> - <has_text_matching expression="x='EKLF'" /> - <has_text_matching expression="y='Cebpa'"/> + <has_text_matching expression="x_field='EKLF'" /> + <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'"/> @@ -885,8 +965,8 @@ </output> <output name="out_png" file="pl.scatter.krumsiek11.png" ftype="png" compare="sim_size"/> </test> - <test> - <!-- test 2: pl.heatmap !--> + <test expect_num_outputs="2"> + <!-- test 3: pl.heatmap --> <param name="adata" value="krumsiek11.h5ad" /> <param name="format" value="png"/> <conditional name="method"> @@ -933,8 +1013,8 @@ </output> <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="sim_size"/> </test> - <test> - <!-- test 2.1: pl.heatmap with symbols !--> + <test expect_num_outputs="2"> + <!-- 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"> @@ -983,8 +1063,8 @@ </assert_contents> </output> </test> - <test> - <!-- test 3: pl.dotplot !--> + <test expect_num_outputs="2"> + <!-- test 5: pl.dotplot --> <param name="adata" value="pbmc68k_reduced.h5ad" /> <param name="format" value="png"/> <conditional name="method"> @@ -1042,8 +1122,8 @@ </output> <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="sim_size"/> </test> - <test> - <!-- test 3.1: pl.dotplot with symbols !--> + <test expect_num_outputs="2"> + <!-- 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"> @@ -1080,8 +1160,8 @@ </assert_contents> </output> </test> - <test> - <!-- test 4: pl.violin !--> + <test expect_num_outputs="2"> + <!-- test 7: pl.violin --> <param name="adata" value="pbmc68k_reduced.h5ad" /> <param name="format" value="png"/> <conditional name="method"> @@ -1137,8 +1217,8 @@ </output> <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="sim_size"/> </test> - <test> - <!-- test 5: pl.stacked_violin !--> + <test expect_num_outputs="2"> + <!-- test 8: pl.stacked_violin --> <param name="adata" value="krumsiek11.h5ad" /> <param name="format" value="png"/> <conditional name="method"> @@ -1197,8 +1277,8 @@ </output> <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="sim_size"/> </test> - <test> - <!-- test 5.1: pl.stacked_violin with symbols !--> + <test expect_num_outputs="2"> + <!-- 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"> @@ -1232,8 +1312,8 @@ </assert_contents> </output> </test> - <test> - <!-- test 6: pl.matrixplot !--> + <test expect_num_outputs="2"> + <!-- test 10: pl.matrixplot --> <param name="adata" value="krumsiek11.h5ad" /> <param name="format" value="png"/> <conditional name="method"> @@ -1276,8 +1356,8 @@ </output> <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="sim_size"/> </test> - <test> - <!-- test 6.1: pl.matrixplot with symbols !--> + <test expect_num_outputs="2"> + <!-- 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"> @@ -1316,8 +1396,8 @@ </assert_contents> </output> </test> - <test> - <!-- test 7: pl.clustermap !--> + <test expect_num_outputs="2"> + <!-- test 12: pl.clustermap --> <param name="adata" value="krumsiek11.h5ad" /> <param name="format" value="png"/> <conditional name="method"> @@ -1348,8 +1428,8 @@ </output> <output name="out_png" file="pl.clustermap.krumsiek11.png" ftype="png" compare="sim_size"/> </test> - <test> - <!-- test 8: pl.highest_expr_genes !--> + <test expect_num_outputs="2"> + <!-- 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"> @@ -1375,8 +1455,8 @@ </output> <output name="out_png" file="pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png" ftype="png" compare="sim_size"/> </test> - <test> - <!-- test 9: pl.highly_variable_genes !--> + <test expect_num_outputs="2"> + <!-- 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"> @@ -1397,8 +1477,8 @@ </output> <output name="out_png" file="pl.highly_variable_genes.seurat.blobs.png" ftype="png" compare="sim_size"/> </test> - <test> - <!-- test 10: pl.pca !--> + <test expect_num_outputs="2"> + <!-- test 15: pl.pca --> <param name="adata" value="pbmc68k_reduced.h5ad" /> <param name="format" value="pdf"/> <conditional name="method"> @@ -1453,13 +1533,13 @@ <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 11: pl.pca_loadings !--> + <test expect_num_outputs="2"> + <!-- test 16: pl.pca_loadings --> <param name="adata" value="pp.pca.krumsiek11.h5ad" /> <param name="format" value="png"/> <conditional name="method"> @@ -1477,8 +1557,8 @@ </output> <output name="out_png" file="pl.pca_loadings.pp.pca.krumsiek11.png" compare="sim_size"/> </test> - <test> - <!-- test 12: pl.pca_variance_ratio !--> + <test expect_num_outputs="2"> + <!-- test 17: pl.pca_variance_ratio --> <param name="adata" value="pp.pca.krumsiek11.h5ad" /> <param name="format" value="png"/> <conditional name="method"> @@ -1498,8 +1578,8 @@ </output> <output name="out_png" file="pl.pca_variance_ratio.pp.pca.krumsiek11.png" compare="sim_size"/> </test> - <test> - <!-- test 13: pl.pca_overview !--> + <test expect_num_outputs="2"> + <!-- test 18: pl.pca_overview --> <param name="adata" value="pp.pca.krumsiek11.h5ad" /> <param name="format" value="png"/> <conditional name="method"> @@ -1541,8 +1621,8 @@ </output> <output name="out_png" file="pl.pca_overview.pp.pca.krumsiek11.png" compare="sim_size"/> </test> - <test> - <!-- test 14: pl.tsne !--> + <test expect_num_outputs="2"> + <!-- test 19: pl.tsne --> <param name="adata" value="tl.tsne.krumsiek11.h5ad" /> <param name="format" value="png"/> <conditional name="method"> @@ -1596,8 +1676,8 @@ </output> <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="sim_size"/> </test> - <test> - <!-- test 15: pl.umap !--> + <test expect_num_outputs="2"> + <!-- 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"> @@ -1656,8 +1736,8 @@ </output> <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/> </test> - <test> - <!-- test 16: pl.diffmap !--> + <test expect_num_outputs="2"> + <!-- 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"> @@ -1707,8 +1787,8 @@ </output> <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/> </test> - <test> - <!-- test 17: pl.draw_graph !--> + <test expect_num_outputs="2"> + <!-- 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"> @@ -1763,22 +1843,48 @@ </output> <output name="out_png" file="pl.draw_graph.png" ftype="png" compare="sim_size"/> </test> - <!--<test> - < test pl.dpt_groups_pseudotime > + <test expect_num_outputs="2"> + <!-- 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> - <has_text_matching expression="sc.pl.dpt_groups_pseudotime"/> - <has_text_matching expression="color_map='viridis'"/> - </assert_stdout> + <section name="advanced_common"> + <param name="show_log" value="true" /> + </section> + <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 18: pl.dpt_timeseries !--> + </test> + <test expect_num_outputs="2"> + <!-- 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"> @@ -1800,15 +1906,14 @@ </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 pl.paga + <test expect_num_outputs="1"> + <!-- 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="labels" value="label" /> + <param name="color" value="louvain"/> <param name="layout" value="fr"/> <param name="random_state" value="0"/> <param name="solid_edges" value="connectivities"/> @@ -1823,19 +1928,40 @@ <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> + <test expect_num_outputs="1"> + <!-- test 27: pl.paga_compare --> + <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_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 19: pl.rank_genes_groups !--> + </test>--> + <test expect_num_outputs="2"> + <!-- 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"/> @@ -1855,8 +1981,8 @@ </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> + <test expect_num_outputs="2"> + <!-- 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"> @@ -1899,13 +2025,13 @@ <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="sim_size"/> </output_collection> </test> - --> - <test> - <!-- test 21: pl.rank_genes_groups_dotplot !--> + <test expect_num_outputs="2"> + <!-- test 30: 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"/> @@ -1933,12 +2059,13 @@ </output> <output name="out_png" file="pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/> </test> - <test> - <!-- test 22: pl.rank_genes_groups_heatmap !--> + <test expect_num_outputs="2"> + <!-- 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"/> @@ -1969,12 +2096,13 @@ </output> <output name="out_png" file="pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/> </test> - <test> - <!-- test 23: pl.rank_genes_groups_matrixplot !--> + <test expect_num_outputs="2"> + <!-- 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"/> @@ -2004,12 +2132,13 @@ </output> <output name="out_png" file="pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/> </test> - <test> - <!-- test 24: pl.rank_genes_groups_stacked_violin !--> + <test expect_num_outputs="2"> + <!-- 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"/> @@ -2057,6 +2186,53 @@ </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`) @@ -2066,7 +2242,7 @@ (`.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`) ======================================================================== @@ -2078,7 +2254,7 @@ 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`) ================================================================= @@ -2095,7 +2271,7 @@ 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`) ================================== @@ -2103,7 +2279,7 @@ 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`) =================================================== @@ -2112,7 +2288,7 @@ 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`) ============================================================================ @@ -2123,7 +2299,7 @@ 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`) =========================================================== @@ -2141,7 +2317,7 @@ 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`) ========================================================================================================= @@ -2153,7 +2329,7 @@ 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`) =================================================================================== @@ -2161,25 +2337,25 @@ 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`) ========================================= @@ -2188,37 +2364,37 @@ 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`) @@ -2231,56 +2407,56 @@ `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>
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