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Scanpy plot new function (galaxyproject#6113)
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* update macros

* update plot.xml

* add test data

* Adding test data

* small change to filter.xml

* Update tools/scanpy/macros.xml

Co-authored-by: Björn Grüning <[email protected]>

---------

Co-authored-by: Björn Grüning <[email protected]>
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@heylf @bgruening
heylf and bgruening authored Aug 20, 2024
1 parent fce5664 commit 0ef475d
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Showing 7 changed files with 111 additions and 2 deletions.
2 changes: 1 addition & 1 deletion tools/scanpy/filter.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -524,7 +524,7 @@ df.to_csv('marker.tsv', sep='\t', index=True)
<has_text_matching expression="adata, key, x, 1.0, 0.2, 'bulk_labels'"/>
</assert_contents>
</output>
<output name="anndata_out" file="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" ftype="h5ad">
<output name="anndata_out" file="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1_out.h5ad" ftype="h5ad">
<assert_contents>
<has_h5_keys keys="obs, var, uns" />
</assert_contents>
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10 changes: 10 additions & 0 deletions tools/scanpy/macros.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -435,6 +435,10 @@ with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
</when>
<when value="customfile">
<param argument="var_names" type="data" format="tabular" label="List of variables to plot" help="This should be a tsv where row = group (e.g. celltypes) and columns = variables."></param>
<param name="header" type="select" label="Header in the list of markers?">
<option value="included">Header incldued</option>
<option value="not_included">Header not included</option>
</param>
</when>
</conditional>
</xml>
Expand Down Expand Up @@ -471,6 +475,12 @@ with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
<expand macro="param_groupby"/>
<expand macro="param_num_categories"/>
</xml>
<token name="@CMD_var_names_header_check@"><![CDATA[
header='infer'
#if $method.var_names.type == 'customfile' and $method.var_names.header == 'not_included' :
header=None
#end if
]]></token>
<token name="@CMD_params_inputs@"><![CDATA[
#if $method.var_names.type == 'custom'
#set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')])
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101 changes: 100 additions & 1 deletion tools/scanpy/plot.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,7 @@ sc.pl.scatter(
frameon=$method.plot.frameon)
#else if $method.method == 'pl.heatmap'
@CMD_var_names_header_check@
sc.pl.heatmap(
@CMD_param_plot_inputs@
#if $method.gene_symbols
Expand All @@ -89,6 +90,7 @@ sc.pl.heatmap(
@CMD_pl_heatmap@)
#else if $method.method == 'pl.dotplot'
@CMD_var_names_header_check@
sc.pl.dotplot(
@CMD_param_plot_inputs@
#if $method.gene_symbols
Expand Down Expand Up @@ -129,6 +131,7 @@ sc.pl.violin(
@CMD_params_seaborn_violinplot@)
#else if $method.method == 'pl.stacked_violin'
@CMD_var_names_header_check@
sc.pl.stacked_violin(
@CMD_param_plot_inputs@
#if $method.gene_symbols
Expand All @@ -139,6 +142,7 @@ sc.pl.stacked_violin(
@CMD_pl_stacked_violin@)
#else if $method.method == 'pl.matrixplot'
@CMD_var_names_header_check@
sc.pl.matrixplot(
@CMD_param_plot_inputs@
#if $method.gene_symbols
Expand Down Expand Up @@ -399,9 +403,26 @@ sc.pl.rank_genes_groups_violin(
scale='$method.violin_plot.scale')
#else if $method.method == 'pl.rank_genes_groups_dotplot'
@CMD_var_names_header_check@
sc.pl.rank_genes_groups_dotplot(
@CMD_param_plot_inputs@
@CMD_pl_rank_genes_groups_ext@
#if $method.var_names.type == 'custom'
#set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')])
var_names=$var_names,
#else if $method.var_names.type == 'customfile'
var_names={key: [v for v in list(value.values()) if pd.notna(v)] for key, value in pd.read_csv('$var_names', sep='\t', index_col=0, header=header).to_dict(orient='index').items()},
#else
n_genes=$method.n_genes,
#end if
#if $method.groupby != ''
groupby='$method.groupby',
#end if
num_categories=$method.num_categories,
#if $method.key != ''
key='$method.key',
#end if
#if $method.gene_symbols
gene_symbols='$method.gene_symbols',
#end if
Expand Down Expand Up @@ -819,6 +840,7 @@ sc.pl.rank_genes_groups_stacked_violin(
</section>
</when>
<when value="pl.rank_genes_groups_dotplot">
<expand macro="params_inputs"/>
<expand macro="pl_rank_genes_groups_ext"/>
<expand macro="params_plots"/>
<expand macro="gene_symbols"/>
Expand Down Expand Up @@ -2033,6 +2055,9 @@ sc.pl.rank_genes_groups_stacked_violin(
<param name="method" value="pl.rank_genes_groups_dotplot"/>
<param name="gene_symbols" value="symbol"/>
<param name="n_genes" value="10"/>
<conditional name="var_names">
<param name="type" value="all"/>
</conditional>
<param name="log" value="False"/>
<param name="use_raw" value="False"/>
<param name="dendrogram" value="False"/>
Expand Down Expand Up @@ -2233,6 +2258,80 @@ sc.pl.rank_genes_groups_stacked_violin(
</output>
<output name="out_png" file="pl.scatter.pbmc68k_reduced.png" ftype="png" compare="sim_size"/>
</test>
<test expect_num_outputs="2">
<!-- test 35: pl.rank_genes_groups_dotplot with marker list -->
<param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" />
<param name="format" value="png"/>
<conditional name="method">
<param name="method" value="pl.rank_genes_groups_dotplot"/>
<conditional name="var_names">
<param name="type" value="customfile"/>
<param name="var_names" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.tsv"/>
</conditional>
<param name="groupby" value="bulk_labels"/>
<param name="log" value="False"/>
<param name="use_raw" value="False"/>
<param name="dendrogram" value="False"/>
<param name="color_map" value="viridis"/>
<section name="matplotlib_pyplot_scatter">
<param name="linewidths" value="0" />
<param name="edgecolors" value="face"/>
</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.rank_genes_groups_dotplot"/>
<has_text_matching expression="groupby='bulk_labels'"/>
<has_text_matching expression="log=False"/>
<has_text_matching expression="use_raw=False"/>
<has_text_matching expression="dendrogram=False"/>
<has_text_matching expression="color_map='viridis'"/>
<has_text_matching expression="lw=0.0"/>
<has_text_matching expression="ec='face'"/>
</assert_contents>
</output>
<output name="out_png" file="pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.png" ftype="png" compare="sim_size"/>
</test>
<test expect_num_outputs="2">
<!-- test 36: pl.rank_genes_groups_dotplot with marker list -->
<param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" />
<param name="format" value="png"/>
<conditional name="method">
<param name="method" value="pl.rank_genes_groups_dotplot"/>
<conditional name="var_names">
<param name="type" value="customfile"/>
<param name="var_names" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.tsv"/>
</conditional>
<param name="groupby" value="bulk_labels"/>
<param name="log" value="False"/>
<param name="use_raw" value="False"/>
<param name="dendrogram" value="False"/>
<param name="color_map" value="viridis"/>
<section name="matplotlib_pyplot_scatter">
<param name="linewidths" value="0" />
<param name="edgecolors" value="face"/>
</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.rank_genes_groups_dotplot"/>
<has_text_matching expression="groupby='bulk_labels'"/>
<has_text_matching expression="log=False"/>
<has_text_matching expression="use_raw=False"/>
<has_text_matching expression="dendrogram=False"/>
<has_text_matching expression="color_map='viridis'"/>
<has_text_matching expression="lw=0.0"/>
<has_text_matching expression="ec='face'"/>
</assert_contents>
</output>
<output name="out_png" file="pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png" ftype="png" compare="sim_size"/>
</test>
</tests>
<help><![CDATA[
Generic: Scatter plot along observations or variables axes (`pl.scatter`)
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