<tool id="liana_plot" name="Liana Plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>visualize ligand-receptor interactions</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="creators"/>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
#if str($method.method) in ['pl.target_metrics', 'pl.contributions', 'pl.interactions']:
cp '$method.mdata' 'misty.h5mu' &&
#else:
cp '$method.adata' 'anndata.h5ad' &&
#end if
cat '$script_file' > '$hidden_output' &&
python '$script_file' >> '$hidden_output' &&
ls . >> '$hidden_output' &&
touch 'anndata_info.txt' &&
cat 'anndata_info.txt' @CMD_PRETTIFY_STDOUT@
 ]]></command>
    <configfiles>
        <configfile name="script_file"><![CDATA[
@CMD_IMPORTS@
import mudata as mu
if os.path.exists("misty.h5mu"):
    import mudata as mu
    mdata = mu.read_h5mu("misty.h5mu")
    # Wrap MuData into LIANA MistyData (this is what plotting expects)
else:
    adata = sc.read_h5ad('anndata.h5ad')


#if str($method.method) == 'pl.dotplot':
fig = li.plotting.dotplot(
    adata=adata,
    uns_key='$method.uns_key',
    #if str($method.colour) != '':
    colour='$method.colour',
    #end if
    #if str($method.size) != '':
    size='$method.size',
    #end if
    @CMD_PLOT_SOURCE_TARGET_LABELS@
    @CMD_PLOT_LIGAND_RECEPTOR_COMPLEX@
    @CMD_PLOT_TOP_N_ORDERBY@
    inverse_colour=$method.inverse_colour,
    inverse_size=$method.inverse_size,
    cmap='$method.cmap',
    size_range=($method.size_range_min, $method.size_range_max),
    figure_size=($method.figure_size_width, $method.figure_size_height),
    return_fig=True)

#else if str($method.method) == 'pl.dotplot_by_sample':
fig = li.plotting.dotplot_by_sample(
    adata=adata,
    uns_key='$method.uns_key',
    sample_key='$method.sample_key',
    #if str($method.colour) != '':
    colour='$method.colour',
    #end if
    #if str($method.size) != '':
    size='$method.size',
    #end if
    @CMD_PLOT_SOURCE_TARGET_LABELS@
    @CMD_PLOT_LIGAND_RECEPTOR_COMPLEX@
    inverse_colour=$method.inverse_colour,
    inverse_size=$method.inverse_size,
    cmap='$method.cmap',
    size_range=($method.size_range_min, $method.size_range_max),
    figure_size=($method.figure_size_width, $method.figure_size_height),
    return_fig=True)

#else if str($method.method) == 'pl.tileplot':
fig = li.plotting.tileplot(
    adata=adata,
    uns_key='$method.uns_key',
    #if str($method.fill) != '':
    fill='$method.fill',
    #end if
    #if str($method.label) != '':
    label='$method.label',
    #end if
    @CMD_PLOT_SOURCE_TARGET_LABELS@
    @CMD_PLOT_LIGAND_RECEPTOR_COMPLEX@
    @CMD_PLOT_TOP_N_ORDERBY@
    #if str($method.source_title) != '':
    source_title='$method.source_title',
    #end if
    #if str($method.target_title) != '':
    target_title='$method.target_title',
    #end if
    cmap='$method.cmap',
    label_size=$method.label_size,
    figure_size=($method.figure_size_width, $method.figure_size_height),
    return_fig=True)

#else if str($method.method) == 'pl.connectivity':
fig = li.plotting.connectivity(
    adata=adata,
    idx=$method.idx,
    spatial_key='$method.spatial_key',
    connectivity_key='$method.connectivity_key',
    size=$method.size,
    figure_size=($method.figure_size_width, $method.figure_size_height),
    return_fig=True)

#else if str($method.method) == 'pl.target_metrics':
fig = li.plotting.target_metrics(
    misty=mdata,
    #if str($method.key) != '':
    key='$method.key',
    #end if
    #if str($method.stat) != '':
    stat='$method.stat',
    #end if
    #if str($method.top_n) != '':
    top_n=$method.top_n,
    #end if
    ascending=$method.ascending,
    figure_size=($method.figure_size_width, $method.figure_size_height),
    return_fig=True)

#else if str($method.method) == 'pl.contributions':
fig = li.plotting.contributions(
    misty=mdata,
    #if str($method.key) != '':
    key='$method.key',
    #end if
    #if str($method.view_names) != '':
    view_names=[x.strip() for x in '$method.view_names'.split(',')],
    #end if
    figure_size=($method.figure_size_width, $method.figure_size_height),
    return_fig=True)

#else if str($method.method) == 'pl.interactions':
fig = li.plotting.interactions(
    misty=mdata,
    #if str($method.key) != '':
    key='$method.key',
    #end if
    #if str($method.view) != '':
    view='$method.view',
    #end if
    #if str($method.top_n) != '':
    top_n=$method.top_n,
    #end if
    ascending=$method.ascending,
    figure_size=($method.figure_size_width, $method.figure_size_height),
    return_fig=True)
#end if

## Save the figure
fig.save('plot.$format', dpi=150)

        ]]>
        </configfile>
    </configfiles>
    <inputs>
        <param name="format" type="select" label="Format for saving figure">
            <option value="png" selected="true">png</option>
            <option value="pdf">pdf</option>
            <option value="svg">svg</option>
        </param>
        <conditional name="method">
            <param argument="method" type="select" label="Plotting method">
                <option value="pl.dotplot">Dotplot: Interactions by source and target cells (dotplot)</option>
                <option value="pl.dotplot_by_sample">Dotplot by sample: Interactions grouped by sample (dotplot_by_sample)</option>
                <option value="pl.tileplot">Tileplot: Interactions as tiles by source and target (tileplot)</option>
                <option value="pl.connectivity">Connectivity: Spatial connectivity weights (connectivity)</option>
                <option value="pl.target_metrics">MISTy Target Metrics: Plot target metrics from MISTy results (target_metrics)</option>
                <option value="pl.contributions">MISTy Contributions: Plot view contributions per target (contributions)</option>
                <option value="pl.interactions">MISTy Interactions: Plot interaction importances (interactions)</option>
            </param>
            <when value="pl.dotplot">
                <expand macro="inputs_anndata"/>
                <expand macro="param_uns_key"/>
                <expand macro="param_plot_colour"/>
                <expand macro="param_plot_size"/>
                <expand macro="param_source_labels"/>
                <expand macro="param_target_labels"/>
                <expand macro="param_ligand_complex"/>
                <expand macro="param_receptor_complex"/>
                <expand macro="param_top_n"/>
                <expand macro="param_orderby"/>
                <expand macro="param_orderby_ascending"/>
                <expand macro="param_orderby_absolute"/>
                <expand macro="param_inverse_colour"/>
                <expand macro="param_inverse_size"/>
                <expand macro="param_cmap"/>
                <expand macro="param_size_range"/>
                <expand macro="param_figure_size"/>
            </when>
            <when value="pl.dotplot_by_sample">
                <expand macro="inputs_anndata"/>
                <expand macro="param_uns_key"/>
                <expand macro="param_sample_key" VALUE="sample"/>
                <expand macro="param_plot_colour"/>
                <expand macro="param_plot_size"/>
                <expand macro="param_source_labels"/>
                <expand macro="param_target_labels"/>
                <expand macro="param_ligand_complex"/>
                <expand macro="param_receptor_complex"/>
                <expand macro="param_inverse_colour"/>
                <expand macro="param_inverse_size"/>
                <expand macro="param_cmap"/>
                <expand macro="param_size_range"/>
                <expand macro="param_figure_size"/>
            </when>
            <when value="pl.tileplot">
                <expand macro="inputs_anndata"/>
                <expand macro="param_uns_key"/>
                <param argument="fill" type="text" value="" optional="true" label="Fill by column" help="Column in liana_res for tile color. E.g., 'magnitude_rank', 'specificity_rank', or p-value columns.">
                    <expand macro="sanitize_query"/>
                </param>
                <param argument="label" type="text" value="" optional="true" label="Label by column" help="Column in liana_res to display inside tiles (e.g., 'lr_names', 'magnitude_rank').">
                    <expand macro="sanitize_query"/>
                </param>
                <expand macro="param_source_labels"/>
                <expand macro="param_target_labels"/>
                <expand macro="param_ligand_complex"/>
                <expand macro="param_receptor_complex"/>
                <expand macro="param_top_n"/>
                <expand macro="param_orderby"/>
                <expand macro="param_orderby_ascending"/>
                <expand macro="param_orderby_absolute"/>
                <param argument="source_title" type="text" value="" optional="true" label="Source axis title" help="Custom title for sender/source cell types axis. Default: 'Source'.">
                    <expand macro="sanitize_query"/>
                </param>
                <param argument="target_title" type="text" value="" optional="true" label="Target axis title" help="Custom title for receiver/target cell types axis. Default: 'Target'.">
                    <expand macro="sanitize_query"/>
                </param>
                <expand macro="param_cmap"/>
                <param argument="label_size" type="integer" value="12" min="1" label="Label text size" help="Font size for labels in tiles. Default: 12.">
                </param>
                <expand macro="param_figure_size" width="5" height="5"/>
            </when>
            <when value="pl.connectivity">
                <expand macro="inputs_anndata"/>
                <param argument="idx" type="integer" value="0" min="0" label="Cell index" help="Index of the cell to plot connectivity for."/>
                <param argument="spatial_key" type="text" value="spatial" label="Spatial key" help="Key in adata.obsm that contains the spatial coordinates.">
                    <expand macro="sanitize_query"/>
                </param>
                <param argument="connectivity_key" type="text" value="spatial_connectivities" label="Connectivity key" help="Key in adata.obsp that contains the spatial connectivity matrix.">
                    <expand macro="sanitize_query"/>
                </param>
                <param argument="size" type="float" value="1" min="0" label="Point size" help="Size of the points."/>
                <expand macro="param_figure_size" width="5.4" height="5"/>
            </when>
            <when value="pl.target_metrics">
                <param name="mdata" type="data" format="h5mu" optional="true" label="MISTy (MuData .h5mu) file" help="" />
                <expand macro="param_misty_key"/>
                <param argument="stat" type="select" optional="true" label="Statistic to plot" help="Target metric to visualize. gain_R2: improvement from multi-view; intra_R2: intra-view variance explained; multi_R2: total variance explained.">
                    <option value="">-- Select statistic --</option>
                    <option value="gain_R2">gain_R2 - R² gain from spatial context</option>
                    <option value="intra_R2">intra_R2 - Intra-view R²</option>
                    <option value="multi_R2">multi_R2 - Total multi-view R²</option>
                    <option value="p_value">p_value - Statistical significance</option>
                </param>
                <param argument="top_n" type="integer" value="" optional="true" min="1" label="Top N targets" help="Number of top targets to display. Empty = all targets.">
                </param>
                <param argument="ascending" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Sort ascending" help="If enabled: sort by increasing values. If disabled: sort by decreasing values (default, shows highest ranking first).">
                </param>
                <expand macro="param_figure_size" width="5" height="5"/>
            </when>
            <when value="pl.contributions">
                <param name="mdata" type="data" format="h5mu" optional="true" label="MISTy (MuData .h5mu) file" help="" />
                <expand macro="param_misty_key"/>
                <param argument="view_names" type="text" value="" optional="true" label="Views to include" help="Comma-separated view names (intra, juxta, para) to plot. Empty = all views. Useful for focusing on specific spatial scales.">
                    <expand macro="sanitize_query"/>
                </param>
                <expand macro="param_figure_size" width="5" height="5"/>
            </when>
            <when value="pl.interactions">
                <param name="mdata" type="data" format="h5mu" optional="true" label="MISTy (MuData .h5mu) file" help="" />
                <expand macro="param_misty_key"/>
                <param argument="view" type="text" value="" optional="true" label="View name" help="Specific view (e.g., 'intra', 'juxta', 'para') to visualize interaction importances. Empty = combined importance across all views.">
                    <expand macro="sanitize_query"/>
                </param>
                <param argument="top_n" type="integer" value="" optional="true" min="1" label="Top N interactions" help="Number of top interactions to display. Empty = show all.">
                </param>
                <param argument="ascending" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Sort ascending" help="If enabled: smallest to largest. If disabled: largest to smallest (default, shows most important first).">
                </param>
                <expand macro="param_figure_size" width="5" height="5"/>
            </when>
        </conditional>
        <expand macro="inputs_common_advanced"/>
    </inputs>
    <outputs>
        <data name="out_png" format="png" from_work_dir="plot.png" label="${tool.name} (${method.method}) on ${on_string}: PNG">
            <filter>format == 'png'</filter>
        </data>
        <data name="out_pdf" format="pdf" from_work_dir="plot.pdf" label="${tool.name} (${method.method}) on ${on_string}: PDF">
            <filter>format == 'pdf'</filter>
        </data>
        <data name="out_svg" format="svg" from_work_dir="plot.svg" label="${tool.name} (${method.method}) on ${on_string}: SVG">
            <filter>format == 'svg'</filter>
        </data>
        <data name="hidden_output" format="txt" label="Log file">
            <filter>advanced_common['show_log']</filter>
        </data>
    </outputs>
    <tests>
        <!-- 1) dotplot -> PNG -->
        <test expect_num_outputs="2">
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.dotplot"/>
                <param name="adata" location="https://zenodo.org/records/18388645/files/pbmc_liana_results.h5ad"/>
                <param name="uns_key" value="liana_res"/>
                <param name="colour" value="magnitude_rank"/>
                <param name="size" value="specificity_rank"/>
                <param name="inverse_colour" value="true"/>
                <param name="inverse_size" value="true"/>
                <param name="cmap" value="viridis"/>
                <param name="size_range_min" value="1"/>
                <param name="size_range_max" value="5"/>
                <param name="figure_size_width" value="8"/>
                <param name="figure_size_height" value="6"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="out_png" ftype="png">
                <assert_contents>
                    <has_size size="390000" delta="150000"/>
                </assert_contents>
            </output>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="li.plotting.dotplot"/>
                </assert_contents>
            </output>
        </test>
        <!-- 2) dotplot_by_sample -> PDF -->
        <test expect_num_outputs="2">
            <param name="format" value="pdf"/>
            <conditional name="method">
                <param name="method" value="pl.dotplot_by_sample"/>
                <param name="adata" location="https://zenodo.org/records/18388645/files/multi_sample_test.h5ad"/>
                <param name="uns_key" value="liana_res"/>
                <param name="sample_key" value="sample"/>
                <param name="colour" value="magnitude_rank"/>
                <param name="size" value="specificity_rank"/>
                <param name="inverse_colour" value="true"/>
                <param name="inverse_size" value="true"/>
                <param name="cmap" value="viridis"/>
                <param name="size_range_min" value="1"/>
                <param name="size_range_max" value="5"/>
                <param name="figure_size_width" value="8"/>
                <param name="figure_size_height" value="6"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="out_pdf" ftype="pdf">
                <assert_contents>
                    <has_size size="280000" delta="100000"/>
                </assert_contents>
            </output>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="li.plotting.dotplot_by_sample"/>
                </assert_contents>
            </output>
        </test>
        <!-- 3) tileplot -> SVG -->
        <test expect_num_outputs="2">
            <param name="format" value="svg"/>
            <conditional name="method">
                <param name="method" value="pl.tileplot"/>
                <param name="adata" location="https://zenodo.org/records/18388645/files/pbmc_liana_results.h5ad"/>
                <param name="uns_key" value="liana_res"/>
                <param name="fill" value="magnitude_rank"/>
                <param name="label" value="magnitude_rank"/>
                <param name="top_n" value="15"/>
                <param name="orderby" value="magnitude_rank"/>
                <param name="orderby_ascending" value="true"/>
                <param name="cmap" value="viridis"/>
                <param name="label_size" value="10"/>
                <param name="figure_size_width" value="6"/>
                <param name="figure_size_height" value="6"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="out_svg" ftype="svg">
                <assert_contents>
                    <has_size size="3300000" delta="1000000"/>
                </assert_contents>
            </output>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="li.plotting.tileplot"/>
                </assert_contents>
            </output>
        </test>
        <!-- 4) connectivity -> PNG -->
        <test expect_num_outputs="2">
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.connectivity"/>
                <param name="adata" location="https://zenodo.org/records/18388645/files/spatial_small.h5ad"/>
                <param name="idx" value="0"/>
                <param name="spatial_key" value="spatial"/>
                <param name="connectivity_key" value="spatial_connectivities"/>
                <param name="size" value="1.5"/>
                <param name="figure_size_width" value="6"/>
                <param name="figure_size_height" value="5"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="out_png" ftype="png">
                <assert_contents>
                    <has_size size="56000" delta="40000"/>
                </assert_contents>
            </output>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="li.plotting.connectivity"/>
                </assert_contents>
            </output>
        </test>
        <!-- 5) MISTy target_metrics -> PDF -->
        <test expect_num_outputs="2">
            <param name="format" value="pdf"/>
            <conditional name="method">
                <param name="method" value="pl.target_metrics"/>
                <param name="mdata" location="https://zenodo.org/records/18388645/files/genericMistyData_rf.h5mu"/>
                <param name="stat" value="gain_R2"/>
                <param name="ascending" value="false"/>
                <param name="figure_size_width" value="5"/>
                <param name="figure_size_height" value="5"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="out_pdf" ftype="pdf">
                <assert_contents>
                    <has_size size="17186" delta="5000"/>
                </assert_contents>
            </output>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="li.plotting.target_metrics"/>
                </assert_contents>
            </output>
        </test>
        <!-- 6) MISTy contributions -> SVG -->
        <test expect_num_outputs="2">
            <param name="format" value="svg"/>
            <conditional name="method">
                <param name="method" value="pl.contributions"/>
                <param name="mdata" location="https://zenodo.org/records/18388645/files/genericMistyData_rf.h5mu"/>
                <param name="view_names" value="intra,juxta,para"/>
                <param name="figure_size_width" value="5"/>
                <param name="figure_size_height" value="5"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="out_svg" ftype="svg">
                <assert_contents>
                     <has_size size="58175" delta="10000"/>
                </assert_contents>
            </output>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="li.plotting.contributions"/>
                </assert_contents>
            </output>
        </test>
        <!-- 7) MISTy interactions -> PNG -->
        <test expect_num_outputs="2">
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.interactions"/>
                <param name="mdata" location="https://zenodo.org/records/18388645/files/genericMistyData_rf.h5mu"/>
                <param name="view" value="para"/>
                <param name="top_n" value="20"/>
                <param name="ascending" value="false"/>
                <param name="figure_size_width" value="5"/>
                <param name="figure_size_height" value="5"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="out_png" ftype="png">
                <assert_contents>
                    <has_size size="52184" delta="8000"/>
                </assert_contents>
            </output>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="li.plotting.interactions"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Liana Plotting Tools
====================

This tool provides visualization methods for LIANA ligand-receptor analysis results.

Available Methods
-----------------

**dotplot**
    Create a dotplot of interactions by source and target cells. The dot size and color
    can be mapped to different columns in the LIANA results (e.g., expression magnitude,
    specificity scores).

**dotplot_by_sample**
    Create a dotplot of interactions grouped by sample. Useful for comparing interactions
    across different conditions or samples.

**tileplot**
    Create a tileplot showing interactions as tiles organized by source and target cells.
    The fill color and labels can be customized.

**connectivity**
    Plot spatial connectivity weights for a specific cell. Requires spatial data with
    connectivity information computed.

**target_metrics** (MISTy)
    Plot target metrics from MISTy spatial modelling results. Shows statistics like
    R² gain, intra R², multi R², or p-values for each target.

**contributions** (MISTy)
    Plot view contributions per target from MISTy results. Shows how different spatial
    views contribute to explaining each target variable.

**interactions** (MISTy)
    Plot interaction importances from MISTy results. Shows the importance of predictor
    variables for explaining targets within a specific view.

Common Parameters
-----------------

**uns_key**
    Key in adata.uns that contains the LIANA results. Default is 'liana_res'.

**colour / size**
    Columns in liana_res to define the color and size of dots/tiles.
    Common options include: 'magnitude_rank', 'specificity_rank', 'lr_means', etc.

**source_labels / target_labels**
    Filter interactions to only show specific source or target cell types.

**ligand_complex / receptor_complex**
    Filter interactions to only show specific ligand or receptor complexes.

**top_n / orderby**
    Show only the top N interactions, ordered by a specific column.

**inverse_colour / inverse_size**
    Apply -log10 transformation to the colour/size values for better visualization.

**cmap**
    Colormap to use for plotting (e.g., 'viridis', 'plasma', 'RdBu_r').

**figure_size**
    Width and height of the figure in inches.

Output
------

The tool outputs a plot in the selected format (PNG, PDF, or SVG).

    ]]></help>
    <expand macro="citations"/>
</tool>