annotate plot.xml @ 1:fee4b4eb0ef5 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c

<tool id="seurat_plot" name="Seurat Visualize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>- Plot cells, features and dimensions</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
@CMD@
    ]]></command>
    <configfiles>
        <configfile name="script_file"><![CDATA[
@CMD_imports@
@CMD_read_inputs@
library(ggplot2)

#if $method.method == 'VlnPlot'

plot<-VlnPlot(
    seurat_obj,
    features = c(unlist(strsplit(gsub(" ", "", '$method.features'), ","))),
    #if $method.idents != ''
    idents = '$method.idents',
    #end if
    sort = $method.sort,
    #if $method.adv.assay != ''
    assay = '$method.adv.assay',
    #end if
    #if $method.adv.layer != ''
    layer = '$method.adv.layer',
    #end if
    #if $method.plot.cols != ''
    cols = c(unlist(strsplit(gsub(" ", "", '$method.plot.cols'), ","))),
    #end if
    #if $method.plot.pt_size
    pt.size = $method.plot.pt_size,
    #end if
    alpha = $method.plot.alpha,
    #if $method.adv.group_by != ''
    group.by = '$method.adv.group_by',
    #end if
    #if $method.adv.split_by != ''
    split.by = '$method.adv.split_by',
    #end if
    adjust = $method.plot.adjust,
    #if $method.plot.y_max
    y.max = $method.plot.y_max,
    #end if
    same.y.lims = $method.plot.same_y_lims,
    log = $method.plot.log,
    #if $method.plot.ncol != ''
    ncol = $method.plot.ncol,
    #end if
    split.plot = $method.adv.split_plot,
    stack = $method.adv.stack,
    fill.by = '$method.plot.fill_by',
    flip = $method.plot.flip,
    add.noise = $method.plot.add_noise,
    combine = TRUE
)

#else if $method.method == 'FeatureScatter'

    #if $method.adv.cells
    cells_list<-paste(readLines('$method.adv.cells'), collapse=",")
    #end if

plot<-FeatureScatter(
    seurat_obj,
    feature1 = '$method.feature1',
    feature2 = '$method.feature2',
    #if $method.adv.cells
    cells = c(unlist(strsplit(cells_list, ","))),
    #end if
    shuffle = $method.plot.shuffle.shuffle,
    #if $method.plot.shuffle.shuffle == 'TRUE'
    seed = $method.plot.shuffle.seed,
    #end if
    #if $method.adv.group_by != ''
    group.by = '$method.adv.group_by',
    #end if
    #if $method.adv.split_by != ''
    split.by = '$method.adv.split_by',
    #end if
    #if $method.plot.cols != ''
    cols = c(unlist(strsplit(gsub(" ", "", '$method.plot.cols'), ","))),
    #end if
    #if $method.plot.pt_size
    pt.size = $method.plot.pt_size,
    #end if
    #if $method.adv.span != ''
    span = '$method.adv.span',
    #end if
    smooth = $method.plot.smooth,
    slot = '$method.adv.slot',
    plot.cor = $method.plot.plot_cor,
    log = $method.plot.log,
    #if $method.plot.ncol
    ncol = $method.plot.ncol,
    #end if
    raster = $method.plot.raster.raster,
    #if $method.plot.raster.raster == 'TRUE'
    raster.dpi = c($method.plot.raster.raster_x, $method.plot.raster.raster_y),
    #end if
    jitter = $method.plot.jitter,
    combine = TRUE
)

#else if $method.method == 'CellScatter'

    #if $method.features
    features_list<-paste(readLines('$method.features'), collapse=",")
    #end if

plot<-CellScatter(
    seurat_obj,
    cell1 = '$method.cell1',
    cell2 = '$method.cell2',
    #if $method.features
    features = c(unlist(strsplit(features_list, ","))),
    #end if
    #if $method.highlight != ''
    highlight = c(unlist(strsplit(gsub(" ", "", '$method.highlight'), ","))),
    #end if
    #if $method.plot.cols != ''
    cols = c(unlist(strsplit(gsub(" ", "", '$method.plot.cols'), ","))),
    #end if
    #if $method.plot.pt_size
    pt.size = $method.plot.pt_size,
    #end if
    smooth = $method.plot.smooth,
    raster = $method.plot.raster.raster,
    #if $method.plot.raster.raster == 'TRUE'
    raster.dpi = c($method.plot.raster.raster_x, $method.plot.raster.raster_y),
    #end if
)

    #if $method.label_points == 'true'
    plot<-LabelPoints(
        plot,
        points = c(unlist(strsplit(gsub(" ", "", '$method.highlight'), ","))),
        repeal = TRUE
    )
    #end if

#else if $method.method == 'VariableFeaturePlot'

plot<-VariableFeaturePlot(
    seurat_obj,
    #if $method.assay != ''
    assay = '$method.assay',
    #end if
    cols = c('$method.plot.cols_1', '$method.plot.cols_2'),
    #if $method.plot.pt_size
    pt.size = $method.plot.pt_size,
    #end if
    raster = $method.plot.raster.raster,
    #if $method.plot.raster.raster == 'TRUE'
    raster.dpi = c($method.plot.raster.raster_x, $method.plot.raster.raster_y),
    #end if
    log =$method.plot.log
)

    #if $method.label_topN.label_topN == 'true'
    N = $method.label_topN.topN
    top_N<-head(VariableFeatures(seurat_obj), N)
    plot<-LabelPoints(plot,
    points = top_N,
    repel = TRUE)
    #end if

#else if $method.method == 'VizDimLoadings'
plot<-VizDimLoadings(
    seurat_obj,
    dims = 1:$method.dims,
    nfeatures = $method.nfeatures,
    reduction = '$method.reduction',
    col = '$method.plot.col',
    projected = $method.projected,
    balanced = $method.balanced,
    #if $method.plot.ncol
    ncol = $method.plot.ncol,
    #end if
    combine = TRUE
)

#else if $method.method == 'DimPlot'

    #if $method.adv.cells
    cells_list<-paste(readLines('$method.adv.cells'), collapse=",")
    #end if

plot<-DimPlot(
    seurat_obj,
    dims = c($method.dims_1, $method.dims_2),
    #if $method.adv.cells
    cells = c(unlist(strsplit(cells_list, ","))),
    #end if
    #if $method.reduction != ''
    reduction = '$method.reduction',
    #end if
    #if $method.plot.cols != ''
    cols = c(unlist(strsplit(gsub(" ", "", '$method.plot.cols'), ","))),
    #end if
    #if $method.plot.pt_size
    pt.size = $method.plot.pt_size,
    #end if
    #if $method.adv.group_by != ''
    group.by = '$method.adv.group_by',
    #end if
    #if $method.adv.split_by != ''
    split.by = '$method.adv.split_by',
    #end if
    #if $method.adv.shape_by != ''
    shape.by = '$method.adv.shape_by',
    #end if
    #if $method.plot.order != ''
    order = c(unlist(strsplit(gsub(" ", "", '$method.plot.order'), ","))),
    #end if
    shuffle = $method.plot.shuffle.shuffle,
    #if $method.plot.shuffle.shuffle == 'TRUE'
    seed = $method.plot.shuffle.seed,
    #end if
    label = $method.plot.label.label,
    #if $method.plot.label.label =='TRUE'
    label.size = $method.plot.label.label_size,
    label.color = '$method.plot.label.label_color',
    label.box = $method.plot.label.label_box,
    repel = $method.plot.label.repel,
    #end if
    alpha = $method.plot.alpha,
    #if $method.plot.highlight.highlight == 'true'
    cells.highlight = c(unlist(strsplit(gsub(" ", "", '$method.plot.highlight.cells_highlight'), ","))),
    cols.highlight = '$method.plot.highlight.cols_highlight',
    sizes.highlight = $method.plot.highlight.sizes_highlight,
    #end if
    na.value = '$method.plot.na_value',
    #if $method.plot.ncol
    ncol = $method.plot.ncol,
    #end if
    raster = $method.plot.raster.raster,
    #if $method.plot.raster.raster == 'TRUE'
    raster.dpi = c($method.plot.raster.raster_x, $method.plot.raster.raster_y),
    #end if
    combine = TRUE
)

#else if $method.method == 'DimHeatmap'
plot<-DimHeatmap(
    seurat_obj,
    dims = $method.dims,
    nfeatures = $method.nfeatures,
    reduction = '$method.reduction',
    #if $method.adv.cells != ''
    cells = $method.adv.cells,
    #end if
    #if $method.plot.disp_min
    disp.min = $method.plot.disp_min,
    #end if
    #if $method.plot.disp_max
    disp.max = $method.plot.disp_max,
    #end if
    projected = $method.adv.projected,
    balanced = $method.adv.balanced,
    #if $method.plot.ncol
    ncol = $method.plot.ncol,
    #end if
    fast = FALSE,
    raster = $method.plot.raster,
    slot = '$method.adv.slot',
    #if $method.adv.assays != ''
    assays = c(unlist(strsplit(gsub(" ", "", '$method.adv.assays'), ","))),
    #end if
    combine = TRUE
)

#else if $method.method == 'ElbowPlot'
plot<-ElbowPlot(
    seurat_obj,
    ndims = $method.ndims,
    reduction = '$method.reduction'
)

#else if $method.method == 'FeaturePlot'

    #if $method.adv.cells
    cells_list<-paste(readLines('$method.adv.cells'), collapse=",")
    #end if

plot<-FeaturePlot(
    seurat_obj,
    features = c(unlist(strsplit(gsub(" ", "", '$method.features'), ","))),
    dims = c('$method.dims_1', '$method.dims_2'),
    #if $method.reduction != ''
    reduction = '$method.reduction',
    #end if
    #if $method.adv.cells
    cells = c(unlist(strsplit(cells_list, ","))),
    #end if
    blend = $method.plot.blend.blend,
    #if $method.plot.blend.blend == 'TRUE'
    cols = c('$method.plot.blend.cols_1', '$method.plot.cols_2', '$method.plot.cols_3'),
    blend.threshold = $method.plot.blend.blend_threshold,
    #else
    cols = c('$method.plot.cols_2', '$method.plot.cols_3'),
    #end if
    #if $method.plot.pt_size
    pt.size = $method.plot.pt_size,
    #end if
    alpha = $method.plot.alpha,
    order = $method.plot.order,
    min.cutoff = 'q$method.adv.min_cutoff',
    max.cutoff = 'q$method.adv.max_cutoff',
    #if $method.adv.split_by != ''
    split.by = '$method.adv.split_by',
    by.col = $method.plot.blend.by_col,
    #end if
    keep.scale = '$method.plot.keep_scale',
    #if $method.adv.shape_by != ''
    shape.by = '$method.adv.shape_by',
    #end if
    slot = '$method.adv.slot',
    label = $method.plot.label.label,
    #if $method.plot.label.label =='TRUE'
    label.size = $method.plot.label.label_size,
    label.color = '$method.plot.label.label_color',
    repel = $method.plot.label.repel,
    #end if
    #if $method.plot.ncol
    ncol = $method.plot.ncol,
    #end if
    coord.fixed = $method.plot.coord_fixed,
    raster = $method.plot.raster.raster,
    #if $method.plot.raster.raster == 'TRUE'
    raster.dpi = c($method.plot.raster.raster_x, $method.plot.raster.raster_y),
    #end if
    combine = TRUE
)

#else if $method.method == 'DoHeatmap'

    #if $method.features
    features_list<-paste(readLines('$method.features'), collapse=",")
    #end if
    #if $method.cells
    cells_list<-paste(readLines('$method.cells'), collapse=",")
    #end if

plot<-DoHeatmap(
    seurat_obj,
    #if $method.features
    features = c(unlist(strsplit(features_list, ","))),
    #end if
    #if $method.cells
    cells = c(unlist(strsplit(cells_list, ","))),
    #end if
    #if $method.adv.group_by != ''
    group.by = '$method.adv.group_by',
    #end if
    group.bar = $method.plot.group_bar,
    #if $method.plot.group_colors != ''
    group.colors = c(unlist(strsplit(gsub(" ", "", '$method.plot.group_colors'), ","))),
    #end if
    #if $method.plot.disp_min
    disp.min = $method.plot.disp_min,
    #end if
    #if $method.plot.disp_max
    disp.max = $method.plot.disp_max,
    #end if
    slot = '$method.adv.slot',
    #if $method.adv.assay != ''
    assay = '$method.adv.assay',
    #end if
    label = $method.plot.label,
    size = $method.plot.size,
    hjust = $method.plot.hjust,
    vjust = $method.plot.vjust,
    angle = $method.plot.angle,
    raster = $method.plot.raster,
    draw.lines = $method.plot.draw_lines,
    #if $method.plot.lines_width
    lines.width = $method.plot.lines_width,
    #end if
    group.bar.height = $method.plot.group_bar_height,
    combine = TRUE
)

#else if $method.method == 'DotPlot'
plot<-DotPlot(
    seurat_obj,
    features = c(unlist(strsplit(gsub(" ", "", '$method.features'), ","))),
    #if $method.plot.cols.cols == 'two'
    cols = c('$method.plot.cols.cols_1', '$method.plot.cols.cols_2'),
    #else if $method.plot.cols.cols == 'more'
    cols = c(unlist(strsplit(gsub(" ", "", '$method.plot.cols.cols_more'), ","))),
    #end if
    col.min = $method.plot.col_min,
    col.max = $method.plot.col_max,
    dot.min = $method.plot.dot_min,
    dot.scale = $method.plot.dot_scale,
    cluster.idents = $method.plot.cluster_idents,
    scale = $method.plot.scale.scale,
    #if $method.plot.scale.scale == 'TRUE'
    scale.by = '$method.plot.scale.scale_by',
        #if $method.plot.scale.scale_min != ''
        scale.min = $method.plot.scale.scale_min,
        #end if
        #if $method.plot.scale.scale_max != ''
        scale.max = $method.plot.scale.scale_max
        #end if
    #end if
    #if $method.adv.assay != ''
    assay = '$method.adv.assay',
    #end if
    #if $method.adv.group_by != ''
    group.by = '$method.adv.group_by',
    #end if
    #if $method.adv.split_by != ''
    split.by = '$method.adv.split_by'
    #end if
)

#end if

#if $plot_format == 'png'
ggsave('plot.png',
    #if $resize.resize == 'true'
    width = $resize.width,
    height = $resize.height,
    units = 'px',
    #end if
    bg = 'white'
)
#else if $plot_format == 'pdf'
ggsave('plot.pdf',
    #if $resize.resize == 'true'
    width = $resize.width,
    height = $resize.height,
    units = 'px',
    #end if
    bg = 'white'
)
#else if $plot_format == 'svg'
ggsave('plot.svg',
    #if $resize.resize == 'true'
    width = $resize.width,
    height = $resize.height,
    units = 'px',
    #end if
    bg = 'white'
)
#else if $plot_format == 'jpeg'
ggsave('plot.jpeg',
    #if $resize.resize == 'true'
    width = $resize.width,
    height = $resize.height,
    units = 'px',
    #end if
    bg = 'white'
)
#else if $plot_format == 'tex'
ggsave('plot.tex',
    #if $resize.resize == 'true'
    width = $resize.width,
    height = $resize.height,
    units = 'px',
    #end if
    bg = 'white'
)
#else if $plot_format == 'tiff'
ggsave('plot.tiff',
    #if $resize.resize == 'true'
    width = $resize.width,
    height = $resize.height,
    units = 'px',
    #end if
    bg = 'white'
)
#else if $plot_format == 'eps'
ggsave('plot.eps',
    #if $resize.resize == 'true'
    width = $resize.width,
    height = $resize.height,
    units = 'px',
    #end if
    bg = 'white'
)
#end if

]]></configfile>
    </configfiles>
    <inputs>
        <expand macro="input_rds"/>
        <expand macro="plot_types"/>
        <conditional name="method">
            <param name="method" type="select" label="Method used">
                <option value="VlnPlot">Violin Plot with 'VlnPlot'</option>
                <option value="FeatureScatter">Scatter Plot with 'FeatureScatter'</option>
                <option value="CellScatter">Scatter Plot with 'CellScatter'</option>
                <option value="VariableFeaturePlot">Plot Variable Genes with 'VariableFeaturePlot'</option>
                <option value="VizDimLoadings">Visualize Reduction Results with 'VizDimLoadings'</option>
                <option value="DimPlot">Visualize Dimensional Reduction with 'DimPlot'</option>
                <option value="DimHeatmap">Visualize Reduction Results with 'DimHeatmap'</option>
                <option value="ElbowPlot">Determine dimensionality with 'ElbowPlot'</option>
                <option value="FeaturePlot">Visualize expression with 'FeaturePlot'</option>
                <option value="DoHeatmap">Visualize expression with 'DoHeatmap'</option>
                <option value="DotPlot">Visualize expression with 'DotPlot'</option>
            </param>
            <when value="VlnPlot">
                <param argument="features" type="text" value="nFeature_RNA" label="Features to plot" help="as variables on y-axis, comma-separated list e.g. nCount_RNA, percent.mt">
                    <expand macro="valid_list"/>
                </param>
                <param argument="idents" type="text" optional="true" value="" label="Ident classes to display on plot" help="as category on x-axis, defauts to all">
                <expand macro="valid_name"/>
                </param>
                <param argument="sort" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Sort identity classes by average expression"/>
                <section name="plot" title="Plot Formatting Options">
                    <expand macro="plot_ncol"/>
                    <expand macro="plot_cols"/>
                    <expand macro="plot_pt_size"/>
                    <expand macro="plot_alpha"/>
                    <param argument="adjust" type="integer" value="1" label="Adjust parameter for geom_violin"/>
                    <param name="y_max" type="float" optional="true" value="" label="Maximum y axis value" help="(y.max)"/>
                    <param name="same_y_lims" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Set all y-axis limits to same value" help="when plotting multiple features (same.y.lims)"/>
                    <expand macro="plot_log_scale"/>
                    <param name="fill_by" type="select" label="Colour violins by feature or ident" help="(fill.by)">
                        <option value="feature" selected="true">feature</option>
                        <option value="ident">ident</option>
                    </param>
                    <param argument="flip" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Flip plot orientation" help="puts identities on y-axis"/>
                    <param name="add_noise" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Add a small noise for plotting" help="(add.noise)"/>
                </section>
                <section name="adv" title="Advanced Options">
                    <expand macro="select_assay"/>
                    <expand macro="select_layer"/>
                    <expand macro="plot_group_by"/>
                    <expand macro="plot_split_by"/>
                    <param name="split_plot" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Plot each group of a split plot as multiple violin shapes" help="(split.plot)"/>
                    <param argument="stack" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Horizontally stack plots for each feature"/>
                </section>
            </when>
            <when value="FeatureScatter">
                <param argument="feature1" type="text" value="nCount_RNA" label="First feature to plot" help="on x-axis">
                <expand macro="valid_name"/>
                </param>
                <param argument="feature2" type="text" value="nFeature_RNA" label="Second feature to plot" help="on y-axis">
                <expand macro="valid_name"/>
                </param>
                <section name="plot" title="Plot Formatting Options">
                    <expand macro="plot_cols"/>
                    <expand macro="plot_pt_size"/>
                    <expand macro="plot_shuffle_and_seed"/>
                    <expand macro="plot_smooth"/>
                    <param name="plot_cor" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Display correlation in plot title" help="(plot.cor)"/>
                    <expand macro="plot_ncol"/>
                    <expand macro="raster_select"/>
                    <expand macro="plot_log_scale"/>
                    <param argument="jitter" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Jitter for easier visualization of crowded points"/>
                </section>
                <section name="adv" title="Advanced Options">
                    <param argument="cells" type="data" format="txt,tabular" optional="true" label="List of cells to include on plot" help="text file with one cell on each line"/>
                    <expand macro="select_slot_data"/>
                    <expand macro="plot_group_by"/>
                    <expand macro="plot_split_by"/>
                    <param argument="span" type="boolean" truevalue="TRUE" falsevalue="NULL" checked="false" label="Spline span in loess function call"/>
                </section>
            </when>
            <when value="CellScatter">
                <param argument="cell1" type="text" value="cell 1" label="First cell to plot" help="on x-axis">
                    <expand macro="valid_cell_name"/>
                </param>
                <param argument="cell2" type="text" value="cell 2" label="Second cell to plot" help="on y-axis">
                    <expand macro="valid_cell_name"/>
                </param>
                <param argument="features" type="data" format="txt,tabular" optional="true" label="List of features to plot" help="text file with one feature on each line, default is all features"/>
                <param argument="highlight" type="text" optional="true" value="" label="Features to highlight">
                    <expand macro="valid_list"/>
                </param>
                <param name="label_points" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Label highlighted features"/>
                <section name="plot" title="Plot Formatting Options">
                    <expand macro="plot_cols"/>
                    <expand macro="plot_pt_size"/>
                    <expand macro="plot_smooth"/>
                    <expand macro="raster_select"/>
                </section>
            </when>
            <when value="VariableFeaturePlot">
                <expand macro="select_assay"/>
                <conditional name="label_topN">
                    <param name="label_topN" type="select" label="Label the top most variable features">
                        <option value="true">Yes</option>
                        <option value="false" selected="true">No</option>
                    </param>
                    <when value="true">
                        <expand macro="set_topN"/>
                    </when>
                    <when value="false">
                    </when>
                </conditional>
                <section name="plot" title="Plot Formatting Options">
                    <param name="cols_1" type="select" label="Colour for non-variable genes">
                        <option value="black" selected="true">black</option>
                        <option value="grey">grey</option>
                    </param>
                    <param name="cols_2" type="select" label="Colour for variable genes">
                        <option value="red" selected="true">red</option>
                        <option value="blue">blue</option>
                        <option value="green">green</option>
                        <option value="orange">orange</option>
                        <option value="magenta">magenta</option>
                        <option value="purple">purple</option>
                        <option value="black">black</option>
                    </param>
                    <expand macro="plot_pt_size"/>
                    <param argument="log" type="boolean" truevalue="TRUE" falsevalue="NULL" checked="false" label="Plot the x-axis in log scale"/>
                    <expand macro="raster_select"/>
                </section>
            </when>
            <when value="VizDimLoadings">
                <param argument="dims" type="integer" value="10" label="Number of dimensions to display"/>
                <param argument="nfeatures" type="integer" value="30" label="Number of genes to display"/>
                <expand macro="select_reduction_pca"/>
                <expand macro="plot_projected_and_balanced"/>
                <section name="plot" title="Plot Formatting Options">
                    <param argument="col" type="select" label="Colour to use for points">
                        <option value="blue" selected="true">blue</option>
                        <option value="red">red</option>
                        <option value="green">green</option>
                        <option value="orange">orange</option>
                        <option value="magenta">magenta</option>
                        <option value="purple">purple</option>
                        <option value="grey">grey</option>
                        <option value="black">black</option>
                    </param>
                    <expand macro="plot_ncol"/>
                </section>
            </when>
            <when value="DimPlot">
                <expand macro="plot_2_dims"/>
                <expand macro="select_reduction_umap"/>
                <section name="plot" title="Plot Formatting Options">
                    <expand macro="plot_cols"/>
                    <expand macro="plot_pt_size"/>
                    <expand macro="plot_order"/>
                    <expand macro="plot_shuffle_and_seed"/>
                    <expand macro="plot_alpha"/>
                    <expand macro="plot_ncol"/>
                    <expand macro="raster_select"/>
                    <conditional name="label">
                        <param argument="label" type="select" label="Add labels to the clusters">
                            <option value="TRUE">Yes</option>
                            <option value="FALSE" selected="true">No</option>
                        </param>
                        <when value="TRUE">
                            <param name="label_size" type="integer" value="4" label="Set size of labels" help="(label.size)"/>
                            <param name="label_color" type="select" label="Set colour of label text" help="(label.color)">
                                <option value="black" selected="true">black</option>
                                <option value="grey">grey</option>
                            </param>
                            <param name="label_box" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Put a box around each label" help="(label.box)"/>
                            <param argument="repel" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Repel labels"/>
                        </when>
                        <when value="FALSE">
                        </when>
                    </conditional>
                    <conditional name="highlight">
                        <param name="highlight" type="select" label="Highlight group(s) of cells">
                            <option value="true">Yes</option>
                            <option value="false" selected="true">No</option>
                        </param>
                        <when value="true">
                            <param name="cells_highlight" type="text" value="" label="List of cells to highlight" help="comma-separated list of e.g. barcodes, clusters, groups (cells.highlight)">
                                <expand macro="valid_cell_list"/>
                            </param>
                            <param name="cols_highlight" type="select" label="Colour for highlighted cells" help="other cells will be black (cols.highlight)">
                                <option value="blue" selected="true">blue</option>
                                <option value="red">red</option>
                                <option value="green">green</option>
                                <option value="orange">orange</option>
                                <option value="magenta">magenta</option>
                                <option value="purple">purple</option>
                                <option value="grey">grey</option>
                            </param>
                            <param name="sizes_highlight" type="integer" value="1" label="Size of highlighted cells" help="(sizes.highlight)"/>
                        </when>
                        <when value="false">
                        </when>
                    </conditional>
                    <param name="na_value" type="select" label="Colour for NA points when using custom scale" help="(na.value)">
                        <option value="lightgrey" selected="true">lightgrey</option>
                        <option value="grey">grey</option>
                        <option value="black">black</option>
                    </param>
                </section>
                <section name="adv" title="Advanced Options">
                    <param argument="cells" type="data" format="txt,tabular" optional="true" label="List of cells to include on plot" help="text file with one cell on each line"/>
                    <expand macro="plot_group_by"/>
                    <expand macro="plot_split_by"/>
                    <param name="shape_by" type="text" optional="true" value="" label="Shape points by a group or identity" help="only when not saving as raster (shape.by)"/>
                </section>
            </when>
            <when value="DimHeatmap">
                <param argument="dims" type="text" value="1:10" label="Dimensions from reduction to plot" help="enter one or a range of dimensions e.g. 3 to plot dim 3, 1:10 to plot dims 1 to 10">
                    <validator type="regex" message="Please only use numbers or colon">^[\d:]+$</validator>
                </param>
                <param argument="nfeatures" type="integer" value="30" label="Number of genes to plot"/>
                <expand macro="select_reduction_pca"/>
                <section name="plot" title="Plot Formatting Options">
                    <expand macro="plot_disp_min_max"/>
                    <expand macro="plot_ncol"/>
                    <expand macro="raster_boolean"/>
                </section>
                <section name="adv" title="Advanced Options">
                    <param argument="cells" type="integer" optional="true" value="" label="Number of top cells to plot"/>
                    <expand macro="select_slot_scale"/>
                    <param argument="assays" type="text" optional="true" value="" label="Vector of assays to pull data from">
                        <expand macro="valid_list"/>
                    </param>
                    <expand macro="plot_projected_and_balanced"/>
                </section>
            </when>
            <when value="ElbowPlot">
                <param argument="ndims" type="integer" value="30" label="Number of dimensions to plot standard deviation for"/>
                <expand macro="select_reduction_pca"/>
            </when>
            <when value="FeaturePlot">
                <param argument="features" type="text" value="" label="Features to plot" help="e.g. gene, percent.mito, PC_1">
                    <expand macro="valid_list"/>
                </param>
                <expand macro="plot_2_dims"/>
                <expand macro="select_reduction_umap"/>
                <section name="plot" title="Plot Formatting Options">
                    <param name="keep_scale" type="select" label="How to handle colour scale across multiple plots" help="(keep.scale)">
                        <option value="feature" selected="true">Scale each feature separately</option>
                        <option value="all">Scale all to same maximum</option>
                    </param>
                    <conditional name="blend">
                        <param argument="blend" type="select" label="Scale and blend expression values to visualize coexpression" help="of two features entered as features to plot">
                            <option value="TRUE">Yes</option>
                            <option value="FALSE" selected="true">No</option>
                        </param>
                        <when value="TRUE">
                            <param name="blend_threshold" type="float" value="0.5" min="0" max="1" label="Colour cutoff from weak signal to strong signal" help="(blend.threshold)"/>
                            <param name="cols_1" type="select" label="Colour for double negatives">
                                <option value="lightgrey" selected="true">lightgrey</option>
                                <option value="grey">grey</option>
                                <option value="black">black</option>
                            </param>
                        </when>
                        <when value="FALSE">
                            <param name="by_col" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="If splitting by a factor, plot the splits per column with features as rows" help="ignored if blend = TRUE (by.col)"/>
                        </when>
                    </conditional>
                    <param name="cols_2" type="select" label="Colour for low values">
                        <option value="lightgrey" selected="true">light grey</option>
                        <option value="grey">grey</option>
                        <option value="lightblue">light blue</option>
                        <option value="blue">blue</option>
                        <option value="palegreen">light green</option>
                        <option value="palegreen4">green</option>
                        <option value="red">red</option>
                        <option value="red4">dark red</option>
                    </param>
                    <param name="cols_3" type="select" label="Colour for high values">
                        <option value="lightgrey">light grey</option>
                        <option value="grey">grey</option>
                        <option value="lightblue">light blue</option>
                        <option value="blue" selected="true">blue</option>
                        <option value="palegreen">light green</option>
                        <option value="palegreen4">green</option>
                        <option value="red">red</option>
                        <option value="red4">dark red</option>
                    </param>
                    <expand macro="plot_pt_size"/>
                    <expand macro="plot_alpha"/>
                    <param argument="order" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Plot cells in order of expression"/>
                    <conditional name="label">
                        <param argument="label" type="select" label="Add labels to the clusters">
                            <option value="TRUE">Yes</option>
                            <option value="FALSE" selected="true">No</option>
                        </param>
                        <when value="TRUE">
                            <param name="label_size" type="integer" value="4" label="Set size of labels" help="(label.size)"/>
                            <param name="label_color" type="select" label="Set colour of label text" help="(label.color)">
                                <option value="black">black</option>
                                <option value="grey">grey</option>
                            </param>
                            <param argument="repel" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Repel labels"/>
                        </when>
                        <when value="FALSE">
                        </when>
                    </conditional>
                    <param name="coord_fixed" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Plot cartesian coordinates with fixed aspect ratio" help="(coord.fixed)"/>
                    <expand macro="plot_ncol"/>
                    <expand macro="raster_select"/>
                </section>
                <section name="adv" title="Advanced Options">
                    <param argument="cells" type="data" format="txt,tabular" optional="true" label="List of cells to include on plot" help="text file with one cell on each line"/>
                    <expand macro="select_slot_data"/>
                    <expand macro="plot_split_by"/>
                    <param name="shape_by" type="text" optional="true" value="" label="Shape points by a group or identity (only if raster is FALSE)" help="(shape.by)"/>
                    <param name="min_cutoff" type="integer" optional="true" value="" label="Minimum cutoff for features - as quantile" help="(min.cutoff)"/>
                    <param name="max_cutoff" type="integer" optional="true" value="" label="Maximum cutoff for features - as quantile" help="(max.cutoff)"/>
                </section>
            </when>
            <when value="DoHeatmap">
                <param argument="features" type="data" format="txt,tabular" optional="true" label="List of features to plot" help="text file with one cell on each line, defaults to VariableFeatures"/>
                <param argument="cells" type="data" format="txt,tabular" optional="true" label="List of cells to include on plot" help="text file with one cell on each line"/>
                <section name="plot" title="Plot Formatting Options">
                    <param name="group_bar" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Add colour bar showing group status for cells" help="(group.bar)"/>
                    <param name="group_colors" type="text" optional="true" value="" label="Colours to use for colour bar" help="comma-separated list of colours, one for each identity(group.colors)">
                        <expand macro="valid_list"/>
                    </param>
                    <expand macro="plot_disp_min_max"/>
                    <param argument="label" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Label cell identities above the colour bar" help="(label)"/>
                    <param argument="size" type="float" value="5.5" label="Size of text above colour bar" help="(size)"/>
                    <param argument="hjust" type="float" value="0" label="Horizontal justification of text above colour bar" help="(hjust)"/>
                    <param argument="vjust" type="float" value="0" label="Vertical justification of text above colour bar" help="(vjust)"/>
                    <param argument="angle" type="integer" value="45" min="0" max="90" label="Angle of text above colour bar" help="(angle)"/>
                    <expand macro="raster_boolean"/>
                    <param name="draw_lines" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Include white lines to separate the groups" help="(draw.lines)"/>
                    <param name="lines_width" type="integer" optional="true" value="" label="Integer number to adjust width of separating lines" help="corresponds to the number of 'cells' between groups (lines.width)"/>
                    <param name="group_bar_height" type="float" value="0.02" label="Scale the height of the colour bar" help="(group.bar.height)"/>
                </section>
                <section name="adv" title="Advanced options">
                    <param name="group_by" type="text" optional="true" value="ident" label="Vector of variables to group cells by" help="use ident to group by cluster (group.by)">
                        <expand macro="valid_list"/>
                    </param>
                    <expand macro="select_slot_scale"/>
                    <expand macro="select_assay"/>
                </section>
            </when>
            <when value="DotPlot">
                <param argument="idents" type="text" optional="true" value="" label="Identity classes to include in plot" help="comma-separated list of clusters/idents, leave blank to include all">
                    <expand macro="valid_list"/>
                </param>
                <param argument="features" type="text" value="" label="Features to plot" help="object or comma-separated list">
                    <expand macro="valid_list"/>
                </param>
                <section name="plot" title="Plot Formatting Options">
                    <conditional name="cols">
                        <param name="cols" type="select" label="" help="">
                            <option value="two" selected="true">two</option>
                            <option value="more">more</option>
                        </param>
                        <when value="two">
                            <param name="cols_1" type="select" label="Colour for low values">
                                <option value="lightgrey" selected="true">light grey</option>
                                <option value="grey">grey</option>
                                <option value="lightblue">light blue</option>
                                <option value="blue">blue</option>
                                <option value="palegreen">light green</option>
                                <option value="palegreen4">green</option>
                                <option value="red">light red</option>
                                <option value="red4">red</option>
                            </param>
                            <param name="cols_2" type="select" label="Colour for high values">
                                <option value="lightgrey">light grey</option>
                                <option value="grey">grey</option>
                                <option value="lightblue">light blue</option>
                                <option value="blue" selected="true">blue</option>
                                <option value="palegreen">light green</option>
                                <option value="palegreen4">green</option>
                                <option value="red">red</option>
                                <option value="red4">dark red</option>
                            </param>
                        </when>
                        <when value="more">
                            <param name="cols_more" type="text" value="RdBu" label="Colours to plot" help="comma-separated list or palette (cols)">
                                <expand macro="valid_list"/>
                            </param>
                        </when>
                    </conditional>
                    <param name="col_min" type="float" value="-2.5" label="Minimum scaled average expression threshold" help="everything smaller will be set to this (col.min"/>
                    <param name="col_max" type="float" value="2.5" label="Maximum scaled average expression threshold" help="everything larger will be set to this (col.max"/>
                    <param name="dot_min" type="float" value="0" min="0" max="1" label="Fraction of cells at which to draw smallest dot" help="no dot drawn for groups where fewer cells express the gene (dot.min)"/>
                    <param name="dot_scale" type="float" value="6" label="Scale size of points" help="(dot.scale)"/>
                    <param name="cluster_idents" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Order identities into hierarchy" help="based on the features being plotted (cluster.idents)"/>
                    <conditional name="scale">
                        <param argument="scale" type="select" label="Scale the data">
                            <option value="TRUE" selected="true">No</option>
                            <option value="FALSE">Yes</option>
                        </param>
                        <when value="FALSE"></when>
                        <when value="TRUE">
                            <param name="scale_by" type="select" label="Scale by" help="(scale.by)">
                                <option value="radius" selected="true">radius</option>
                                <option value="size">size</option>
                            </param>
                            <param name="scale_min" type="float" optional="true" value="" label="Lower limit for scaling" help="leave blank to use default (scale.min)"/>
                            <param name="scale_max" type="float" optional="true" value="" label="Upper limit for scaling" help="leave blank to use default (scale.max)"/>
                        </when>
                    </conditional>
                </section>
                <section name="adv" title="Advanced Options">
                    <expand macro="select_assay"/>
                    <expand macro="plot_group_by"/>
                    <expand macro="plot_split_by"/>
                </section>
            </when>
        </conditional>
        <expand macro="plot_sizes"/>
        <expand macro="inputs_common_advanced"/>
    </inputs>
    <outputs>
        <expand macro="plot_out"/>
        <expand macro="outputs_common_advanced"/>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <!-- test1: VlnPlot PNG -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/filtered.rds"/>
            <param name="plot_format" value="png"/>
            <conditional name="method">
                <param name="method" value="VlnPlot"/>
                <param name="features" value="nFeature_RNA, nCount_RNA, percent.mt"/>
                <section name="plot">
                    <param name="ncol" value="2"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="VlnPlot"/>
                </assert_contents>
            </output>
            <output name="plot_out_png" location="https://zenodo.org/records/13732784/files/VlnPlot.png" ftype="png" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test2: FeatureScatter PDF -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/filtered.rds"/>
            <param name="plot_format" value="png"/>
            <conditional name="method">
                <param name="method" value="FeatureScatter"/>
                <param name="feature1" value="nCount_RNA"/>
                <param name="feature2" value="percent.mt"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="FeatureScatter"/>
                </assert_contents>
            </output>
            <output name="plot_out_png" location="https://zenodo.org/records/13732784/files/FeatureScatter.png" ftype="png" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test3: CellScatter PDF -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/variablefeatures.rds"/>
            <param name="plot_format" value="pdf"/>
            <conditional name="method">
                <param name="method" value="CellScatter"/>
                <param name="cell1" value="X16cell"/>
                <param name="cell2" value="midblast.9"/>
                <param name="highlight" value="Pkd2l2, Gm4850, Nlrp9b"/>
                <param name="label_points" value="true"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="CellScatter"/>
                </assert_contents>
            </output>
            <output name="plot_out_pdf" location="https://zenodo.org/records/13732784/files/CellScatter.pdf" ftype="pdf" compare="diff" lines_diff="50"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test4: VariableFeaturePlot SVG -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/variablefeatures.rds"/>
            <param name="plot_format" value="svg"/>
            <conditional name="method">
                <param name="method" value="VariableFeaturePlot"/>
                <conditional name="label_topN">
                    <param name="label_topN" value="true"/>
                    <param name="topN" value="5"/>
                </conditional>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="VariableFeaturePlot"/>
                </assert_contents>
            </output>
            <output name="plot_out_svg" location="https://zenodo.org/records/13732784/files/VariableFeaturePlot.svg" ftype="svg" compare="diff" lines_diff="50"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test5: VizDimLoadings JPEG -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/pca.rds"/>
            <param name="plot_format" value="jpeg"/>
            <conditional name="method">
                <param name="method" value="VizDimLoadings"/>
                <param name="dims" value="5"/>
                <param name="nfeatures" value="10"/>
                <param name="reduction" value="pca"/>
                <section name="plot">
                    <param name="col" value="magenta"/>
                </section>
                <param name="projected" value="FALSE"/>
                <param name="balanced" value="TRUE"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="VizDimLoadings"/>
                </assert_contents>
            </output>
            <output name="plot_out_jpeg" location="https://zenodo.org/records/13732784/files/VizDimLoadings.jpeg" ftype="jpeg" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test6: DimPlot TEX -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/umap.rds"/>
            <param name="plot_format" value="tex"/>
            <conditional name="method">
                <param name="method" value="DimPlot"/>
                <param name="dims" value="1, 2"/>
                <param name="reduction" value="umap"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="DimPlot"/>
                </assert_contents>
            </output>
            <output name="plot_out_tex" location="https://zenodo.org/records/13732784/files/DimPlot.tex" ftype="tex">
                <assert_contents>
                    <has_text_matching expression="beginpicture"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">
            <!-- test7: DimHeatmap TIFF -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/pca.rds"/>
            <param name="plot_format" value="tiff"/>
            <conditional name="method">
                <param name="method" value="DimHeatmap"/>
                <param name="dims" value="1:3"/>
                <param name="nfeatures" value="30"/>
                <param name="reduction" value="pca"/>
                <section name="adv">
                    <param name="cells" value="50"/>
                    <param name="slot" value="scale.data"/>
                    <param name="balanced" value="TRUE"/>
                </section>
                <section name="plot">
                    <param name="raster" value="TRUE"/>
                    <param name="ncol" value="1"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="DimHeatmap"/>
                </assert_contents>
            </output>
            <output name="plot_out_tiff" location="https://zenodo.org/records/13732784/files/DimHeatmap.tiff" ftype="tiff" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test8: ElbowPlot EPS -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/pca.rds"/>
            <param name="plot_format" value="eps"/>
            <conditional name="method">
                <param name="method" value="ElbowPlot"/>
                <param name="ndims" value="50"/>
                <param name="reduction" value="pca"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="ElbowPlot"/>
                </assert_contents>
            </output>
            <output name="plot_out_eps" location="https://zenodo.org/records/13732784/files/ElbowPlot.eps" ftype="eps"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test9: FeaturePlot PNG -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/umap.rds"/>
            <param name="plot_format" value="png"/>
            <conditional name="method">
                <param name="method" value="FeaturePlot"/>
                <param name="features" value="Obox6"/>
                <param name="dims" value="1, 2"/>
                <param name="reduction" value="umap"/>
                <section name="plot">
                    <param name="cols_2" value="blue"/>
                    <param name="cols_3" value="lightblue"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="FeaturePlot"/>
                </assert_contents>
            </output>
            <output name="plot_out_png" location="https://zenodo.org/records/13732784/files/FeaturePlot.png" ftype="png" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test10: DoHeatmap PNG -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/clusters.rds"/>
            <param name="plot_format" value="png"/>
            <conditional name="method">
                <param name="method" value="DoHeatmap"/>
                <section name="plot">
                    <param name="raster" value="TRUE"/>
                </section>
                <section name="adv">
                    <param name="group_by" value="ident"/>
                </section>
            </conditional>
            <conditional name="resize">
                <param name="resize" value="true"/>
                <param name="width" value="2100"/>
                <param name="height" value="3100"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="DoHeatmap"/>
                </assert_contents>
            </output>
            <output name="plot_out_png" location="https://zenodo.org/records/13732784/files/DoHeatmap.png" ftype="png" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test11: DotPlot PNG -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/clusters.rds"/>
            <param name="plot_format" value="png"/>
            <conditional name="method">
                <param name="method" value="DotPlot"/>
                <param name="features" value="Pkd2l2, Gm4850, Nlrp9b, Dnajb4, Siah2"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="DotPlot"/>
                </assert_contents>
            </output>
            <output name="plot_out_png" location="https://zenodo.org/records/13732784/files/DotPlot.png" ftype="png" compare="image_diff"/>
        </test>
    </tests>
    <help><![CDATA[
Seurat
======

Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data.

Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.

You can choose which type of file you want to produce, but be aware that some types (e.g. tex) may not be viewable on Galaxy, although you will be able to download them to use elsewhere.

VlnPlot
=======

Draw a violin plot of single cell data (gene expression, metrics, PC scores, etc.)

More details on the `seurat documentation
<https://satijalab.org/seurat/reference/vlnplot>`__

FeatureScatter
==============

Create a scatter plot of two features (typically feature expression), across a set of single cells. Cells are colored by their identity class.
Pearson correlation between the two features is displayed above the plot.

More details on the `seurat documentation
<https://satijalab.org/seurat/reference/featurescatter>`__

CellScatter
===========

Creates a plot of scatter plot of features across two single cells. Pearson correlation between the two cells is displayed above the plot.

More details on the `seurat documentation
<https://satijalab.org/seurat/reference/cellscatter>`__

VariableFeaturePlot
===================

View selected variable features on a plot of variances.

More details on the `seurat documentation
<https://satijalab.org/seurat/reference/variablefeatureplot>`__

VizDimLoadings
==============

Visualize top genes associated with reduction components - default reduction is PCA.

More details on the `seurat documentation
<https://satijalab.org/seurat/reference/vizdimloadings>`__

DimPlot
=======

Graph the output of a dimensional reduction technique on a 2D scatter plot where each point is a cell and it's positioned based on the cell embeddings determined by the reduction technique.
By default, cells are colored by their identity class (can be changed with the group.by parameter).

More details on the `seurat documentation
<https://satijalab.org/seurat/reference/dimplot>`__

DimHeatmap
==========

Draw a heatmap focusing on a principal component. Both cells and genes are sorted by their principal component scores.
Allows for nice visualization of sources of heterogeneity in the dataset.

More details on the `seurat documentation
<https://satijalab.org/seurat/reference/dimheatmap>`__

ElbowPlot
=========

Plot the standard deviations of the principal components for easy identification of an elbow in the graph - plots PCA as default reduction.

More details on the `seurat documentation
<https://satijalab.org/seurat/reference/elbowplot>`__

FeaturePlot
===========

Color single cells on a dimensional reduction plot according to a 'feature' (i.e. gene expression, PC scores, number of genes detected, etc.)

More details on the `seurat documentation
<https://satijalab.org/seurat/reference/featureplot>`__

DoHeatmap
=========

Draw a heatmap of single cell feature expression.

More details on the `seurat documentation
<https://satijalab.org/seurat/reference/doheatmap>`__

DotPlot
=======

Visualize how feature expression changes across different identity classes (e.g. clusters).
The size of the dot encodes the percentage of cells within a class that express the gene, while the color encodes the AverageExpression level across all cells within a class.

More details on the `seurat documentation
<https://satijalab.org/seurat/reference/dotplot>`__

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