Mercurial > repos > iuc > scanpy_plot
changeset 3:a8f865950ac4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
| author | iuc |
|---|---|
| date | Thu, 12 Dec 2019 09:24:59 -0500 |
| parents | 4bfb75bb7c8e |
| children | cb18f2388815 |
| files | macros.xml plot.xml test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png test-data/pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad |
| diffstat | 7 files changed, 539 insertions(+), 251 deletions(-) [+] |
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--- a/macros.xml Thu Dec 05 07:10:37 2019 -0500 +++ b/macros.xml Thu Dec 12 09:24:59 2019 -0500 @@ -1,7 +1,7 @@ <macros> <token name="@version@">1.4.4.post1</token> <token name="@profile@">19.01</token> - <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token> + <token name="@galaxy_version@"><![CDATA[@version@+galaxy1]]></token> <xml name="requirements"> <requirements> <requirement type="package" version="@version@">scanpy</requirement> @@ -351,10 +351,10 @@ <option value="gist_ncar">gist_ncar (Miscellaneous)</option> </xml> <xml name="param_groupby"> - <param argument="groupby" type="text" value="" optional="true" label="The key of the observation grouping to consider" help="If it is given, the heatmap is ordered by the respective group. It is expected that to be a categorical. If it is not a categorical observation, it would be subdivided into `num_categories`."/> + <param argument="groupby" type="text" value="" optional="true" label="The key of the observation grouping to consider" help="If it is given, the plot is ordered by the respective group. It is expected that to be a categorical. If it is not a categorical observation, it would be subdivided into 'num_categories'."/> </xml> <xml name="param_use_raw"> - <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use `raw` attribute of input if present" help=""/> + <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use 'raw' attribute of input if present" help=""/> </xml> <xml name="param_log"> <param argument="log" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use the log of the values?"/> @@ -378,12 +378,12 @@ <xml name="pl_var_names"> <conditional name="var_names"> <param name="type" type="select" label="Variables to plot (columns of the heatmaps)" > - <option value="all">All variables in `adata.var_names`</option> - <option value="custom">Subset of variables in `adata.var_names`</option> + <option value="all">All variables in 'adata.var_names'</option> + <option value="custom">Subset of variables in 'adata.var_names'</option> </param> <when value="all"/> <when value="custom"> - <param argument="var_names" type="text" value="" label="List of variables to plot" help="They should be a valid subset of `adata.var_names`, and separated by comma"/> + <param argument="var_names" type="text" value="" label="List of variables to plot" help="They should be a valid subset of 'adata.var_names', and separated by comma"/> </when> </conditional> </xml> @@ -404,27 +404,20 @@ <param argument="var_group_rotation" type="float" value="" optional="true" label="Label rotation degrees" help="By default, labels larger than 4 characters are rotated 90 degrees"/> </xml> <xml name="param_layer"> - <param argument="layer" type="text" value="" label="Name of the AnnData object layer that wants to be plotted" help="By default `adata.raw.X` is plotted. If `use_raw=False` is set, then `adata.X` is plotted. If layer is set to a valid layer name, then the layer is plotted. layer takes precedence over `use_raw`."/> + <param argument="layer" type="text" value="" label="Name of the AnnData object layer that wants to be plotted" help="By default 'adata.raw.X' is plotted. If 'use_raw=False' is set, then 'adata.X' is plotted. If layer is set to a valid layer name, then the layer is plotted. layer takes precedence over 'use_raw'."/> </xml> <token name="@CMD_param_plot_inputs@"><![CDATA[ adata, save='.$format', show=False, ]]></token> - <xml name="params_plots"> + <xml name="params_inputs"> <expand macro="pl_var_names"/> <expand macro="param_groupby"/> - <expand macro="param_log"/> - <expand macro="param_use_raw"/> <expand macro="param_num_categories"/> - <expand macro="param_dendrogram"/> - <expand macro="pl_var_group_positions"/> - <expand macro="param_var_group_rotation"/> - <expand macro="pl_figsize"/> - <expand macro="param_layer"/> </xml> - <token name="@CMD_params_plots@"><![CDATA[ -#if $method.var_names.type == 'all' + <token name="@CMD_params_inputs@"><![CDATA[ + #if $method.var_names.type == 'all' var_names=adata.var_names, #else #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')]) @@ -433,9 +426,20 @@ #if str($method.groupby) != '' groupby='$method.groupby', #end if + num_categories=$method.num_categories, + ]]></token> + <xml name="params_plots"> + <expand macro="param_log"/> + <expand macro="param_use_raw"/> + <expand macro="param_dendrogram"/> + <expand macro="pl_var_group_positions"/> + <expand macro="param_var_group_rotation"/> + <expand macro="pl_figsize"/> + <expand macro="param_layer"/> + </xml> + <token name="@CMD_params_plots@"><![CDATA[ log=$method.log, use_raw=$method.use_raw, - num_categories=$method.num_categories, dendrogram=$method.dendrogram, #if len($method.var_group_positions) > 0: #set $var_group_positions=[] @@ -673,7 +677,7 @@ <option value="False">No</option> </param> <when value="True"> - <param argument="size" type="integer" min="0" value="1" label="Size of the jitter points" help=""/> + <param argument="size" type="float" min="0" value="1" label="Size of the jitter points" help=""/> </when> <when value="False"/> </conditional> @@ -742,7 +746,7 @@ saturation=$method.seaborn_violinplot.saturation, ]]></token> <xml name="param_color"> - <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either `.obs` or `.var`"/> + <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either '.obs' or '.var'"/> </xml> <token name="@CMD_param_color@"><![CDATA[ #if str($method.color) != '' @@ -750,10 +754,10 @@ color=$color, #end if ]]></token> - <xml name="pl_groups"> - <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations, comma-separated" help=""/> + <xml name="param_groups"> + <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations to plot" help="Comma-separated"/> </xml> - <token name="@CMD_params_pl_groups@"><![CDATA[ + <token name="@CMD_params_groups@"><![CDATA[ #if str($method.groups) != '' #set $groups=([x.strip() for x in str($method.groups).split(',')]) groups=$groups, @@ -761,8 +765,8 @@ ]]></token> <xml name="pl_components"> <repeat name="components" title="Component"> - <param argument="axis1" type="text" value="1" label="Axis 1" help=""/> - <param argument="axis2" type="text" value="2" label="Axis 2" help=""/> + <param argument="axis1" type="text" value="1" label="X-Axis" help=""/> + <param argument="axis2" type="text" value="2" label="Y-Axis" help=""/> </repeat> </xml> <token name="@CMD_params_pl_components@"><![CDATA[ @@ -802,6 +806,12 @@ <xml name="param_legend_fontsize"> <param argument="legend_fontsize" type="integer" optional="true" value="" label="Legend font size" help=""/> </xml> + <token name="@CMD_param_legend_fontsize@"><![CDATA[ + #if str($method.plot.legend_fontsize) != '' + legend_fontsize=$method.plot.legend_fontsize, + #end if + ]]> + </token> <xml name="param_legend_fontweight"> <param argument="legend_fontweight" type="select" label="Legend font weight" help=""> <option value="light">light</option> @@ -814,12 +824,14 @@ </param> </xml> <xml name="param_palette"> - <param argument="palette" type="select" label="Colors to use for plotting g categorical annotation groups" help=""> + <param argument="palette" type="select" label="Colors to use for plotting categorical annotation groups" help=""> + <option value="">Default</option> <expand macro="matplotlib_pyplot_colormap"/> </param> </xml> <xml name="param_color_map"> - <param argument="color_map" type="select" label="Colors to use for plotting categorical annotation groups" help=""> + <param argument="color_map" type="select" label="Color map to use for continous variables" help=""> + <option value="">Default</option> <expand macro="matplotlib_pyplot_colormap"/> </param> </xml> @@ -835,9 +847,21 @@ <xml name="param_size"> <param argument="size" type="float" optional="true" value="" label="Point size" help=""/> </xml> + <token name="@CMD_param_size@"><![CDATA[ + #if str($method.plot.size) != '' + size=$method.plot.size, + #end if + ]]> + </token> <xml name="param_title"> <param argument="title" type="text" value="" optional="true" label="Title for panels" help="Titles must be separated by a comma"/> </xml> + <token name="@CMD_param_title@"><![CDATA[ + #if $method.plot.title + title='$method.plot.title', + #end if + ]]> + </token> <xml name="param_sort_order"> <param argument="sort_order" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Sort order?" help="For continuous annotations used as color parameter, plot data points with higher values on top of others."/> </xml> @@ -879,7 +903,7 @@ ]]> </token> <xml name="param_arrows"> - <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run `tl.rna_velocity` before."/> + <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run 'tl.rna_velocity' before."/> </xml> <xml name="param_cmap"> <param argument="cmap" type="select" label="Colors to use for plotting categorical annotation groups" help=""> @@ -894,6 +918,7 @@ <expand macro="param_legend_fontsize"/> <expand macro="param_legend_fontweight"/> <expand macro="param_size"/> + <expand macro="param_color_map"/> <expand macro="param_palette"/> <expand macro="param_frameon"/> <expand macro="param_ncols"/> @@ -905,21 +930,20 @@ <token name="@CMD_pl_attribute_section@"><![CDATA[ projection='$method.plot.projection', legend_loc='$method.plot.legend_loc', - #if str($method.plot.legend_fontsize) != '' - legend_fontsize=$method.plot.legend_fontsize, - #end if + @CMD_param_legend_fontsize@ legend_fontweight='$method.plot.legend_fontweight', - #if str($method.plot.size) != '' - size=$method.plot.size, + @CMD_param_size@ + #if str($method.plot.color_map) != '' + color_map='$method.plot.color_map', #end if + #if str($method.plot.palette) != '' palette='$method.plot.palette', + #end if frameon=$method.plot.frameon, ncols=$method.plot.ncols, wspace=$method.plot.wspace, hspace=$method.plot.hspace, - #if $method.plot.title - title='$method.plot.title', - #end if + @CMD_param_title@ ]]> </token> <xml name="options_layout"> @@ -937,22 +961,22 @@ </param> </xml> <xml name="param_root"> - <param argument="root" type="text" value="" label="Comma-separated roots" help="If choosing a tree layout, this is the index of the root node or a list of root node indices. If this is a non-empty vector then the supplied node IDs are used as the roots of the trees (or a single tree if the graph is connected). If this is `None` or an empty list, the root vertices are automatically calculated based on topological sorting."/> + <param argument="root" type="text" value="" label="Comma-separated roots" help="If choosing a tree layout, this is the index of the root node or a list of root node indices. If this is a non-empty vector then the supplied node IDs are used as the roots of the trees (or a single tree if the graph is connected). If this is 'None' or an empty list, the root vertices are automatically calculated based on topological sorting."/> </xml> <xml name="param_random_state"> - <param argument="random_state" type="integer" value="0" label="Random state" help="For layouts with random initialization like 'fr', change this to use different intial states for the optimization. If `None`, the initial state is not reproducible."/> + <param argument="random_state" type="integer" value="0" label="Random state" help="For layouts with random initialization like 'fr', change this to use different intial states for the optimization. If 'None', the initial state is not reproducible."/> </xml> <xml name="inputs_paga"> <param argument="threshold" type="float" min="0" value="0.01" label="Threshold to draw edges" help="Do not draw edges for weights below this threshold. Set to 0 if you want all edges. Discarding low-connectivity edges helps in getting a much clearer picture of the graph."/> - <expand macro="pl_groups"/> + <expand macro="param_groups"/> <param argument="color" type="text" value="" label="The node colors" help="Gene name or obs. annotation, and also plots the degree of the abstracted graph when passing 'degree_dashed', 'degree_solid'."/> <param argument="pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for drawing" help=""/> - <param argument="labels" type="text" value="" label="Comma-separated node labels" help="If none is provided, this defaults to the group labels stored in the categorical for which `tl.paga` has been computed."/> + <param argument="labels" type="text" value="" label="Comma-separated node labels" help="If none is provided, this defaults to the group labels stored in the categorical for which 'tl.paga' has been computed."/> <expand macro="param_layout"/> <param argument="init_pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for initializing the layout" help=""/> <expand macro="param_random_state"/> <expand macro="param_root"/> - <param argument="transitions" type="text" value="" label="Key corresponding to the matrix storing the arrows" help="Key for `.uns['paga']`, e.g. 'transistions_confidence'"/> + <param argument="transitions" type="text" value="" label="Key corresponding to the matrix storing the arrows" help="Key for '.uns['paga']', e.g. 'transistions_confidence'"/> <param argument="solid_edges" type="text" value="connectivities" label="Key corresponding to the matrix storing the edges to be drawn solid black" help="Key for uns/paga"/> <param argument="dashed_edges" type="text" value="" optional="true" label="Key corresponding to the matrix storing the edges to be drawn dashed grey" help="Key for uns/paga. If not set, no dashed edges are drawn."/> <param argument="single_component" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Restrict to largest connected component?" help=""/> @@ -1022,12 +1046,158 @@ ]]> </token> <xml name="param_swap_axes"> - <param argument="swap_axes" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Swap axes?" help="By default, the x axis contains `var_names` (e.g. genes) and the y axis the `groupby` categories (if any). By setting `swap_axes` then x are the `groupby` categories and y the `var_names`."/> + <param argument="swap_axes" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Swap axes?" help="By default, the x axis contains 'var_names' (e.g. genes) and the y axis the 'groupby' categories (if any). By setting 'swap_axes' then x are the 'groupby' categories and y the 'var_names'."/> </xml> <xml name="gene_symbols"> - <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in `.var` that stores gene symbols"/> + <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in '.var' that stores gene symbols"/> + </xml> + <xml name="param_n_genes"> + <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help=""/> + </xml> + <xml name="pl_dotplot"> + <param argument="color_map" type="select" label="Color palette"> + <expand macro="matplotlib_pyplot_colormap"/> + </param> + <param argument="dot_max" type="float" value="" min="0" max="1" optional="true" label="Maximum dot size" help="If none, the maximum dot size is set to the maximum fraction value found (e.g. 0.6). If given, the value should be a number between 0 and 1. All fractions larger than dot_max are clipped to this value."/> + <param argument="dot_min" type="float" value="" min="0" max="1" optional="true" label="Minimum dot size" help="If none, the minimum dot size is set to 0. If given, the value should be a number between 0 and 1. All fractions smaller than dot_min are clipped to this value."/> + <expand macro="section_matplotlib_pyplot_scatter"/> + </xml> + <token name="@CMD_pl_dotplot@"><![CDATA[ + color_map='$method.color_map', + #if str($method.dot_max) != '' + dot_max=$method.dot_max, + #end if + #if str($method.dot_min) != '' + dot_min=$method.dot_min, + #end if + @CMD_params_matplotlib_pyplot_scatter@ + ]]> + </token> + <xml name="param_key"> + <param argument="key" type="text" value="" label="Key used to store the ranking results in 'uns'"/> + </xml> + <xml name="pl_heatmap"> + <expand macro="param_swap_axes"/> + <param argument="show_gene_labels" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show gene labels?" help="By default gene labels are shown when there are 50 or less genes. Otherwise the labels are removed."/> + <section name="matplotlib_pyplot_imshow" title="Parameters for matplotlib.pyplot.imshow"> + <expand macro="param_cmap"/> + <param name="interpolation" type="select" label="Interpolation method" help=""> + <option value="None">none</option> + <option value="nearest">nearest</option> + <option value="bilinear">bilinear</option> + <option value="bicubic">bicubic</option> + <option value="spline16">spline16</option> + <option value="spline36">spline36</option> + <option value="hanning">hanning</option> + <option value="hamming">hamming</option> + <option value="hermite">hermite</option> + <option value="kaiser">kaiser</option> + <option value="quadric">quadric</option> + <option value="catrom">catrom</option> + <option value="gaussian">gaussian</option> + <option value="bessel">bessel</option> + <option value="sinc">sinc</option> + <option value="mitchell">mitchell</option> + <option value="lanczos">lanczos</option> + </param> + <expand macro="param_alpha"/> + <expand macro="param_vmin"/> + <expand macro="param_vmax"/> + <param name="origin" type="select" label="Place the [0,0] index of the array in the upper left or lower left corner of the axes" help=" The convention 'upper' is typically used for matrices and images."> + <option value="upper">Upper</option> + <option value="lower">Lower</option> + </param> + </section> </xml> - <xml name="n_genes"> - <param argument="n_genes" type="integer" min="0" value="20" label="Number of genes to show" help=""/> - </xml> + <token name="@CMD_pl_heatmap@"><![CDATA[ + swap_axes=$method.swap_axes, + show_gene_labels=$method.show_gene_labels, + cmap='$method.matplotlib_pyplot_imshow.cmap', + #if str($method.matplotlib_pyplot_imshow.interpolation) != 'None' + interpolation='$method.matplotlib_pyplot_imshow.interpolation', + #end if + #if $method.matplotlib_pyplot_imshow.alpha + alpha=$method.matplotlib_pyplot_imshow.alpha, + #end if + #if $method.matplotlib_pyplot_imshow.vmin + vmin=$method.matplotlib_pyplot_imshow.vmin, + #end if + #if $method.matplotlib_pyplot_imshow.vmax + vmax=$method.matplotlib_pyplot_imshow.vmax, + #end if + origin='$method.matplotlib_pyplot_imshow.origin' + ]]> + </token> + <xml name="pl_rank_genes_groups_ext"> + <expand macro="param_groups"/> + <expand macro="param_n_genes"/> + <expand macro="param_key"/> + </xml> + <token name="@CMD_pl_rank_genes_groups_ext@"><![CDATA[ + @CMD_params_groups@ + #if str($method.n_genes) != '' + n_genes=$method.n_genes, + #end if + #if str($method.key) != '' + key='$method.key', + #end if + ]]> + </token> + <xml name="pl_matrixplot"> + <expand macro="param_swap_axes"/> + <section name="matplotlib_pyplot_pcolor" title="Parameters for matplotlib.pyplot.pcolor"> + <param argument="cmap" type="select" label="Color palette"> + <expand macro="seaborn_color_palette_options"/> + </param> + <param argument="vmin" type="float" value="" optional="true" label="Minimum value to anchor the colormap" help=""/> + <param argument="vmax" type="float" value="" optional="true" label="Maximum value to anchor the colormap" help=""/> + <expand macro="param_matplotlib_pyplot_edgecolors"/> + <expand macro="param_alpha"/> + <param argument="snap" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Snap the mesh to pixel boundaries?" help=""/> + </section> + </xml> + <token name="@CMD_pl_matrixplot@"><![CDATA[ + swap_axes=$method.swap_axes, + cmap='$method.matplotlib_pyplot_pcolor.cmap', + #if $method.matplotlib_pyplot_pcolor.vmin + vmin=$method.matplotlib_pyplot_pcolor.vmin, + #end if + #if $method.matplotlib_pyplot_pcolor.vmax + vmax=$method.matplotlib_pyplot_pcolor.vmax, + #end if + edgecolors='$method.matplotlib_pyplot_pcolor.edgecolors', + #if $method.matplotlib_pyplot_pcolor.alpha + alpha=$method.matplotlib_pyplot_pcolor.alpha, + #end if + snap=$method.matplotlib_pyplot_pcolor.snap + ]]> + </token> + <xml name="pl_stacked_violin"> + <expand macro="param_swap_axes"/> + <section name="violin_plot" title="Violin plot attributes"> + <expand macro="conditional_stripplot"/> + <expand macro="param_scale"/> + </section> + <param argument="row_palette" type="select" label="Colors to use in each of the stacked violin plots"> + <option value="muted">muted</option> + <expand macro="seaborn_color_palette_options"/> + </param> + <param argument="standard_scale" type="select" label="Standardize a dimension between 0 and 1" help="Each variable or observation is subtracted by the minimum and divided each by its maximum."> + <option value="None">No standardization</option> + <option value="var">Standardization on variable</option> + <option value="obs">Standardization on observation</option> + </param> + <expand macro="seaborn_violinplot"/> + </xml> + <token name="@CMD_pl_stacked_violin@"><![CDATA[ + swap_axes=$method.swap_axes, + @CMD_conditional_stripplot@ + scale='$method.violin_plot.scale', + row_palette='$method.row_palette', + #if str($method.standard_scale) != 'None' + standard_scale='$method.standard_scale', + #end if + @CMD_params_seaborn_violinplot@ + ]]> + </token> </macros>
--- a/plot.xml Thu Dec 05 07:10:37 2019 -0500 +++ b/plot.xml Thu Dec 12 09:24:59 2019 -0500 @@ -37,53 +37,33 @@ #end if use_raw=$method.use_raw, sort_order=$method.sort_order, - @CMD_params_pl_groups@ + @CMD_params_groups@ @CMD_params_pl_components@ projection='$method.plot.projection', legend_loc='$method.plot.legend_loc', - legend_fontsize=$method.plot.legend_fontsize, + @CMD_param_legend_fontsize@ legend_fontweight='$method.plot.legend_fontweight', color_map='$method.plot.color_map', + #if str($method.plot.palette) != '' palette='$method.plot.palette', + #end if frameon=$method.plot.frameon, - #if $method.plot.title - title='$method.plot.title', - #end if - size=$method.plot.size) + @CMD_param_title@ + @CMD_param_size@) #else if $method.method == 'pl.heatmap' sc.pl.heatmap( @CMD_param_plot_inputs@ + @CMD_params_inputs@ @CMD_params_plots@ - swap_axes=$method.swap_axes, - show_gene_labels=$method.show_gene_labels, - cmap='$method.matplotlib_pyplot_imshow.cmap', - #if str($method.matplotlib_pyplot_imshow.interpolation) != 'None' - interpolation='$method.matplotlib_pyplot_imshow.interpolation', - #end if - #if $method.matplotlib_pyplot_imshow.alpha - alpha=$method.matplotlib_pyplot_imshow.alpha, - #end if - #if $method.matplotlib_pyplot_imshow.vmin - vmin=$method.matplotlib_pyplot_imshow.vmin, - #end if - #if $method.matplotlib_pyplot_imshow.vmax - vmax=$method.matplotlib_pyplot_imshow.vmax, - #end if - origin='$method.matplotlib_pyplot_imshow.origin') + @CMD_pl_heatmap@) #else if $method.method == 'pl.dotplot' sc.pl.dotplot( @CMD_param_plot_inputs@ + @CMD_params_inputs@ @CMD_params_plots@ - color_map='$method.color_map', - #if $method.dot_max - dot_max=$method.dot_max, - #end if - #if $method.dot_min - dot_min=$method.dot_min, - #end if - @CMD_params_matplotlib_pyplot_scatter@) + @CMD_pl_dotplot@) #else if $method.method == 'pl.violin' sc.pl.violin( @@ -118,33 +98,16 @@ #else if $method.method == 'pl.stacked_violin' sc.pl.stacked_violin( @CMD_param_plot_inputs@ + @CMD_params_inputs@ @CMD_params_plots@ - swap_axes=$method.swap_axes, - @CMD_conditional_stripplot@ - scale='$method.violin_plot.scale', - row_palette='$method.row_palette', - #if str($method.standard_scale) != 'None' - standard_scale='$method.standard_scale', - #end if - @CMD_params_seaborn_violinplot@) + @CMD_pl_stacked_violin@) #else if $method.method == 'pl.matrixplot' sc.pl.matrixplot( @CMD_param_plot_inputs@ + @CMD_params_inputs@ @CMD_params_plots@ - swap_axes=$method.swap_axes, - cmap='$method.matplotlib_pyplot_pcolor.cmap', - #if $method.matplotlib_pyplot_pcolor.vmin - vmin=$method.matplotlib_pyplot_pcolor.vmin, - #end if - #if $method.matplotlib_pyplot_pcolor.vmax - vmax=$method.matplotlib_pyplot_pcolor.vmax, - #end if - edgecolors='$method.matplotlib_pyplot_pcolor.edgecolors', - #if $method.matplotlib_pyplot_pcolor.alpha - alpha=$method.matplotlib_pyplot_pcolor.alpha, - #end if - snap=$method.matplotlib_pyplot_pcolor.snap) + @CMD_pl_matrixplot@) #else if $method.method == 'pl.clustermap' sc.pl.clustermap( @@ -190,8 +153,7 @@ log=$method.log, save='.$format', show=False, - highly_variable_genes=$method.highly_variable_genes - ) + highly_variable_genes=$method.highly_variable_genes) #else if $method.method == 'pl.pca' sc.pl.pca( @@ -199,7 +161,7 @@ @CMD_param_color@ use_raw=$method.use_raw, sort_order=$method.sort_order, - @CMD_params_pl_groups@ + @CMD_params_groups@ @CMD_params_pl_components@ @CMD_pl_attribute_section@ @CMD_params_matplotlib_pyplot_scatter@) @@ -222,7 +184,7 @@ @CMD_param_color@ use_raw=$method.use_raw, sort_order=$method.sort_order, - @CMD_params_pl_groups@ + @CMD_params_groups@ @CMD_params_pl_components@ @CMD_pl_attribute_section@ @CMD_params_matplotlib_pyplot_scatter@) @@ -235,7 +197,7 @@ @CMD_pl_edges@ arrows=$method.arrows, sort_order=$method.sort_order, - @CMD_params_pl_groups@ + @CMD_params_groups@ @CMD_params_pl_components@ @CMD_pl_attribute_section@ @CMD_params_matplotlib_pyplot_scatter@) @@ -248,7 +210,7 @@ @CMD_pl_edges@ arrows=$method.arrows, sort_order=$method.sort_order, - @CMD_params_pl_groups@ + @CMD_params_groups@ @CMD_params_pl_components@ @CMD_pl_attribute_section@ @CMD_params_matplotlib_pyplot_scatter@) @@ -259,7 +221,7 @@ @CMD_param_color@ use_raw=$method.use_raw, sort_order=$method.sort_order, - @CMD_params_pl_groups@ + @CMD_params_groups@ @CMD_params_pl_components@ @CMD_pl_attribute_section@ @CMD_params_matplotlib_pyplot_scatter@) @@ -282,7 +244,7 @@ #end if arrows=$method.arrows, sort_order=$method.sort_order, - @CMD_params_pl_groups@ + @CMD_params_groups@ @CMD_params_pl_components@ @CMD_pl_attribute_section@ @CMD_params_matplotlib_pyplot_scatter@) @@ -290,13 +252,18 @@ #else if $method.method == 'pl.dpt_groups_pseudotime' sc.pl.dpt_groups_pseudotime( @CMD_param_plot_inputs@ - color_map='$method.color_map') + #if str($method.color_map) != '' + color_map='$method.color_map' + #end if + ) #else if $method.method == 'pl.dpt_timeseries' sc.pl.dpt_timeseries( @CMD_param_plot_inputs@ #if $method.heatmap.as_heatmap == "True" + #if str($method.heatmap.color_map) != '' color_map='$method.heatmap.color_map', + #end if #end if as_heatmap=$method.heatmap.as_heatmap) @@ -322,7 +289,9 @@ #set $annotations=([x.strip() for x in str($method.annotations).split(',')]) annotations=$annotations, #end if + #if str($method.color_map) != '' color_map='$method.color_map', + #end if n_avg=$method.n_avg, #if str($method.annotations) != '' groups_key='$method.groups_key', @@ -336,7 +305,7 @@ #else if $method.method == 'pl.rank_genes_groups' sc.pl.rank_genes_groups( @CMD_param_plot_inputs@ - @CMD_params_pl_groups@ + @CMD_params_groups@ n_genes=$method.n_genes, #if str($method.gene_symbols) != '' gene_symbols='$method.gene_symbols', @@ -348,14 +317,16 @@ #else if $method.method == 'pl.rank_genes_groups_violin' sc.pl.rank_genes_groups_violin( @CMD_param_plot_inputs@ - @CMD_params_pl_groups@ + @CMD_params_groups@ #if $method.genes.select == 'n_genes' n_genes=$method.genes.n_genes, #else #set $gene_names = ([x.strip() for x in str($method.genes.gene_names).split(',')]) gene_names=$gene_names, #end if + #if str($method.gene_symbols) != '' gene_symbols='$method.gene_symbols', + #end if use_raw=$method.use_raw, split=$method.split, strip=$method.violin_plot.stripplot.stripplot, @@ -367,6 +338,34 @@ #end if scale='$method.violin_plot.scale') +#else if $method.method == 'pl.rank_genes_groups_dotplot' +sc.pl.rank_genes_groups_dotplot( + @CMD_param_plot_inputs@ + @CMD_pl_rank_genes_groups_ext@ + @CMD_params_plots@ + @CMD_pl_dotplot@) + +#else if $method.method == 'pl.rank_genes_groups_heatmap' +sc.pl.rank_genes_groups_heatmap( + @CMD_param_plot_inputs@ + @CMD_pl_rank_genes_groups_ext@ + @CMD_params_plots@ + @CMD_pl_heatmap@) + +#else if $method.method == 'pl.rank_genes_groups_matrixplot' +sc.pl.rank_genes_groups_matrixplot( + @CMD_param_plot_inputs@ + @CMD_pl_rank_genes_groups_ext@ + @CMD_params_plots@ + @CMD_pl_matrixplot@) + +#else if $method.method == 'pl.rank_genes_groups_stacked_violin' +sc.pl.rank_genes_groups_stacked_violin( + @CMD_param_plot_inputs@ + @CMD_pl_rank_genes_groups_ext@ + @CMD_params_plots@ + @CMD_pl_stacked_violin@) + #end if ]]></configfile> </configfiles> @@ -375,43 +374,36 @@ <expand macro="param_plot_format"/> <conditional name="method"> <param argument="method" type="select" label="Method used for plotting"> - <option value="pl.scatter">Generic: Scatter plot along observations or variables axes, using `pl.scatter`</option> - <option value="pl.heatmap">Generic: Heatmap of the expression values of set of genes, using `pl.heatmap`</option> - <option value="pl.dotplot">Generic: Makes a dot plot of the expression values, using `pl.dotplot`</option> - <option value="pl.violin">Generic: Violin plot, using `pl.violin`</option> - <option value="pl.stacked_violin">Generic: Stacked violin plots, using `pl.stacked_violin`</option> - <option value="pl.matrixplot">Generic: Heatmap of the mean expression values per cluster, using `pl.matrixplot`</option> - <option value="pl.clustermap">Generic: Hierarchically-clustered heatmap, using `pl.clustermap`</option> + <option value="pl.scatter">Generic: Scatter plot along observations or variables axes, using 'pl.scatter'</option> + <option value="pl.heatmap">Generic: Heatmap of the expression values of set of genes, using 'pl.heatmap'</option> + <option value="pl.dotplot">Generic: Makes a dot plot of the expression values, using 'pl.dotplot'</option> + <option value="pl.violin">Generic: Violin plot, using 'pl.violin'</option> + <option value="pl.stacked_violin">Generic: Stacked violin plots, using 'pl.stacked_violin'</option> + <option value="pl.matrixplot">Generic: Heatmap of the mean expression values per cluster, using 'pl.matrixplot'</option> + <option value="pl.clustermap">Generic: Hierarchically-clustered heatmap, using 'pl.clustermap'</option> <!--<option value="pl.ranking">Generic: </option>!--> - <option value="pl.highest_expr_genes">Preprocessing: Plot the fraction of counts assigned to each gene over all cells, using `pl.highest_expr_genes`</option> - <!--<option value="pl.filter_genes_dispersion">Preprocessing: Plot dispersions versus means for genes, using `pl.filter_genes_dispersion`</option>--> - <option value="pl.highly_variable_genes">Preprocessing: Plot dispersions versus means for genes, using `pl.highly_variable_genes`</option> - <!--<option value="pl.calculate_qc_metrics">Preprocessing: </option>!--> - <option value="pl.pca">PCA: Scatter plot in PCA coordinates, using `pl.pca`</option> - <option value="pl.pca_loadings">PCA: Rank genes according to contributions to PCs, using `pl.pca_loadings`</option> - <option value="pl.pca_variance_ratio">PCA: Scatter plot in PCA coordinates, using `pl.pca_variance_ratio`</option> - <option value="pl.pca_overview">PCA: Plot PCA results, using `pl.pca_overview`</option> - <option value="pl.tsne">Embeddings: Scatter plot in tSNE basis, using `pl.tsne`</option> - <option value="pl.umap">Embeddings: Scatter plot in UMAP basis, using `pl.umap`</option> - <option value="pl.diffmap">Embeddings: Scatter plot in Diffusion Map basis, using `pl.diffmap`</option> - <option value="pl.draw_graph">Embeddings: Scatter plot in graph-drawing basis, using `pl.draw_graph`</option> - <option value="pl.dpt_groups_pseudotime">Branching trajectories and pseudotime, clustering: Plot groups and pseudotime, using `pl.dpt_groups_pseudotime`</option> - <option value="pl.dpt_timeseries">Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series, using `pl.dpt_timeseries`</option> - <option value="pl.paga">Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges, using `pl.paga`</option> - <option value="pl.paga_compare">Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side, using `pl.paga_compare`</option> - <option value="pl.paga_path">Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths, using `pl.paga_path`</option> - <option value="pl.rank_genes_groups">Marker genes: Plot ranking of genes using dotplot plot, using `pl.rank_genes_groups`</option> - <!--<option value="pl.rank_genes_groups_dotplot">Marker genes: </option>!--> - <!--<option value="pl.rank_genes_groups_heatmap">Marker genes: </option>!--> - <!--<option value="pl.rank_genes_groups_matrixplot">Marker genes: </option>!--> - <!--<option value="pl.rank_genes_groups_stacked_violin">Marker genes: </option>!--> - <option value="pl.rank_genes_groups_violin">Marker genes: Plot ranking of genes for all tested comparisons, using `pl.rank_genes_groups_violin`</option> - <!--<option value="pl.phate">Misc: </option>!--> - <!--<option value="pl.matrix">Misc: </option>!--> - <!--<option value="pl.paga_adjacency">Misc: </option>!--> - <!--<option value="pl.timeseries">Misc: </option>!--> - <!--<option value="pl.timeseries_as_heatmap">Misc: </option>!--> - <!--<option value="pl.timeseries_subplot">Misc: </option>!--> + <option value="pl.highest_expr_genes">Preprocessing: Plot the fraction of counts assigned to each gene over all cells, using 'pl.highest_expr_genes'</option> + <!--<option value="pl.filter_genes_dispersion">Preprocessing: Plot dispersions versus means for genes, using 'pl.filter_genes_dispersion'</option>--> + <option value="pl.highly_variable_genes">Preprocessing: Plot dispersions versus means for genes, using 'pl.highly_variable_genes'</option> + <option value="pl.pca">PCA: Scatter plot in PCA coordinates, using 'pl.pca'</option> + <option value="pl.pca_loadings">PCA: Rank genes according to contributions to PCs, using 'pl.pca_loadings'</option> + <option value="pl.pca_variance_ratio">PCA: Scatter plot in PCA coordinates, using 'pl.pca_variance_ratio'</option> + <option value="pl.pca_overview">PCA: Plot PCA results, using 'pl.pca_overview'</option> + <option value="pl.tsne">Embeddings: Scatter plot in tSNE basis, using 'pl.tsne'</option> + <option value="pl.umap">Embeddings: Scatter plot in UMAP basis, using 'pl.umap'</option> + <option value="pl.diffmap">Embeddings: Scatter plot in Diffusion Map basis, using 'pl.diffmap'</option> + <option value="pl.draw_graph">Embeddings: Scatter plot in graph-drawing basis, using 'pl.draw_graph'</option> + <option value="pl.dpt_groups_pseudotime">Branching trajectories and pseudotime, clustering: Plot groups and pseudotime, using 'pl.dpt_groups_pseudotime'</option> + <option value="pl.dpt_timeseries">Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series, using 'pl.dpt_timeseries'</option> + <option value="pl.paga">Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges, using 'pl.paga'</option> + <option value="pl.paga_compare">Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side, using 'pl.paga_compare'</option> + <option value="pl.paga_path">Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths, using 'pl.paga_path'</option> + <option value="pl.rank_genes_groups">Marker genes: Plot ranking of genes using dotplot plot, using 'pl.rank_genes_groups'</option> + <option value="pl.rank_genes_groups_violin">Marker genes: Plot ranking of genes as violin plot, using 'pl.rank_genes_groups_violin'</option> + <option value="pl.rank_genes_groups_dotplot">Marker genes: Plot ranking of genes as dotplot plot, using 'pl.rank_genes_groups_dotplot'</option> + <option value="pl.rank_genes_groups_heatmap">Marker genes: Plot ranking of genes as heatmap plot, using 'pl.rank_genes_groups_heatmap'</option> + <option value="pl.rank_genes_groups_matrixplot">Marker genes: Plot ranking of genes as matrixplot plot, using 'pl.rank_genes_groups_matrixplot'</option> + <option value="pl.rank_genes_groups_stacked_violin">Marker genes: Plot ranking of genes as stacked violin plot, using 'pl.rank_genes_groups_stacked_violin'</option> </param> <when value="pl.scatter"> <conditional name="type"> @@ -420,35 +412,35 @@ <option value="basis">Using tool that computes coordinates</option> </param> <when value="xy"> - <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either `.obs` or `.var`"/> - <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either `.obs` or `.var`"/> + <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either '.obs' or '.var'"/> + <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either '.obs' or '.var'"/> <conditional name="layers"> <param argument="use_layers" type="select" label="Use the layers attribute?"> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> - <param argument="layer_x" type="text" value="" optional="true" label="Layers for x coordinate" help="Use the `layers` attribute of `adata` if present"/> - <param argument="layer_y" type="text" value="" optional="true" label="Layers for y coordinate" help="Use the `layers` attribute of `adata` if present"/> - <param argument="layer_color" type="text" value="" optional="true" label="Layers for color" help="Use the `layers` attribute of `adata` if present"/> + <param argument="layer_x" type="text" value="" optional="true" label="Layers for x coordinate" help="Use the 'layers' attribute of 'adata' if present"/> + <param argument="layer_y" type="text" value="" optional="true" label="Layers for y coordinate" help="Use the 'layers' attribute of 'adata' if present"/> + <param argument="layer_color" type="text" value="" optional="true" label="Layers for color" help="Use the 'layers' attribute of 'adata' if present"/> </when> <when value="false"/> </conditional> </when> <when value="basis"> <param argument="basis" type="select" label="Plotting tool that computes coordinates" help=""> - <option value="pca">pca (need to run on `tl.pca` output)</option> - <option value="tsne">tsne (need to run on `tl.tsne` output)</option> - <option value="umap">umap (need to run on `tl.umap` output)</option> - <option value="diffmap">diffmap (need to run on `tl.diffmap` output)</option> - <option value="draw_graph_fr">draw_graph_fr (need to run on `tl.draw_graph` output)</option> + <option value="pca">pca (need to run on 'tl.pca' output)</option> + <option value="tsne">tsne (need to run on 'tl.tsne' output)</option> + <option value="umap">umap (need to run on 'tl.umap' output)</option> + <option value="diffmap">diffmap (need to run on 'tl.diffmap' output)</option> + <option value="draw_graph_fr">draw_graph_fr (need to run on 'tl.draw_graph' output)</option> </param> <expand macro="param_color"/> </when> </conditional> <expand macro="param_use_raw"/> <param argument="sort_order" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot data points with higher values on top of others?" help="For continuous annotations used as color parameter"/> - <expand macro="pl_groups"/> + <expand macro="param_groups"/> <section name="plot" title="Plot attributes"> <expand macro="pl_components"/> <expand macro="param_projection"/> @@ -463,59 +455,26 @@ </section> </when> <when value="pl.heatmap"> + <expand macro="params_inputs"/> <expand macro="params_plots"/> - <expand macro="param_swap_axes"/> - <param argument="show_gene_labels" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show gene labels?" help="By default gene labels are shown when there are 50 or less genes. Otherwise the labels are removed."/> - <section name="matplotlib_pyplot_imshow" title="Parameters for matplotlib.pyplot.imshow"> - <expand macro="param_cmap"/> - <param name="interpolation" type="select" label="Interpolation method" help=""> - <option value="None">none</option> - <option value="nearest">nearest</option> - <option value="bilinear">bilinear</option> - <option value="bicubic">bicubic</option> - <option value="spline16">spline16</option> - <option value="spline36">spline36</option> - <option value="hanning">hanning</option> - <option value="hamming">hamming</option> - <option value="hermite">hermite</option> - <option value="kaiser">kaiser</option> - <option value="quadric">quadric</option> - <option value="catrom">catrom</option> - <option value="gaussian">gaussian</option> - <option value="bessel">bessel</option> - <option value="sinc">sinc</option> - <option value="mitchell">mitchell</option> - <option value="lanczos">lanczos</option> - </param> - <expand macro="param_alpha"/> - <expand macro="param_vmin"/> - <expand macro="param_vmax"/> - <param name="origin" type="select" label="Place the [0,0] index of the array in the upper left or lower left corner of the axes" help=" The convention 'upper' is typically used for matrices and images."> - <option value="upper">Upper</option> - <option value="lower">Lower</option> - </param> - </section> + <expand macro="pl_heatmap"/> </when> <when value="pl.dotplot"> + <expand macro="params_inputs"/> <expand macro="params_plots"/> - <param argument="color_map" type="select" label="Color palette"> - <expand macro="matplotlib_pyplot_colormap"/> - </param> - <param argument="dot_max" type="float" value="" min="0" max="1" optional="true" label="Maximum dot size" help="If none, the maximum dot size is set to the maximum fraction value found (e.g. 0.6). If given, the value should be a number between 0 and 1. All fractions larger than dot_max are clipped to this value."/> - <param argument="dot_min" type="float" value="" min="0" max="1" optional="true" label="Minimum dot size" help="If none, the minimum dot size is set to 0. If given, the value should be a number between 0 and 1. All fractions smaller than dot_min are clipped to this value."/> - <expand macro="section_matplotlib_pyplot_scatter"/> + <expand macro="pl_dotplot"/> </when> <when value="pl.violin"> <conditional name="key_variables"> <param name="type" type="select" label="Keys for accessing variables"> - <option value="var_names">All variables in `.var_names`</option> - <option value="obs">All fields in `.obs`</option> - <option value="custom">Subset of variables in `adata.var_names` or fields of `.obs`</option> + <option value="var_names">All variables in '.var_names'</option> + <option value="obs">All fields in '.obs'</option> + <option value="custom">Subset of variables in 'adata.var_names' or fields of '.obs'</option> </param> <when value="var_names"/> <when value="obs"/> <when value="custom"> - <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from `.var_names` or fields of `.obs`"/> + <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'"/> </when> </conditional> <expand macro="param_groupby"/> @@ -524,7 +483,7 @@ <section name="violin_plot" title="Violin plot attributes"> <expand macro="conditional_stripplot"/> <conditional name="multi_panel"> - <param argument="multi_panel" type="select" label="Display keys in multiple panels" help="Also when `groupby is not provided"> + <param argument="multi_panel" type="select" label="Display keys in multiple panels" help="Also when 'groupby is not provided"> <option value="True">Yes</option> <option value="False" selected="true">No</option> </param> @@ -536,41 +495,19 @@ </conditional> <expand macro="param_scale"/> </section> - <param argument="xlabel" type="text" value="" optional="true" label="Label of the x axis" help="Defaults to `groupby` if `rotation` is `None`, otherwise, no label is shown."/> + <param argument="xlabel" type="text" value="" optional="true" label="Label of the x axis" help="Defaults to 'groupby' if 'rotation' is 'None', otherwise, no label is shown."/> <param argument="rotation" type="float" value="" optional="true" label="Rotation of xtick labels" help=""/> <expand macro="seaborn_violinplot"/> </when> <when value="pl.stacked_violin"> + <expand macro="params_inputs"/> <expand macro="params_plots"/> - <expand macro="param_swap_axes"/> - <section name="violin_plot" title="Violin plot attributes"> - <expand macro="conditional_stripplot"/> - <expand macro="param_scale"/> - </section> - <param argument="row_palette" type="select" label="Colors to use in each of the stacked violin plots"> - <option value="muted">muted</option> - <expand macro="seaborn_color_palette_options"/> - </param> - <param argument="standard_scale" type="select" label="Standardize a dimension between 0 and 1" help="Each variable or observation is subtracted by the minimum and divided each by its maximum."> - <option value="None">No standardization</option> - <option value="var">Standardization on variable</option> - <option value="obs">Standardization on observation</option> - </param> - <expand macro="seaborn_violinplot"/> + <expand macro="pl_stacked_violin"/> </when> <when value="pl.matrixplot"> + <expand macro="params_inputs"/> <expand macro="params_plots"/> - <expand macro="param_swap_axes"/> - <section name="matplotlib_pyplot_pcolor" title="Parameters for matplotlib.pyplot.pcolor"> - <param argument="cmap" type="select" label="Color palette"> - <expand macro="seaborn_color_palette_options"/> - </param> - <param argument="vmin" type="float" value="" optional="true" label="Minimum value to anchor the colormap" help=""/> - <param argument="vmax" type="float" value="" optional="true" label="Maximum value to anchor the colormap" help=""/> - <expand macro="param_matplotlib_pyplot_edgecolors"/> - <expand macro="param_alpha"/> - <param argument="snap" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Snap the mesh to pixel boundaries?" help=""/> - </section> + <expand macro="pl_matrixplot"/> </when> <when value="pl.clustermap"> <param argument="obs_keys" type="text" value="" optional="true" label="Categorical annotation to plot with a different color map" help="Currently, only a single key is supported."/> @@ -608,7 +545,7 @@ </when> <when value="pl.highest_expr_genes"> <param argument="n_top" type="integer" min="0" value="30" label="Number of top genes" help=""/> - <param argument="gene_symbols" type="text" optional="true" label="Key for field in `.var` that stores gene symbols" help="Fill it if you do not want to use `.var_names`."/> + <param argument="gene_symbols" type="text" optional="true" label="Key for field in '.var' that stores gene symbols" help="Fill it if you do not want to use '.var_names'."/> <section name="setseaborn_boxplot" title="Plot settings" expanded="false"> <param argument="color" type="text" value="" optional="true" label="Color for all of the elements, or seed for a gradient palette" help=""/> <param argument="palette" type="select" optional="true" label="Colors to use for the different levels of the hue variable" help="See https://seaborn.pydata.org/tutorial/color_palettes.html for more details."> @@ -621,12 +558,12 @@ <expand macro="param_color"/> <expand macro="param_use_raw"/> <expand macro="param_sort_order"/> - <expand macro="pl_groups"/> + <expand macro="param_groups"/> <expand macro="pl_attribute_section"/> <expand macro="section_matplotlib_pyplot_scatter"/> </when> <when value="pl.pca_loadings"> - <param argument="components" type="text" value="1,2,3" label="Lsit of comma-separated components" help="1, 2, 3 means first, second and third principal components"/> + <param argument="components" type="text" value="1,2,3" label="List of comma-separated components" help="1, 2, 3 means first, second and third principal components"/> </when> <when value="pl.pca_variance_ratio"> <param argument="n_pcs" type="integer" min="0" value="30" label="Number of PCs to show" help=""/> @@ -636,7 +573,7 @@ <expand macro="param_color"/> <expand macro="param_use_raw"/> <expand macro="param_sort_order"/> - <expand macro="pl_groups"/> + <expand macro="param_groups"/> <expand macro="pl_attribute_section"/> <expand macro="section_matplotlib_pyplot_scatter"/> </when> @@ -646,7 +583,7 @@ <expand macro="pl_edges"/> <expand macro="param_arrows"/> <expand macro="param_sort_order"/> - <expand macro="pl_groups"/> + <expand macro="param_groups"/> <expand macro="pl_attribute_section"/> <expand macro="section_matplotlib_pyplot_scatter"/> </when> @@ -656,7 +593,7 @@ <expand macro="pl_edges"/> <expand macro="param_arrows"/> <expand macro="param_sort_order"/> - <expand macro="pl_groups"/> + <expand macro="param_groups"/> <expand macro="pl_attribute_section"/> <expand macro="section_matplotlib_pyplot_scatter"/> </when> @@ -664,7 +601,7 @@ <expand macro="param_color"/> <expand macro="param_use_raw"/> <expand macro="param_sort_order"/> - <expand macro="pl_groups"/> + <expand macro="param_groups"/> <expand macro="pl_attribute_section"/> <expand macro="section_matplotlib_pyplot_scatter"/> </when> @@ -678,7 +615,7 @@ <expand macro="pl_edges"/> <expand macro="param_arrows"/> <expand macro="param_sort_order"/> - <expand macro="pl_groups"/> + <expand macro="param_groups"/> <expand macro="pl_attribute_section"/> <expand macro="section_matplotlib_pyplot_scatter"/> </when> @@ -706,7 +643,7 @@ <when value="pl.paga_path"> <param argument="nodes" type="text" value="" label="A path through nodes of the abstracted graph" help="Each node is represented by its indice (within .categories) for the groups that have been used to run PAGA. Comma-separated"/> - <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from `.var_names` or fields of `.obs`"/> + <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'"/> <expand macro="param_use_raw"/> <param argument="annotations" type="text" value="" optional="true" label="Key to plot" help="Keys for obs, comma-separated"/> <expand macro="param_color_map"/> @@ -719,22 +656,22 @@ <param argument="normalize_to_zero_one" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Shift and scale the running average to [0, 1] per gene?"/> </when> <when value="pl.rank_genes_groups"> - <expand macro="pl_groups"/> - <expand macro="n_genes"/> + <expand macro="param_groups"/> + <expand macro="param_n_genes"/> <expand macro="gene_symbols"/> <param argument="fontsize" type="integer" min="0" value="8" label="Font size for gene names"/> <expand macro="param_ncols"/> <param argument="sharey" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Should the y-axis of each panels be shared?" help="If not, each panel has its own y-axis range"/> </when> <when value="pl.rank_genes_groups_violin"> - <expand macro="pl_groups"/> + <expand macro="param_groups"/> <conditional name="genes"> <param argument="select" type="select" label="Which genes to plot?" help=""> <option value="n_genes">A number of genes</option> <option value="gene_names">A custom list of genes</option> </param> <when value="n_genes"> - <expand macro="n_genes"/> + <expand macro="param_n_genes"/> </when> <when value="gene_names"> <param argument="gene_names" type="text" value="" label="List of genes to plot" help="A list of comma-separated names"/> @@ -748,6 +685,26 @@ <expand macro="param_scale"/> </section> </when> + <when value="pl.rank_genes_groups_dotplot"> + <expand macro="pl_rank_genes_groups_ext"/> + <expand macro="params_plots"/> + <expand macro="pl_dotplot"/> + </when> + <when value="pl.rank_genes_groups_heatmap"> + <expand macro="pl_rank_genes_groups_ext"/> + <expand macro="params_plots"/> + <expand macro="pl_heatmap"/> + </when> + <when value="pl.rank_genes_groups_matrixplot"> + <expand macro="pl_rank_genes_groups_ext"/> + <expand macro="params_plots"/> + <expand macro="pl_matrixplot"/> + </when> + <when value="pl.rank_genes_groups_stacked_violin"> + <expand macro="pl_rank_genes_groups_ext"/> + <expand macro="params_plots"/> + <expand macro="pl_stacked_violin"/> + </when> </conditional> </inputs> <outputs> @@ -755,21 +712,21 @@ <filter>format == 'png' and method['method'] != 'pl.rank_genes_groups_violin'</filter> </data> <collection name="collection_png" type="list" label="${tool.name} (${method.method}) on ${on_string}"> - <discover_datasets pattern="rank_genes_groups_cell_type_(?P<designation>.*).png" format="png"/> + <discover_datasets pattern="rank_genes_groups_(?P<designation>.*).png" format="png"/> <filter>format == 'png' and method['method'] == 'pl.rank_genes_groups_violin'</filter> </collection> <data name="out_pdf" format="pdf" from_work_dir="*.pdf" label="${tool.name} (${method.method}) on ${on_string}"> <filter>format == 'pdf' and method['method'] != pl.rank_genes_groups_violin</filter> </data> <collection name="collection_pdf" type="list" label="${tool.name} (${method.method}) on ${on_string}"> - <discover_datasets pattern="rank_genes_groups_cell_type_(?P<designation>.*).pdf" format="pdf"/> + <discover_datasets pattern="rank_genes_groups_(?P<designation>.*).pdf" format="pdf"/> <filter>format == 'pdf' and method['method'] == 'pl.rank_genes_groups_violin'</filter> </collection> <data name="out_svg" format="svg" from_work_dir="*.svg" label="${tool.name} (${method.method}) on ${on_string}"> <filter>format == 'svg' and method['method'] != pl.rank_genes_groups_violin</filter> </data> <collection name="collection_svg" type="list" label="${tool.name} (${method.method}) on ${on_string}"> - <discover_datasets pattern="rank_genes_groups_cell_type_(?P<designation>.*).svg" format="svg"/> + <discover_datasets pattern="rank_genes_groups_(?P<designation>.*).svg" format="svg"/> <filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter> </collection> </outputs> @@ -852,7 +809,6 @@ <has_text_matching expression="legend_loc='right margin'"/> <has_text_matching expression="legend_fontsize=1"/> <has_text_matching expression="legend_fontweight='normal'"/> - <has_text_matching expression="color_map='viridis'"/> <has_text_matching expression="palette='bwr'"/> <has_text_matching expression="frameon=False"/> <has_text_matching expression="size=1.0"/> @@ -870,9 +826,9 @@ <param name="type" value="all"/> </conditional> <param name="groupby" value="cell_type"/> + <param name="num_categories" value="7"/> <param name="log" value="False"/> <param name="use_raw" value="False"/> - <param name="num_categories" value="7"/> <conditional name="figsize"> <param name="test" value="yes"/> <param name="width" value="10" /> @@ -914,9 +870,9 @@ <param name="var_names" value="CD79A, MS4A1, CD8A, CD8B, LYZ, GNLY, NKG7, RP3-467N11.1, FCGR3A, FCER1A, CST3, POU2AF1, LINC00402"/> </conditional> <param name="groupby" value="louvain"/> + <param name="num_categories" value="7"/> <param name="log" value="False"/> <param name="use_raw" value="False"/> - <param name="num_categories" value="7"/> <param name="dendrogram" value="True"/> <repeat name="var_group_positions"> <param name="start" value="0"/> @@ -1020,9 +976,9 @@ <param name="type" value="all"/> </conditional> <param name="groupby" value="cell_type"/> + <param name="num_categories" value="7"/> <param name="log" value="False"/> <param name="use_raw" value="False"/> - <param name="num_categories" value="7"/> <param name="dendrogram" value="True"/> <conditional name="figsize"> <param name="test" value="no"/> @@ -1611,13 +1567,151 @@ <has_text_matching expression="scale='width'"/> </assert_stdout> <output_collection name="collection_png"> - <element name="Ery" file="pl.rank_genes_groups_violin.Ery.png" ftype="png" compare="sim_size"/> - <element name="Mk" file="pl.rank_genes_groups_violin.Mk.png" ftype="png" compare="sim_size"/> - <element name="Mo" file="pl.rank_genes_groups_violin.Mo.png" ftype="png" compare="sim_size"/> - <element name="Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="sim_size"/> - <element name="progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="sim_size"/> + <element name="cell_type_Ery" file="pl.rank_genes_groups_violin.Ery.png" ftype="png" compare="sim_size"/> + <element name="cell_type_Mk" file="pl.rank_genes_groups_violin.Mk.png" ftype="png" compare="sim_size"/> + <element name="cell_type_Mo" file="pl.rank_genes_groups_violin.Mo.png" ftype="png" compare="sim_size"/> + <element name="cell_type_Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="sim_size"/> + <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="sim_size"/> </output_collection> </test> + <test> + <!-- test 22: pl.rank_genes_groups_dotplot !--> + <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> + <param name="format" value="png"/> + <conditional name="method"> + <param name="method" value="pl.rank_genes_groups_dotplot"/> + <param name="n_genes" value="10"/> + <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> + <assert_stdout> + <has_text_matching expression="sc.pl.rank_genes_groups_dotplot"/> + <has_text_matching expression="n_genes=10"/> + <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="linewidths=0.0"/> + <has_text_matching expression="edgecolors='face'"/> + </assert_stdout> + <output name="out_png" file="pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/> + </test> + <test> + <!-- test 23: pl.rank_genes_groups_heatmap !--> + <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> + <param name="format" value="png"/> + <conditional name="method"> + <param name="method" value="pl.rank_genes_groups_heatmap"/> + <param name="n_genes" value="10"/> + <param name="log" value="False"/> + <param name="use_raw" value="False"/> + <param name="dendrogram" value="False"/> + <param name="swap_axes" value="False"/> + <param name="show_gene_labels" value="False"/> + <section name="matplotlib_pyplot_imshow"> + <param name="cmap" value="viridis"/> + <param name="interpolation" value="None"/> + <param name="origin" value="upper"/> + </section> + </conditional> + <assert_stdout> + <has_text_matching expression="sc.pl.rank_genes_groups_heatmap"/> + <has_text_matching expression="n_genes=10"/> + <has_text_matching expression="log=False"/> + <has_text_matching expression="use_raw=False"/> + <has_text_matching expression="dendrogram=False"/> + <has_text_matching expression="swap_axes=False"/> + <has_text_matching expression="show_gene_labels=False"/> + <has_text_matching expression="cmap='viridis'"/> + <has_text_matching expression="origin='upper'"/> + </assert_stdout> + <output name="out_png" file="pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/> + </test> + <test> + <!-- test 24: pl.rank_genes_groups_matrixplot !--> + <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> + <param name="format" value="png"/> + <conditional name="method"> + <param name="method" value="pl.rank_genes_groups_matrixplot"/> + <param name="n_genes" value="10"/> + <param name="log" value="False"/> + <param name="use_raw" value="False"/> + <param name="dendrogram" value="False"/> + <param name="swap_axes" value="False"/> + <section name="matplotlib_pyplot_pcolor"> + <param name="cmap" value="viridis"/> + <param name="edgecolors" value="face"/> + <param name="snap" value="False"/> + </section> + </conditional> + <assert_stdout> + <has_text_matching expression="sc.pl.rank_genes_groups_matrixplot"/> + <has_text_matching expression="n_genes=10"/> + <has_text_matching expression="log=False"/> + <has_text_matching expression="use_raw=False"/> + <has_text_matching expression="dendrogram=False"/> + <has_text_matching expression="swap_axes=False"/> + <has_text_matching expression="cmap='viridis'"/> + <has_text_matching expression="edgecolors='face'"/> + <has_text_matching expression="snap=False"/> + </assert_stdout> + <output name="out_png" file="pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/> + </test> + <test> + <!-- test 25: pl.rank_genes_groups_stacked_violin !--> + <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> + <param name="format" value="png"/> + <conditional name="method"> + <param name="method" value="pl.rank_genes_groups_stacked_violin"/> + <param name="n_genes" value="10"/> + <param name="log" value="False"/> + <param name="use_raw" value="False"/> + <param name="dendrogram" value="True"/> + <param name="swap_axes" value="True"/> + <section name="violin_plot"> + <conditional name="stripplot"> + <param name="stripplot" value="True"/> + <param name="jitter" value="True"/> + <param name="size" value="1"/> + </conditional> + <param name="scale" value="width"/> + </section> + <param name="row_palette" value="muted"/> + <param name="standard_scale" value="None"/> + <section name="seaborn_violinplot"> + <param name="bw" value="scott"/> + <param name="linewidth" value="0"/> + <param name="color" value="AliceBlue"/> + <param name="palette" value="viridis"/> + <param name="saturation" value="0.75"/> + </section> + </conditional> + <assert_stdout> + <has_text_matching expression="sc.pl.rank_genes_groups_stacked_violin"/> + <has_text_matching expression="n_genes=10"/> + <has_text_matching expression="log=False"/> + <has_text_matching expression="use_raw=False"/> + <has_text_matching expression="dendrogram=True"/> + <has_text_matching expression="swap_axes=True"/> + <has_text_matching expression="stripplot=True"/> + <has_text_matching expression="jitter=True"/> + <has_text_matching expression="size=1"/> + <has_text_matching expression="scale='width'"/> + <has_text_matching expression="bw='scott'"/> + <has_text_matching expression="scale='width'"/> + <has_text_matching expression="linewidth=0.0"/> + <has_text_matching expression="color='AliceBlue'"/> + <has_text_matching expression="palette='viridis'"/> + <has_text_matching expression="saturation=0.75"/> + </assert_stdout> + <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/> + </test> </tests> <help><![CDATA[ Generic: Scatter plot along observations or variables axes (`pl.scatter`) @@ -1813,11 +1907,35 @@ More details on the `scanpy documentation <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups.html>`__ -Marker genes: Plot ranking of genes for all tested comparisons (`pl.rank_genes_groups_violin`) -============================================================================================== +Marker genes: Plot ranking of genes as violin plot (`pl.rank_genes_groups_violin`) +================================================================================== More details on the `scanpy documentation <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_violin.html>`__ + +Marker genes: Plot ranking of genes as dotplot plot (`pl.rank_genes_groups_dotplot`) +==================================================================================== + +More details on the `scanpy documentation +<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_dotplot.html>`__ + +Marker genes: Plot ranking of genes as heatmap plot (`pl.rank_genes_groups_heatmap`) +==================================================================================== + +More details on the `scanpy documentation +<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_heatmap.html>`__ + +Marker genes: Plot ranking of genes as matrixplot plot (`pl.rank_genes_groups_matrixplot`) +========================================================================================== + +More details on the `scanpy documentation +<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_matrixplot.html>`__ + +Marker genes: Plot ranking of genes as stacked violin plot (`pl.rank_genes_groups_stacked_violin`) +================================================================================================== + +More details on the `scanpy documentation +<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_stacked_violin.html>`__ ]]></help> <expand macro="citations"/> </tool>