Mercurial > repos > iuc > ggplot2_histogram
changeset 2:f52035800250 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
| author | iuc |
|---|---|
| date | Mon, 11 Jun 2018 16:05:18 -0400 |
| parents | d3d92fb20389 |
| children | 63a595b451d1 |
| files | ggplot_histogram.xml macros.xml test-data/ggplot_heatmap_result1.pdf test-data/ggplot_pca_result1.pdf test-data/mtcars.txt |
| diffstat | 4 files changed, 229 insertions(+), 109 deletions(-) [+] |
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--- a/ggplot_histogram.xml Tue Aug 29 09:02:13 2017 -0400 +++ b/ggplot_histogram.xml Mon Jun 11 16:05:18 2018 -0400 @@ -1,9 +1,10 @@ -<tool id="ggplot2_histogram" name="Histogram w ggplot2" version="@VERSION@"> +<tool id="ggplot2_histogram" name="Histogram w ggplot2" version="@VERSION@+galaxy0"> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> - <requirement type="package" version="1.4.2">r-reshape2</requirement> + <requirement type="package" version="1.4.3">r-reshape2</requirement> + <requirement type="package" version="1.2.1">r-svglite</requirement> </expand> <command detect_errors="exit_code"><![CDATA[ cat '$script' && @@ -11,61 +12,59 @@ ]]></command> <configfiles> <configfile name="script"><![CDATA[ - @R_INIT@ ## Import library -library("reshape2") -library("ggplot2") +library(reshape2) +library(ggplot2) integrated <- read.csv('$input1', sep='\t', header=TRUE) input <- melt(integrated) -## Show/hide legend -#if $legend == "yes" - gg_legend = NULL -#else - gg_legend = theme(legend.position="none") -#end if +@LEGEND@ ## density -#if $density == "counts" +#if $adv.density == "counts" gg_density = ggplot(input,aes(value, color=variable)) gg_freq = NULL -#elif $density == "nfreq" +#elif $adv.density == "nfreq" gg_density = ggplot(input,aes(value, ..ncount.., color=variable)) gg_freq = NULL -#elif $density == "freq" +#elif $adv.density == "freq" gg_density = ggplot(input,aes(value, color=variable)) gg_freq = aes(y=..count../sum(..count..)) #end if +@TRANSFORM@ + @XY_SCALING@ -gg_width = $with_output_dim -gg_height = $height_output_dim - +@THEME@ -@TRANSFORM@ - -#if $facet == "facet" +#if $adv.facet == "facet" gg_facet = facet_wrap(~ variable) #else gg_facet = NULL #end if -#if $coloring.colorscheme == "Default" +#if $adv.coloring.colorscheme == "Default" gg_colorscale = NULL #else - gg_colorscale = scale_color_brewer(palette=$coloring.colors, direction=$coloring.colororder) + gg_colorscale = scale_color_brewer(palette=$adv.coloring.colors, direction=$adv.coloring.colororder) #end if -gg_density+ -geom_freqpoly(gg_freq, binwidth=$binwidth, size=$size)+gg_facet+gg_colorscale+ -gg_scalex+gg_scaley+theme_bw()+xlab('$xlab')+ylab('$ylab')+gg_legend+ggtitle('$title') +plot_out <- gg_density + + geom_freqpoly(gg_freq, binwidth=$binwidth, size=$size) + gg_facet + gg_colorscale + + gg_scalex + + gg_scaley + + gg_theme + + xlab('$xlab') + + ylab('$ylab') + + gg_legend + + ggtitle('$title') + + theme(plot.title = element_text(hjust = 0.5)) -ggsave(file='Rplot.pdf') -dev.off() +@SAVE_OUTPUT@ ]]></configfile> </configfiles> <inputs> @@ -74,54 +73,51 @@ <expand macro="xy_lab" /> <param name="size" type="float" value="1.0" label="relative line width" /> <param name="binwidth" type="float" value="0.5" label="Bin width for plotting"/> - - <expand macro="transform" /> - - <param name="density" type="select" label="Advanced - plot counts or density"> - <option value="counts">Plot counts on the y-axis</option> - <option value="freq">Plot frequency on the y-axis</option> - <option value="nfreq">Plot normalized frequency on the y-axis</option> - </param> - <param name="facet" type="select" label="Advanced - faceting"> - <option value="none">Plot my groups on one plot</option> - <option value="facet">Plot my groups on individual plots</option> - </param> - <conditional name="coloring"> - <param name="colorscheme" type="select" label="Advanced - coloring groups" > - <option value="Default" selected="True">No thanks - just use the default scheme to color code my groups (columns)</option> - <option value="Defined">I want to use defined color palettes to differentiate my groups (columns) </option> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="density" type="select" label="Plot counts or density"> + <option value="counts">Plot counts on the y-axis</option> + <option value="freq">Plot frequency on the y-axis</option> + <option value="nfreq">Plot normalized frequency on the y-axis</option> + </param> + <param name="facet" type="select" label="Faceting"> + <option value="none">Plot my groups on one plot</option> + <option value="facet">Plot my groups on individual plots</option> </param> - <when value="Default"> - </when> - <when value="Defined"> - <expand macro="colors" /> - <param name="colororder" type="select" label="Reverse color scheme" > - <option value="1">Default order of color scheme</option> - <option value="-1">Reverse the order of my color scheme</option> - </param> - </when> - </conditional> - <expand macro="xy_scaling" /> - <expand macro="dimensions" /> - <param name="legend" type="select" label="Legend options"> - <option value="yes">Include legend on plot</option> - <option value="no">Hide legend</option> - </param> + <conditional name="coloring"> + <param name="colorscheme" type="select" label="Coloring groups" > + <option value="Default" selected="true">No thanks - just use the default scheme to color code my groups (columns)</option> + <option value="Defined">I want to use defined color palettes to differentiate my groups (columns) </option> + </param> + <when value="Default"> + </when> + <when value="Defined"> + <expand macro="colors" /> + <param name="colororder" type="select" label="Reverse color scheme" > + <option value="1">Default order of color scheme</option> + <option value="-1">Reverse the order of my color scheme</option> + </param> + </when> + </conditional> + <expand macro="transform" /> + <expand macro="xy_scaling" /> + <expand macro="theme" /> + <expand macro="legend" /> + </section> + <section name="out" title="Output Options" expanded="true"> + <expand macro="dimensions" /> + </section> </inputs> <outputs> - <!-- <data name="output1" format="png" from_work_dir="Rplot.png"/> - ToDo: It would be nice to have different output formats for all tools - --> - <data name="output1" format="pdf" from_work_dir="Rplot.pdf"/> + <expand macro="additional_output" /> </outputs> <tests> <test> <param name="input1" value="mtcars.txt"/> - <output name="output1" file="ggplot_histogram_result1.pdf" compare="sim_size"/> + <param name="additional_output_format" value="pdf" /> + <output name="output2" file="ggplot_histogram_result1.pdf" compare="sim_size"/> </test> </tests> <help><![CDATA[ - This tool will generate a histogram representing the distrinutions of each numerical column. Each column should have a descriptive header with no spaces, which will be used in the plot legend to represent the corresponding column (group). Input data example: @@ -132,7 +128,6 @@ gene_D 6 9 gene_E 9 13.5 gene_F 8 12 - ]]></help> <expand macro="citations"/> </tool>
--- a/macros.xml Tue Aug 29 09:02:13 2017 -0400 +++ b/macros.xml Mon Jun 11 16:05:18 2018 -0400 @@ -9,27 +9,116 @@ <token name="@VERSION@">2.2.1</token> <token name="@R_INIT@"><![CDATA[ -## Setup R error handling to go to stderr -options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)}) + ## Setup R error handling to go to stderr + options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)}) -## Unify locale settings -loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + ## Unify locale settings + loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") ]]></token> <token name="@TRANSFORM@"><![CDATA[ -#if $transform == "log2" - input["value"] <- log2(input["value"]) -#elif $transform == "log2plus1" - input["value"] <- log2(input["value"]+1) -#elif $transform == "log10" - input["value"] <- log10(input["value"]) -#elif $transform == "log10plus1" - input["value"] <- log10(input["value"]+1) -#end if + #if $adv.transform == "log2" + input["value"] <- log2(input["value"]) + #elif $adv.transform == "log2plus1" + input["value"] <- log2(input["value"]+1) + #elif $adv.transform == "log10" + input["value"] <- log10(input["value"]) + #elif $adv.transform == "log10plus1" + input["value"] <- log10(input["value"]+1) + #end if + ]]></token> + + <token name="@XY_SCALING@"><![CDATA[ + #Choose between automatically scaled x and y axis or user defined + #if $adv.scaling.plot_scaling == "Automatic" + gg_scalex = NULL + gg_scaley = NULL + #else + gg_scalex = xlim($adv.scaling.xaxismin, $adv.scaling.xaxismax) + gg_scaley = ylim($adv.scaling.yaxismin, $adv.scaling.yaxismax) + cat("\n xaxismin: ", $adv.scaling.xaxismin) + cat("\n xaxismax: ", $adv.scaling.xaxismax) + cat("\n yaxismin: ", $adv.scaling.yaxismin) + cat("\n yaxismax: ", $adv.scaling.yaxismax) + #end if + ]]></token> + + <token name="@THEME@"><![CDATA[ + ## Choose theme for plot + #if $adv.theme == "bw" + gg_theme = theme_bw() + #else + gg_theme = NULL + #end if ]]></token> + <token name="@LEGEND@"><![CDATA[ + ## Show/hide legend + #if $adv.legend == "yes" + gg_legend = theme(legend.position="right") + #else + gg_legend = theme(legend.position="none") + cat("\n no legend") + #end if + ]]></token> + <token name="@SAVE_OUTPUT@"><![CDATA[ + ## output options need to be in out section + gg_width <- as.double('$out.width_output_dim') + gg_height <- as.double('$out.height_output_dim') + gg_unit <- '$out.unit_output_dim' + gg_dpi <- as.double('$out.dpi_output_dim') + gg_add_device <- '$out.additional_output_format' + output1 <- '$output1' + output2 <- '$output2' + + ## ggsave to png + ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png") + if(gg_add_device != "none"){ + ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device) + } + ]]></token> + <xml name="read_complex_input"> + <param name="input1" type="data" format="tabular" label="Select table"/> + <conditional name="inputdata"> + <param name="input_type" type="select" label="Select input dataset options" help="specific dataset input for reading"> + <option value="with_header" selected="true">Dataset with header</option> + <option value="with_rownames">Dataset with row names</option> + <option value="with_header_rownames">Dataset with header and row names</option> + <option value="no_header_rownames">Dataset without header or row names</option> + </param> + <when value="with_header"> + <param name="header" type="hidden" value="TRUE"/> + <param name="row_names_index" type="hidden" value="0"/> + <param name="sample_name_orientation" type="select" display="radio" multiple="false" label="Sample names orientation" help="Default horizontal: header names are interpreted as sample names"> + <option value="TRUE" selected="true">horizontal</option> + <option value="FALSE">vertial</option> + </param> + </when> + <when value="with_rownames"> + <param name="header" type="hidden" value="FALSE"/> + <param name="row_names_index" type="data_column" data_ref="input1" label="Select column, for row names" help="WARNING: please consider that using row names might shift the grouping columns"/> + <param name="sample_name_orientation" type="select" display="radio" label="Sample names orientation" help="default vertial: row names are interpreted as sample names"> + <option value="TRUE">horizontal</option> + <option value="FALSE" selected="true">vertial</option> + </param> + </when> + <when value="with_header_rownames"> + <param name="header" type="hidden" value="TRUE"/> + <param name="row_names_index" type="data_column" data_ref="input1" label="Select column, for row names" help="WARNING: please consider that using row names might shift the grouping columns"/> + <param name="sample_name_orientation" type="select" label="Sample names orientation" display="radio" multiple="false" help="deside whether header names or row names are interpreted as sample names"> + <option value="TRUE" selected="true">horizontal</option> + <option value="FALSE">vertial</option> + </param> + </when> + <when value="no_header_rownames"> + <param name="header" type="hidden" value="FALSE"/> + <param name="row_names_index" type="hidden" value="0"/> + <param name="sample_name_orientation" type="hidden" value="TRUE"/> + </when> + </conditional> + </xml> <xml name="transform"> - <param name="transform" type="select" label="Advanced - log transformation"> + <param name="transform" type="select" label="Data transformation"> <option value="none">Plot the data as it is</option> <option value="log2">Log2(value) transform my data</option> <option value="log2plus1">Log2(value+1) transform my data</option> @@ -37,23 +126,11 @@ <option value="log10plus1">Log10(value+1) transform my data</option> </param> </xml> - - <token name="@XY_SCALING@"><![CDATA[ -#Choose between automatically scaled x and y axis or user defined -#if $scaling.plot_scaling == "Automatic" - gg_scalex = NULL - gg_scaley = NULL -#else - gg_scalex = xlim($scaling.xaxismin, $scaling.xaxismax) - gg_scaley = ylim($scaling.yaxismin, $scaling.yaxismax) -#end if - ]]></token> - <xml name="xy_scaling"> <conditional name="scaling"> - <param name="plot_scaling" type="select" label="Advanced - Axis scaling"> - <option value="Automatic" selected="True">Automatic axis scaling</option> - <option value="Defined">User deined axis scales</option> + <param name="plot_scaling" type="select" label="Axis scaling"> + <option value="Automatic" selected="true">Automatic axis scaling</option> + <option value="Defined">User-defined axis scales</option> </param> <when value="Automatic"> <!--Do nothing here --> @@ -67,33 +144,68 @@ </conditional> </xml> <xml name="title"> - <param name="title" type="text" value="plot title" label="Title of plot" /> + <param name="title" type="text" value="" label="Plot title"> + <!--<sanitizer sanitize="false"/> --> + </param> </xml> <xml name="xy_lab"> - <param name="xlab" type="text" value="title of x-axis" label="Label for x-axis"/> - <param name="ylab" type="text" value="title of y-axis" label="Label for y-axis"/> + <param name="xlab" type="text" value="title of x-axis" label="Label for x axis"> + <sanitizer sanitize="false"/> + </param> + <param name="ylab" type="text" value="title of y-axis" label="Label for y axis"> + <sanitizer sanitize="false"/> + </param> + </xml> + <xml name="legend"> + <param name="legend" type="select" label="Legend options"> + <option value="yes">Include legend on plot</option> + <option value="no">Hide legend</option> + </param> + </xml> + <xml name="theme"> + <param name="theme" type="select" label="Backgound theme for plot"> + <option value="bw">Black and white</option> + <option value="Default">Default (grey)</option> + </param> </xml> <xml name="dimensions"> - <param name="with_output_dim" type="float" value="7" label="width of output" help="in inches" /> - <param name="height_output_dim" type="float" value="7" label="height of output" help="in inches" /> + <param name="unit_output_dim" type="select" label="Unit of output dimensions" help="default inches"> + <option value="in" selected="true">Inches (in)</option> + <option value="cm">Centimeters (cm)</option> + <option value="mm">Millimeters (mm)</option> + </param> + <param name="width_output_dim" type="float" value="7" label="width of output"/> + <param name="height_output_dim" type="float" value="7" label="height of output"/> + <param name="dpi_output_dim" type="float" value="300" label="dpi of output" help="Plot resolution. Applies only to raster output types."/> + <param name="additional_output_format" type="select" label="Additional output format" help="PNG is always selected as output format"> + <option value="none" selected="true">only PNG</option> + <option value="pdf">PDF</option> + <option value="svg">SVG</option> + <option value="eps">EPS</option> + <option value="ps">PS</option> + <option value="tex">TEX (pictex)</option> + <option value="jpeg">JPEG</option> + <option value="tiff">TIFF</option> + <option value="bmp">BMP</option> + </param> </xml> <xml name="citations"> <citations> - <citation type="bibtex">@Book{ + <citation type="bibtex">@book{wickham2009ggplot2, author = {Hadley Wickham}, title = {ggplot2: Elegant Graphics for Data Analysis}, publisher = {Springer-Verlag New York}, year = {2009}, isbn = {978-0-387-98140-6}, - url = {http://ggplot2.org} + url = {http://ggplot2.org}, } </citation> + <yield /> </citations> </xml> - - <xml name="axis_customization" token_label="Advanced - axis title options"> + <xml name="axis_customization" token_label="Axis title options"> <param name="axis_customization" type="select" label="@LABEL@"> - <option value="default" selected="True">Default</option> + <option value="default" selected="true">Default</option> <option value="defined">User defined label options</option> </param> <when value="default"> @@ -113,7 +225,7 @@ <option value="magenta">Magenta</option> <option value="cyan">Cyan</option> <option value="grey">Grey</option> - <option value="gold">Gold</option> + <option value="gold">Gold</option> </param> <param name="face" type="select" label="Font effect of axis label"> <option value="plain">Normal (default)</option> @@ -122,7 +234,6 @@ </param> </when> </xml> - <xml name="colors"> <param name="colors" type="select" label="Color schemes to differentiate your groups" > <option value="Default">Default color scheme</option> @@ -159,8 +270,22 @@ <option value="RdBu">Red to blue (discrete, max=11 colors)</option> <option value="PuOr">Purple to orange (discrete, max=11 colors)</option> <option value="PRGn">Purple to green (discrete, max=11 colors)</option> - <option value="BrBG">Brown to teal (discrete, max=11 colors)</option> + <option value="BrBG">Brown to teal (discrete, max=11 colors)</option> </param> </xml> - + <xml name="additional_output"> + <data name="output1" format="png" label="${tool.name} on ${on_string}: png"/> + <data format="pdf" name="output2" label="${tool.name} on ${on_string}: ${out.additional_output_format}"> + <change_format> + <when input="out.additional_output_format" value="svg" format="svg" /> + <when input="out.additional_output_format" value="eps" format="eps" /> + <when input="out.additional_output_format" value="ps" format="ps" /> + <when input="out.additional_output_format" value="tex" format="txt" /> + <when input="out.additional_output_format" value="jpeg" format="jpg" /> + <when input="out.additional_output_format" value="tiff" format="tiff" /> + <when input="out.additional_output_format" value="bmp" format="bmp" /> + </change_format> + <filter>out['additional_output_format'] != "none"</filter> + </data> + </xml> </macros>