Mercurial > repos > kuyt002 > vennerable_r
changeset 0:77bbf955e8de default tip
initial commit
| author | eric |
|---|---|
| date | Thu, 06 Nov 2014 15:07:54 +0100 |
| parents | |
| children | |
| files | .directory .project vennerable/Vennerable.R vennerable/Vennerable.xml vennerable/static/images/Vennerable.R_backup.png vennerable/static/images/Vennerable.pdf vennerable/static/images/Vennerable.xml_backup.png vennerable/static/images/VennerablePlot.png vennerable/test/Vennerable.DemoTable.tab vennerable/tool_dependencies.xml vennerable/unused/Vennerable.R_backup_png_xml vennerable/unused/Vennerable.xml_backup_png |
| diffstat | 12 files changed, 594 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.directory Thu Nov 06 15:07:54 2014 +0100 @@ -0,0 +1,5 @@ +[Dolphin] +Timestamp=2014,6,17,13,13,59 + +[Settings] +HiddenFilesShown=true
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.project Thu Nov 06 15:07:54 2014 +0100 @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<projectDescription> + <name>vennerable(testtoolshed)</name> + <comment></comment> + <projects> + </projects> + <buildSpec> + </buildSpec> + <natures> + </natures> +</projectDescription>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vennerable/Vennerable.R Thu Nov 06 15:07:54 2014 +0100 @@ -0,0 +1,67 @@ +#!/usr/bin/R + +# R script to call Vennerable package from galaxy +# info: alex.bossers@wur.nl + +# R --slave --vanilla --file=PlotBar.R --args inputFile x_data weighting outputFile plottype resolution imagetype +# 1 2 3 4 5 6 7 8 9 10 11 12 + +#get cmd line args +args <- commandArgs() + in.file <- args[6] + xData <- args[7] # data labels xData of format "a, b, c" and can include spaces + weighting <- args[8] + out.file <- args[9] + plottype <- args[10] + resolution <- args[11] # in dpi + imagetype <- args[12] # svg, pdf or png + +#open lib +library(Vennerable) +options(bitmapType='cairo') + +# for labels of bars or bar groups presume column names from data +if (xData != "default") { + # read without header input file (must be tabular) + annot_data <- read.table(in.file, header=F, sep="\t") + colnames (annot_data) <- strsplit(xData,",")[[1]] + Vannot <- Venn(annot_data) +} else { + # read without header input file (must be tabular) + annot_data <- read.table(in.file, header=T, sep="\t") + Vannot <- Venn(annot_data) +} + +#set output imagetype (svg pdf or png) +#R 3.0.2 and default cairo libs should handle it all ok +#it could be that X11 should be loaded for non-pdf +if (imagetype == "svg") { + svg(out.file) +} else if (imagetype == "png") { + png(out.file, width = 1600, height = 1600, res = resolution) +} else { + pdf(out.file) +} + +# plot it +if (plottype == "ChowRuskey") { + plot(Vannot, type = plottype) + +} else if (plottype == "AWFE") { + plot(Vannot, doWeights = weighting, type = plottype) + +} else if (plottype == "circles") { + plot(Vannot) + +} else if (plottype == "ellipses"){ + plot(Vannot, type = "ellipses") + +} else if (plottype == "squares"){ + plot(Vannot, type = "squares") + +} else if (plottype == "battle"){ + plot(Vannot, type = "battle") +} + +cat ("Wrapper version 1.2, running Vennerable v3.0-82\n Info/bugs: alex.bossers@wur.nl\n") +dev.off()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vennerable/Vennerable.xml Thu Nov 06 15:07:54 2014 +0100 @@ -0,0 +1,135 @@ +<tool id="Vennerable" name="Vennerable" version="1.2c" > + <description>: Plot data in Venn or Edwards/Venn-like diagrams</description> + <command> + R --slave --vanilla --file=\$VENNERABLE_SCRIPT_PATH/vennerable/Vennerable.R + --args $inputFile + #if $opt.userSpecified == "Yes" + default + #else + "$opt.xNames" + #end if + $weighting + #if $imagetype.value == "svg" + $outputFile_svg + $plottype + $resolution + svg + #else if $imagetype.value == "png" + $outputFile_png + $plottype + $resolution + png + #else + $outputFile_pdf + $plottype + $resolution + pdf + #end if + 2>$Vennerable_log + 1>>$Vennerable_log + </command> + <inputs> + <param name="inputFile" format="tabular" type="data" label="Data set" /> + <conditional name="opt"> + <param name="userSpecified" type="select" label="Use column headers as dataset names?"> + <option value="Yes">Yes</option> + <option value="No">No</option> + </param> + <when value="Yes"> + </when> + <when value="No"> + <param name="xNames" type="text" label="Alternative data names" value="A,B,C,D" help="(comma-separated)"/> + </when> + </conditional> + <param name="plottype" type="select" label="Plot type to use" help="some other options might get disabled for certain plottypes" > + <option value="AWFE" selected="True">AWFE: Edwards-Venn (Non-weighted up to 5 datasets)</option> + <option value="ChowRuskey">Chow-Ruskey (always weigthed max 9 sets common intersect not 0)</option> + <option value="ellipses">Ellipses (4 datasets only and always non-weighted)</option> + <option value="circles">Circles (max 3 datasets)</option> + <option value="squares">Squares (max 4 datasets non-weighted)</option> + <option value="battle">Edwards-Venn Squares battle (max 9 datasets, non-weighted)</option> + </param> + <param name="weighting" type="select" label="Use weighting for data in plot" > + <option value="FALSE" selected="True">Non-weighted</option> + <option value="TRUE">Weighted</option> + </param> + <param name="resolution" type="integer" label="Resolution to use (dpi)" value="150" help="Plot features can be sized with this setting (PNG only). Lower (50) is larger text.<br /><i>Default is vector graphics format SVG!</i>" /> + <param name="imagetype" type="select" label="Image output format" help="Scalable Vector Graphics (SVG) format is best for post processing" > + <option value="pdf" selected="True">PDF</option> + <option value="svg">SVG</option> + <option value="png">PNG</option> + </param> + </inputs> + <outputs> + <data name="outputFile_svg" format="svg" label="Venn diagram svg of ${inputFile.name}"> + <filter>imagetype=="svg"</filter> + </data> + <data name="outputFile_png" format="png" label="Venn diagram png of ${inputFile.name}"> + <filter>imagetype=="png"</filter> + </data> + <data name="outputFile_pdf" format="pdf" label="Venn diagram pdf of ${inputFile.name}"> + <filter>imagetype=="pdf"</filter> + </data> + <data name="Vennerable_log" format="tabular" label="Vennerable output and error log file" /> + </outputs> + <tests> + <test> + </test> + </tests> + <requirements> + <requirement type="package" version="3.0.3">R</requirement> + <requirement type="package" version="1.0">vennerable_r_packages</requirement> + <requirement type="set_environment">VENNERABLE_SCRIPT_PATH</requirement> + </requirements> + <help> +| + + +**What it does** + +Vennerable V3.0 (07-10-2014) + +This tool will use the Vennerable R package to plot data as weighted or un-weighted diagrams such as Venn, Edwards-Venn and Chow-Rusky. + +The tool can take from 2 to 9 collumns (in battle mode) of data but more are adviced not to be used (for speed and clarity). + +Since version Vennerable version 3 it supports up to 9 datasets in battle mode. Wrapper version 1.2 and up support output in svg, pdf and png. + +----- + +**Input** + +It takes a tabular file containing identifiers. Matches will be calculated automatically. + +Be sure to specify headers if you haven't any in your dataset! Otherwise the top row of data will be excluded. + +:: + + DataA DataB DataC DataD + HUM1 AGK2 AGK2 RTT3 + AGK2 ZZE3 ERT3 ZPD3 + ZPD3 AAW3 RTT3 WER2 + WER2 HUM1 RRW4 DUM1 + +----- + +**Example** + +.. image:: ../static/images/WURtools/VennerablePlot.png + +----- + +**References** + +- alex.bossers@wur.nl +- Vennerable R package: http://r-forge.r-project.org/projects/vennerable/ + +----- + +.. class:: infomark + +**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* + + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vennerable/static/images/Vennerable.R_backup.png Thu Nov 06 15:07:54 2014 +0100 @@ -0,0 +1,56 @@ +#!/usr/bin/R + +# R script to call Vennerable package from galaxy +# info: alex.bossers@wur.nl + +# R --slave --vanilla --file=PlotBar.R --args inputFile x_data weighting outputFile plottype resolution +# 1 2 3 4 5 6 7 8 9 10 11 + +#get cmd line args +args <- commandArgs() + in.file <- args[6] + xData <- args[7] # data labels xData of format "a, b, c" and can include spaces + weighting <- args[8] + out.file <- args[9] + plottype <- args[10] + resolution <- args[11] #in dpi + +#open lib +library(Vennerable) + +# for labels of bars or bar groups presume column names from data +if (xData != "default") { + # read without header input file (must be tabular) + annot_data <- read.table(in.file, header=F, sep="\t") + colnames (annot_data) <- strsplit(xData,",")[[1]] + Vannot <- Venn(annot_data) +} else { + # read without header input file (must be tabular) + annot_data <- read.table(in.file, header=T, sep="\t") + Vannot <- Venn(annot_data) +} + +#png(out.file,width = 1600, height = 1600, res = resolution) +png(out.file, res = resolution) + +# plot it +if (plottype == "ChowRuskey") { + plot(Vannot, type = plottype) + +} else if (plottype == "AWFE") { + plot(Vannot, doWeights = weighting, type = plottype) + +} else if (plottype == "circles") { + plot(Vannot) + +} else if (plottype == "ellipses"){ + plot(Vannot, type = "ellipses") + +} else if (plottype == "squares"){ + plot(Vannot, type = "squares") + +} + +cat ("version 1.0, info: alex.bossers@wur.nl\n") +dev.off() +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vennerable/static/images/Vennerable.xml_backup.png Thu Nov 06 15:07:54 2014 +0100 @@ -0,0 +1,112 @@ +<tool id="Vennerable" name="Vennerable" version="0.9" > + <description>: Plot data in Venn or Venn-like diagrams</description> + <command> + #if $opt.userSpecified == "Yes" + R --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/WURtools/R_tools/Vennerable.R + --args $inputFile + default + $weighting + $outputFile + $plottype + $resolution + 2>$Vennerable_log + 1>>$Vennerable_log + #else + R --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/WURtools/R_tools/Vennerable.R + --args $inputFile + "$opt.xNames" + $weighting + $outputFile + $plottype + $resolution + 2>$Vennerable_log + 1>>$Vennerable_log + #end if + </command> + <inputs> + <param name="inputFile" format="tabular" type="data" label="Data set" /> + <conditional name="opt"> + <param name="userSpecified" type="select" label="Use column headers as dataset names?"> + <option value="Yes">Yes</option> + <option value="No">No</option> + </param> + <when value="Yes"> + </when> + <when value="No"> + <param name="xNames" type="text" label="Alternative data names" value="A,B,C,D" help="(comma-separated)"/> + </when> + </conditional> + <param name="plottype" type="select" label="Plot type to use" help="some other options might get disabled for certain plottypes" > + <option value="AWFE" selected="True">AWFE: Edwards-Venn (Non-weighted)</option> + <option value="ChowRuskey">Chow-Ruskey (always weigthed)</option> + <option value="ellipses">Ellipses (4 datasets only and always non-weighted)</option> + <option value="circles">Circles (max 3 datasets)</option> + <option value="squares">Squares (max 4 datasets non-weighted)</option> + </param> + <param name="weighting" type="select" label="Use weighting for data in plot" > + <option value="FALSE" selected="True">Non-weighted</option> + <option value="TRUE">Weighted</option> + </param> + <param name="resolution" type="integer" label="Resolution to use (dpi)" value="150" help="Plot features can be sized with this setting. Lower (50) is larger text." /> + </inputs> + <outputs> + <data name="outputFile" format="png" label="Venn diagram of ${inputFile.name}"/> + <data name="Vennerable_log" format="tabular" label="Vennerable output and error log file" /> + </outputs> + <tests> + <test> + </test> + </tests> + <requirements> + <requirement type="binary">R</requirement> + </requirements> + <help> +| + + +**What it does** + +Vennerable V2.0 (09-10-2009) + +This tool will use the Vennerable R package to plot data as weighted or un-weighted diagrams such as Venn, Edwards-Venn and Chow-Rusky. + +The tool can take 2 to 7 collumns of data but more are adviced not to be used (for speed and clarity). + +----- + +**Input** + +It takes a tabular file containing identifiers. Matches will be calculated automatically. + +Be sure to specify headers if you haven't any in your dataset! Otherwise the top row of data will be excluded. + +:: + + DataA DataB DataC DataD + HUM1 AGK2 AGK2 RTT3 + AGK2 ZZE3 ERT3 ZPD3 + ZPD3 AAW3 RTT3 WER2 + WER2 HUM1 RRW4 DUM1 + +----- + +**Example** + +.. image:: ../static/images/WURtools/VennerablePlot.png + +----- + +**References** + +- alex.bossers@wur.nl +- Vennerable R package: http://r-forge.r-project.org/projects/vennerable/ + +----- + +.. class:: infomark + +**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* + + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vennerable/test/Vennerable.DemoTable.tab Thu Nov 06 15:07:54 2014 +0100 @@ -0,0 +1,8 @@ +Data1 Data2 Data3 Data4 Data5 Data6 +aa bb aa aa bb cc +bb gg bb bb dd bb +cc dd ii ii gg qq +dd hh gg ii xx ww +ee jj gg kl ee +ff yy uy tt + pp uu \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vennerable/tool_dependencies.xml Thu Nov 06 15:07:54 2014 +0100 @@ -0,0 +1,32 @@ +<?xml version="1.0"?> +<tool_dependency> + <set_environment> + <environment_variable name="VENNERABLE_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> + <package name="R" version="3.0.3"> + <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu/" prior_installation_required="True"/> + </package> + <package name="vennerable_r_packages" version="1.0"> + <install version="1.0"> + <actions> + <action type="setup_r_environment"> + <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu/"> + <package name="R" version="3.0.3" /> + </repository> + <package>http://www.bioconductor.org/packages/2.13/bioc/src/contrib/BiocGenerics_0.8.0.tar.gz</package> + <package>http://www.bioconductor.org/packages/2.13/bioc/src/contrib/graph_1.40.1.tar.gz</package> + <package>http://www.bioconductor.org/packages/2.13/bioc/src/contrib/RBGL_1.38.0.tar.gz</package> + <package>http://cran.r-project.org/src/contrib/Archive/RColorBrewer/RColorBrewer_1.0-4.tar.gz</package> + <package>http://cran.r-project.org/src/contrib/Archive/Rcpp/Rcpp_0.11.2.tar.gz</package> + <package>http://cran.r-project.org/src/contrib/Archive/plyr/plyr_1.8.tar.gz</package> + <package>http://cran.r-project.org/src/contrib/Archive/reshape/reshape_0.8.4.tar.gz</package> + <package>http://cran.r-project.org/src/contrib/Archive/gtools/gtools_3.4.0.tar.gz</package> + <package>http://cran.r-project.org/src/contrib/Archive/xtable/xtable_1.7-3.tar.gz</package> + <package>http://download.r-forge.r-project.org/src/contrib/Vennerable_3.0.tar.gz</package> + </action> + </actions> + </install> + <readme></readme> + </package> +</tool_dependency> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vennerable/unused/Vennerable.R_backup_png_xml Thu Nov 06 15:07:54 2014 +0100 @@ -0,0 +1,56 @@ +#!/usr/bin/R + +# R script to call Vennerable package from galaxy +# info: alex.bossers@wur.nl + +# R --slave --vanilla --file=PlotBar.R --args inputFile x_data weighting outputFile plottype resolution +# 1 2 3 4 5 6 7 8 9 10 11 + +#get cmd line args +args <- commandArgs() + in.file <- args[6] + xData <- args[7] # data labels xData of format "a, b, c" and can include spaces + weighting <- args[8] + out.file <- args[9] + plottype <- args[10] + resolution <- args[11] #in dpi + +#open lib +library(Vennerable) + +# for labels of bars or bar groups presume column names from data +if (xData != "default") { + # read without header input file (must be tabular) + annot_data <- read.table(in.file, header=F, sep="\t") + colnames (annot_data) <- strsplit(xData,",")[[1]] + Vannot <- Venn(annot_data) +} else { + # read without header input file (must be tabular) + annot_data <- read.table(in.file, header=T, sep="\t") + Vannot <- Venn(annot_data) +} + +#png(out.file,width = 1600, height = 1600, res = resolution) +png(out.file, res = resolution) + +# plot it +if (plottype == "ChowRuskey") { + plot(Vannot, type = plottype) + +} else if (plottype == "AWFE") { + plot(Vannot, doWeights = weighting, type = plottype) + +} else if (plottype == "circles") { + plot(Vannot) + +} else if (plottype == "ellipses"){ + plot(Vannot, type = "ellipses") + +} else if (plottype == "squares"){ + plot(Vannot, type = "squares") + +} + +cat ("version 1.0, info: alex.bossers@wur.nl\n") +dev.off() +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vennerable/unused/Vennerable.xml_backup_png Thu Nov 06 15:07:54 2014 +0100 @@ -0,0 +1,112 @@ +<tool id="Vennerable" name="Vennerable" version="0.9" > + <description>: Plot data in Venn or Venn-like diagrams</description> + <command> + #if $opt.userSpecified == "Yes" + R --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/WURtools/R_tools/Vennerable.R + --args $inputFile + default + $weighting + $outputFile + $plottype + $resolution + 2>$Vennerable_log + 1>>$Vennerable_log + #else + R --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/WURtools/R_tools/Vennerable.R + --args $inputFile + "$opt.xNames" + $weighting + $outputFile + $plottype + $resolution + 2>$Vennerable_log + 1>>$Vennerable_log + #end if + </command> + <inputs> + <param name="inputFile" format="tabular" type="data" label="Data set" /> + <conditional name="opt"> + <param name="userSpecified" type="select" label="Use column headers as dataset names?"> + <option value="Yes">Yes</option> + <option value="No">No</option> + </param> + <when value="Yes"> + </when> + <when value="No"> + <param name="xNames" type="text" label="Alternative data names" value="A,B,C,D" help="(comma-separated)"/> + </when> + </conditional> + <param name="plottype" type="select" label="Plot type to use" help="some other options might get disabled for certain plottypes" > + <option value="AWFE" selected="True">AWFE: Edwards-Venn (Non-weighted)</option> + <option value="ChowRuskey">Chow-Ruskey (always weigthed)</option> + <option value="ellipses">Ellipses (4 datasets only and always non-weighted)</option> + <option value="circles">Circles (max 3 datasets)</option> + <option value="squares">Squares (max 4 datasets non-weighted)</option> + </param> + <param name="weighting" type="select" label="Use weighting for data in plot" > + <option value="FALSE" selected="True">Non-weighted</option> + <option value="TRUE">Weighted</option> + </param> + <param name="resolution" type="integer" label="Resolution to use (dpi)" value="150" help="Plot features can be sized with this setting. Lower (50) is larger text." /> + </inputs> + <outputs> + <data name="outputFile" format="png" label="Venn diagram of ${inputFile.name}"/> + <data name="Vennerable_log" format="tabular" label="Vennerable output and error log file" /> + </outputs> + <tests> + <test> + </test> + </tests> + <requirements> + <requirement type="binary">R</requirement> + </requirements> + <help> +| + + +**What it does** + +Vennerable V2.0 (09-10-2009) + +This tool will use the Vennerable R package to plot data as weighted or un-weighted diagrams such as Venn, Edwards-Venn and Chow-Rusky. + +The tool can take 2 to 7 collumns of data but more are adviced not to be used (for speed and clarity). + +----- + +**Input** + +It takes a tabular file containing identifiers. Matches will be calculated automatically. + +Be sure to specify headers if you haven't any in your dataset! Otherwise the top row of data will be excluded. + +:: + + DataA DataB DataC DataD + HUM1 AGK2 AGK2 RTT3 + AGK2 ZZE3 ERT3 ZPD3 + ZPD3 AAW3 RTT3 WER2 + WER2 HUM1 RRW4 DUM1 + +----- + +**Example** + +.. image:: ../static/images/WURtools/VennerablePlot.png + +----- + +**References** + +- alex.bossers@wur.nl +- Vennerable R package: http://r-forge.r-project.org/projects/vennerable/ + +----- + +.. class:: infomark + +**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* + + + </help> +</tool>