Mercurial > repos > moheydarian > ggplot_scatterplot

changeset 12:8df1c60db1c4 draft

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author moheydarian
date Wed, 11 Jan 2017 10:34:42 -0500
parents 70131ebcabce
children 08ae6379dfbb
files Galaxy-wrapper-for-ggplot2-scatterplot.git ggplot_point.xml ggplotpointscript.R tool_dependency.xml
diffstat 4 files changed, 0 insertions(+), 1347 deletions(-) [+]
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--- a/Galaxy-wrapper-for-ggplot2-scatterplot.git	Wed Jan 11 10:34:22 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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-            <span class="css-truncate css-truncate-target"><time-ago datetime="2017-01-11T15:32:51Z">Jan 11, 2017</time-ago></span>
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-      README.md
-    </h3>
-
-      <article class="markdown-body entry-content" itemprop="text"><h1><a id="user-content-galaxy-wrapper-for-ggplot2-scatterplot" class="anchor" href="#galaxy-wrapper-for-ggplot2-scatterplot" aria-hidden="true"><svg aria-hidden="true" class="octicon octicon-link" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Galaxy-wrapper-for-ggplot2-scatterplot</h1>
-
-<p>This Galalxy wrapper is for the creation of scatterplots using the geom_point() function of ggplot2. </p>
-
-<p>This wrapper is under development and will soon move to the Galaxy toolshed. </p>
-</article>
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--- a/ggplot_point.xml	Wed Jan 11 10:34:22 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,390 +0,0 @@
-<tool id="ggplot_point" name="Scatterplot w ggplot2 to pdf 8.10.2" version="0.1.2">
-    <requirements>
-        <requirement type="package">getopt</requirement>
-        <requirement type="package">ggplot2</requirement>
-    </requirements>
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
-    <command><![CDATA[
-        Rscript '$__tool_directory__/ggplotpointscript.R' --input "$input1" --title "$title" 
-        --theme "${theme.theme_selector}" --xplot "$xplot" --yplot "$yplot" --scaling "$scaling.Plot_scaling" --points "$points.pointoptions" --dim "$dimensions.plotdim" --factor "$factor.factoring" --transform "$transformation.transform" --xlab "$xlab" --ylab "$ylab" 
-        --axistitlecust "$axistitlecustomization.axistitlecust" --axistextcust "$axistextcustomization.axistextcust" 
-        --plottitlecust "$plottitlecustomization.plottitlecust" --gridlinecust "$gridlinecustomization.gridlinecust" --output "Rplot.pdf"
-        #if str( $factor.factoring ) == "Single":
-            --factorcol ${factor.factorcol}
-            --colors ${factor.colors}
-            --colororder ${factor.colororder}
-        #elif str( $factor.factoring ) == "Multiple":
-            --factorcol ${factor.factorcol}
-            --colors=irrelevant
-            --colororder=1
-        #else:
-           --factorcol=1
-           --colors=irrelevant
-           --colororder=1
-        #end if
-
-        #if str( $points.pointoptions ) == "Defined":
-            --size ${points.size}
-            --alpha ${points.alpha}
-            --pointcolor ${points.pointcolor}
-        #else:
-           --size=1
-           --alpha=1
-           --pointcolor=black
-        #end if
-
-        #if str( $scaling.Plot_scaling ) == "Defined":
-            --xaxismin=${scaling.xaxismin}
-            --xaxismax=${scaling.xaxismax}
-            --yaxismin=${scaling.yaxismin}
-            --yaxismax=${scaling.yaxismax}
-        #else:
-           --xaxismin=0
-           --xaxismax=1
-           --yaxismin=2
-           --yaxismax=3
-        #end if
-
-        #if str( $axistitlecustomization.axistitlecust ) == "Defined":
-            --axistitlesize ${axistitlecustomization.axistitlesize}
-            --axistitlecolor ${axistitlecustomization.axistitlecolor}
-            --axistitleface ${axistitlecustomization.axistitleface}
-        #else:
-            --axistitlesize=12
-            --axistitlecolor=black
-            --axistitleface=plain
-        #end if
-
-        #if str( $axistextcustomization.axistextcust ) == "Defined":
-            --axistextsize ${axistextcustomization.axistextsize}
-            --axistextcolor ${axistextcustomization.axistextcolor}
-            --axistextface ${axistextcustomization.axistextface}
-        #else:
-            --axistextsize=12
-            --axistextcolor=black
-            --axistextface=plain
-        #end if
-
-        #if str( $plottitlecustomization.plottitlecust ) == "Defined":
-            --plottitlesize ${plottitlecustomization.plottitlesize}
-            --plottitlecolor ${plottitlecustomization.plottitlecolor}
-            --plottitleface ${plottitlecustomization.plottitleface}
-        #else:
-            --plottitlesize=12
-            --plottitlecolor=black
-            --plottitleface=plain
-        #end if
-
-        #if str( $dimensions.plotdim ) == "Defined":
-            --woutputdim ${dimensions.woutputdim}
-            --houtputdim ${dimensions.houtputdim}
-        #else:
-           --woutputdim=7
-           --houtputdim=7
-        #end if
-
-    ]]></command>
-    <inputs>
-        <param name="input1" type="data" format="tabular" label="Input (tabular format)" />
-        <param name="xplot" type="integer" value="8" label="Column to plot on x-axis" />
-        <param name="yplot" type="integer" value="9" label="Column to plot on y-axis" />
-        <param name="title" size="30" type="text" value="plot title" label="Title of plot" />
-        <param name="xlab" size="30" type="text" value="title of x-axis" label="Label for x-axis"/>
-        <param name="ylab" size="30" type="text" value="title of y-axis" label="Label for y-axis"/> 
-        <conditional name="points">
-            <param name="pointoptions" type="select" label="Advanced - data point options">
-                <option value="Default" selected="True">Default</option>
-                <option value="Defined">User defined point options</option>
-            </param>
-            <when value="Default">
-                <!--Do nothing here -->
-            </when>
-            <when value="Defined">
-                <param name="size" size="4" type="float" value="1" label="relative size of points" />
-                <param name="alpha" size="4" type="float" value="1" label="Transparency of points (On a scale of 0-1; 0=transparent, 1=default)" />
-                <param name="pointcolor" type="select" label="Color of data points" >
-                    <option value="black">Black (default)</option>
-                    <option value="red">Red</option>
-                    <option value="white">White</option>
-                    <option value="blue">Blue</option>
-                    <option value="orange">Orange</option>
-                    <option value="yellow">Yellow</option>
-                    <option value="green">Green</option>
-                    <option value="purple">Purple</option>
-                    <option value="magenta">Magenta</option>
-                    <option value="cyan">Cyan</option>
-                    <option value="grey">Grey</option>
-                    <option value="gold">Gold</option>
-                </param>
-            </when>
-        </conditional>
-        <conditional name="factor">
-            <param name="factoring" type="select" label="Advanced - plotting multiple groups" >
-                <option value="Default" selected="True">No thanks - just plot the data as one group</option>
-                <option value="Single">Plot multiple groups of data on one plot</option>
-                <option value="Multiple">Plot multiple groups of data on individual plots</option>
-            </param>
-            <when value="Default">
-                <!--Do nothing here -->
-            </when>
-            <when value="Single">
-                <param name="factorcol" size="4" type="integer" value="1" label="column differentiating the different groups" />
-                <param name="colors" type="select" label="Color schemes to differentiate your groups" >
-                    <option value="Default">Default color scheme</option>
-                    <option value="YlOrRd">Yellow to orange to red (discrete, max=9 colors)</option>
-                    <option value="YlOrBr">Yellow to orange to brown (discrete, max=9 colors)</option>                    
-                    <option value="YlGnBu">Yellow to green to blue (discrete, max=9 colors)</option>
-                    <option value="YlGn">Yellow to green (discrete, max=9 colors)</option>
-                    <option value="Reds">Shades of red from light to dark (discrete, max=9 colors)</option>
-                    <option value="RdPu">Red to purple (discrete, max=9 colors)</option>
-                    <option value="Purples">Shades of purple from light to dark (discrete, max=9 colors)</option>
-                    <option value="PuRd">Purple to red (discrete, max=9 colors)</option>
-                    <option value="PuBuGn">Purple to blue to green (discrete, max=9 colors)</option>
-                    <option value="PuBu">Purple to blue(discrete, max=9 colors)</option>
-                    <option value="OrRd">Orange to red (discrete, max=9 colors)</option>
-                    <option value="Oranges">Shades of orange from light to dark (discrete, max=9 colors)</option>
-                    <option value="Greys">Shades of grey from light to dark (discrete, max=9 colors)</option>
-                    <option value="Greens">Shades of greens from light to dark (discrete, max=9 colors)</option>
-                    <option value="GnBu">Green to blue (discrete, max=9 colors)</option>
-                    <option value="BuPu">Blue to purple (discrete, max=9 colors)</option>
-                    <option value="BuGn">Blue to green (discrete, max=9 colors)</option>
-                    <option value="Blues">Shades of blue from light to dark (discrete, max=9 colors)</option>
-                    <option value="Set1">Set 1 - predefined color pallete (discrete, max=9 colors)</option>
-                    <option value="Set2">Set 2 - predefined color pallete (discrete, max=8 colors)</option>
-                    <option value="Set3">Set 3 - predefined color pallete (discrete, max=12 colors)</option>
-                    <option value="Pastel1">Pastel 1 - predefined pastel color pallete (discrete, max=9 colors)</option>
-                    <option value="Pastel2">Pastel 2 - predefined pastel color pallete (discrete, max=8 colors)</option>
-                    <option value="Paired">Paired - predefined color pallete (discrete, max=12 colors)</option>
-                    <option value="Dark2">Dark 2 - predefined color pallete (discrete, max=12 colors)</option>
-                    <option value="Accent">Accent - predefined color pallete (discrete, max=12 colors)</option>
-                    <option value="Spectral">Spectral - Red to yellow to purple (discrete, max=11 colors)</option>
-                    <option value="RdYlGn">Red to yellow to green (discrete, max=11 colors)</option>
-                    <option value="RdYlBu">Red to yellow to blue (discrete, max=11 colors)</option>
-                    <option value="RdGy">Red to grey (discrete, max=11 colors)</option>
-                    <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> 
-                </param>
-                <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>
-            <when value="Multiple">
-                <param name="factorcol" size="4" type="integer" value="1" label="column differentiating the different groups" />
-            </when>
-        </conditional>
-        <conditional name="transformation">
-            <param name="transform" type="select" label="Advanced - log 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>
-              <option value="log10">Log10(value) transform my data</option>
-              <option value="log10plus1">Log10(value+1) transform my data</option>
-            </param>
-             <when value="none">
-                <!--Do nothing here -->
-            </when>
-             <when value="log2">
-                <!--Do nothing here -->
-            </when>
-             <when value="log2plus1">
-                <!--Do nothing here -->
-            </when>
-             <when value="log10">
-                <!--Do nothing here -->
-            </when>
-             <when value="log10plus1">
-                <!--Do nothing here -->
-            </when>
-        </conditional>
-        <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 defined axis scales</option>
-            </param>
-            <when value="Automatic">
-                <!--Do nothing here -->
-            </when>
-            <when value="Defined">
-                <param name="xaxismin" size="4" type="integer" value="0" label="minimal range of x-axis" />
-                <param name="xaxismax" size="4" type="integer" value="3" label="maximal range of x-axis" />
-                <param name="yaxismin" size="4" type="integer" value="0" label="minimal range of y-axis" />
-                <param name="yaxismax" size="4" type="integer" value="3" label="maximal range of y-axis" />
-            </when>
-        </conditional>
-        <conditional name="theme">
-            <param name="theme_selector" type="select" label="Advanced - backgound theme for plot">
-              <option value="bw">Black and white</option>
-              <option value="Default">Default (grey)</option>
-            </param>
-            <when value="bw"/>
-            <when value="Default"></when>
-        </conditional>
-        <conditional name="axistitlecustomization">
-            <param name="axistitlecust" type="select" label="Advanced - axis label options">
-                <option value="Default" selected="True">Default</option>
-                <option value="Defined">User defined label options</option>
-            </param>
-            <when value="Default">
-                <!--Do nothing here -->
-            </when>
-            <when value="Defined">
-                <param name="axistitlesize" size="4" type="float" value="12" label="Axis label size (default = 12)"/>
-                <param name="axistitlecolor" type="select" label="Color of axis label">
-                    <option value="black">Black (default)</option>
-                    <option value="red">Red</option>
-                    <option value="white">White</option>
-                    <option value="blue">Blue</option>
-                    <option value="orange">Orange</option>
-                    <option value="yellow">Yellow</option>
-                    <option value="green">Green</option>
-                    <option value="purple">Purple</option>
-                    <option value="magenta">Magenta</option>
-                    <option value="cyan">Cyan</option>
-                    <option value="grey">Grey</option>
-                    <option value="gold">Gold</option> 
-                </param>
-                <param name="axistitleface" size="4" type="select" label="Font effect of axis label">
-                    <option value="plain">Normal (default)</option>
-                    <option value="bold">Bold</option>
-                    <option value="italic">Italic</option>
-                </param>    
-            </when>
-        </conditional>
-        <conditional name="axistextcustomization">
-            <param name="axistextcust" type="select" label="Advanced - axis text options">
-                <option value="Default" selected="True">Default</option>
-                <option value="Defined">User defined axis text options</option>
-            </param>
-            <when value="Default">
-                <!--Do nothing here -->
-            </when>
-            <when value="Defined">
-                <param name="axistextsize" size="4" type="float" value="12" label="Axis text size (default = 12)"/>
-                <param name="axistextcolor" type="select" label="Color of axis text">
-                    <option value="black">Black (default)</option>
-                    <option value="red">Red</option>
-                    <option value="white">White</option>
-                    <option value="blue">Blue</option>
-                    <option value="orange">Orange</option>
-                    <option value="yellow">Yellow</option>
-                    <option value="green">Green</option>
-                    <option value="purple">Purple</option>
-                    <option value="magenta">Magenta</option>
-                    <option value="cyan">Cyan</option>
-                    <option value="grey">Grey</option>
-                    <option value="gold">Gold</option> 
-                </param>
-                <param name="axistextface" size="4" type="select" label="Font effect of axis text">
-                    <option value="plain">Normal (default)</option>
-                    <option value="bold">Bold</option>
-                    <option value="italic">Italic</option>
-                </param>    
-            </when>
-        </conditional>
-        <conditional name="plottitlecustomization">
-            <param name="plottitlecust" type="select" label="Advanced - Plot title options">
-                <option value="Default" selected="True">Default</option>
-                <option value="Defined">User defined plot title options</option>
-            </param>
-            <when value="Default">
-                <!--Do nothing here -->
-            </when>
-            <when value="Defined">
-                <param name="plottitlesize" size="4" type="float" value="12" label="Plot title size (default = 12)"/>
-                <param name="plottitlecolor" type="select" label="Color of plot title">
-                    <option value="black">Black (default)</option>
-                    <option value="red">Red</option>
-                    <option value="white">White</option>
-                    <option value="blue">Blue</option>
-                    <option value="orange">Orange</option>
-                    <option value="yellow">Yellow</option>
-                    <option value="green">Green</option>
-                    <option value="purple">Purple</option>
-                    <option value="magenta">Magenta</option>
-                    <option value="cyan">Cyan</option>
-                    <option value="grey">Grey</option>
-                    <option value="gold">Gold</option> 
-                </param>
-                <param name="plottitleface" size="4" type="select" label="Font effect of plot title">
-                    <option value="plain">Normal (default)</option>
-                    <option value="bold">Bold</option>
-                    <option value="italic">Italic</option>
-                </param>    
-            </when>
-        </conditional>
-        <conditional name="gridlinecustomization">
-            <param name="gridlinecust" type="select" label="Advanced - grid lines">
-              <option value="Default">Default grid lines</option>
-              <option value="hidemajor">Hide major grid lines</option>
-              <option value="hideminor">Hide minor grid lines</option>
-              <option value="hideboth">Hide major and minor grid lines</option>
-            </param>
-             <when value="Default">
-                <!--Do nothing here -->
-            </when>
-             <when value="hidemajor">
-                <!--Do nothing here -->
-            </when>
-             <when value="hideminor">
-                <!--Do nothing here -->
-            </when>
-             <when value="hideboth">
-                <!--Do nothing here -->
-            </when>
-        </conditional>
-        <conditional name="dimensions">
-            <param name="plotdim" type="select" label="Advanced - output dimensions">
-                <option value="Default" selected="True">Default</option>
-                <option value="Defined">User defined output dimensions</option>
-            </param>
-            <when value="Default">
-                <!--Do nothing here -->
-            </when>
-            <when value="Defined">
-                <param name="woutputdim" size="4" type="float" value="7" label="width of output (inches)" />
-                <param name="houtputdim" size="4" type="float" value="7" label="height of output (inches)" />
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <!-- <data name="output1" format="png" from_work_dir="Rplot.png"/> -->
-        <data name="output1" format="pdf" from_work_dir="Rplot.pdf"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input1" value="input.txt"/>
-            <output name="output1" file="Rplot.pdf"/>
-        </test>
-    </tests>
-    <help><![CDATA[
-        This tool will generate a scatterplot representing data from two groups/conditions. 
-
-        The input data should be in tabular format and the user can determine which groups (columns) to plot.
-
-        Multiple groups can be plotted on the same or multiple plots by providing a column with a group identifier under "Advanced - plotting multiple groups".
-
-        Feel free to explore the (many) advanced options to customize your plot. Galaxy makes this type optimization easy for the user!  
-
-        The ouput is a pdf file with your scatterplot. The dimensions of this file can be modified under "Advanced - output dimensions"
-
-
-
-
-        Please report issues at: https://github.com/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot
-    ]]></help>
-     <citations>
-        <citation type="bibtex">
-    @misc{renameTODO,
-      author = {8.5.2016, FirstTODO},
-      year = {TODO},
-      title = {TODO},
-      url = {http://docs.ggplot2.org/current/geom_point.html},
-    }</citation>
-        </citations>
-    </tool>      
-
--- a/ggplotpointscript.R	Wed Jan 11 10:34:22 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,230 +0,0 @@
-#TO ACCOMPANY ggplot_point.xml version 0.1.2
-# Setup R error handling to go to stderr
-options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
-
-# We need to not crash galaxy with an UTF8 error on German LC settings.
-loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
-
-
-# Import library
-library("getopt")
-library("ggplot2")
-options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
-# Take in trailing command line arguments
-args <- commandArgs(trailingOnly = TRUE)
-
-
-# get options, using the spec as defined by the enclosed list.
-# we read the options from the default: commandArgs(TRUE).
-option_specification = matrix(c(
-  'input', 'i', 2, 'character',
-  'title', 't',2, 'character',
-  'size', 's', 2, 'double',
-  'xlab', 'x', 2, 'character',
-  'ylab', 'y', 2, 'character',
-  'xplot', 'z', 2, 'integer',
-  'yplot', 'j', 2, 'integer',
-  'xaxismin', 'e', 2, 'integer',
-  'xaxismax', 'f', 2, 'integer',
-  'yaxismin', 'g', 2, 'integer',
-  'yaxismax', 'h', 2, 'integer',
-  'alpha', 'a', 2, 'double',
-  'points', 'p', 2, 'character',
-  'theme', 'l', 2, 'character',
-  'scaling', 'b', 2, 'character',
-  'transform', 'w', 2, 'character',
-  'dim', 'k', 2, 'character',
-  'woutputdim', 'c', 2, 'integer',
-  'houtputdim', 'd', 2, 'integer',
-  'factor', 'n', 2, 'character',
-  'factorcol', 'm', 2, 'integer',
-  'colors', 'q', 2, 'character', 
-  'colororder', 'r', 2, 'integer', 
-  'pointcolor', 'u', 2, 'character', 
-  'axistitlecust', 'v', 2, 'character',
-  'axistitlecolor', '1', 2, 'character',
-  'axistitlesize', '2', 2, 'integer',
-  'axistitleface', '3', 2, 'character',
-  'axistextcust', '4', 2, 'character',
-  'axistextcolor', '5', 2, 'character',
-  'axistextsize', '6', 2, 'integer',
-  'axistextface', '7', 2, 'character',
-  'plottitlecust', '8', 2, 'character',
-  'plottitlecolor', '9', 2, 'character',
-  'plottitlesize', '10', 2, 'integer',
-  'plottitleface', '11', 2, 'character',
-  'gridlinecust', '12', 2, 'character',
-  'output', 'o', 2, 'character'
-  ), byrow=TRUE, ncol=4);
-
-# Parse options
-options = getopt(option_specification);
-
-
-
-# Print options to see what is going on
-cat("\n input: ",options$input)
-cat("\n title: ",options$title)
-cat("\n xlab: ",options$xlab)
-cat("\n ylab: ",options$ylab)
-cat("\n points: ",options$points)
-cat("\n theme: ",options$theme)
-cat("\n scaling: ",options$scaling)
-cat("\n transform: ",options$transform)
-
-
-
-#Choose between automatically scaled x and y axis or user defined
-if(options$scaling == "Automatic"){
-    gg_scalex = NULL
-    gg_scaley = NULL
-} else {
-    gg_scalex = xlim(options$xaxismin,options$xaxismax)
-    gg_scaley = ylim(options$yaxismin,options$yaxismax)
-    cat("\n xaxismin: ",options$xaxismin)
-    cat("\n xaxismax: ",options$xaxismax)
-    cat("\n yaxismin: ",options$yaxismin)
-    cat("\n yaxismax: ",options$yaxismax)
-}
-
-# Choose theme for plot
-if(options$theme == "bw"){
-    gg_theme = theme_bw()
-} else {
-    gg_theme = NULL
-}
-
-#Choose dimensions of output pdf
-if(options$dim == "Default"){
-    gg_width = 7
-    gg_height = 7
-} else {
-    gg_width = options$woutputdim
-    gg_height = options$houtputdim 
-}
-
-input <-read.table(options$input, check.names=TRUE, header=TRUE, row.names=NULL)
-
-#renaming columns so ggplot can use them
-names(input)[options$xplot] <- "xcol"
-names(input)[options$yplot] <- "ycol"
-
-#choosing whether to plot data as multiple groups on one plot(factoring) OR multiple groups on different plots
-if(options$factor == "Multiple"){
-     gg_facet = facet_wrap( ~ factor)
-     gg_factor = NULL
-     color_scale = NULL
-          
-          if(options$points == "Default"){
-            gg_point = geom_point(size=1, alpha=1, gg_factor)
-        } else {
-            gg_point = geom_point(size=options$size, alpha=options$alpha, colour=options$pointcolor)
-            cat("\n size: ",options$size)
-            cat("\n alpha: ",options$alpha)
-            cat("\n pointcolor: ",options$pointcolor)
-        }
-
-    names(input)[options$factorcol] <- "factor"
-   
-    cat("\n factor: ",options$factor)
-    cat("\n factorcol: ",options$factorcol)
-} else if(options$factor == "Single"){
-    gg_facet = NULL
-    gg_factor = aes(colour=factor(factor))
-
-          if(options$points == "Default"){
-            gg_point = geom_point(size=1, alpha=1, gg_factor)
-        } else {
-            gg_point = geom_point(size=options$size, alpha=options$alpha, gg_factor)
-            cat("\n size: ",options$size)
-            cat("\n alpha: ",options$alpha)
-            cat("\n pointcolor: ",options$pointcolor)
-        }
-
-      if(options$colors == "Default"){
-          color_scale = scale_colour_hue(direction=options$colororder)
-      } else {
-          color_scale = scale_color_brewer(palette=options$colors, direction=options$colororder)
-      }
-
-    names(input)[options$factorcol] <- "factor"
-    
-    cat("\n factor: ",options$factor)
-    cat("\n factorcol: ",options$factorcol)
-    cat("\n color_scale: ",options$colors)
-    cat("\n color_order: ",options$colororder)
-} else{
-      gg_facet = NULL
-      gg_factor = NULL
-      color_scale = NULL
-
-        if(options$points == "Default"){
-            gg_point = geom_point(size=1, alpha=1, gg_factor)
-        } else {
-            gg_point = geom_point(size=options$size, alpha=options$alpha, colour=options$pointcolor)
-            cat("\n size: ",options$size)
-            cat("\n alpha: ",options$alpha)
-            cat("\n pointcolor: ",options$pointcolor)
-        }    
-}
-
-
-#Selecting whether or not to log transform data
-if(options$transform == "log2"){
-    input[, options$xplot] <- log2(input[options$xplot])
-    input[, options$yplot] <- log2(input[options$yplot])
-}else if(options$transform == "log2plus1"){
-    input[, options$xplot] <- log2(input[options$xplot]+1)
-    input[, options$yplot] <- log2(input[options$yplot]+1)
-}else if(options$transform == "log10"){
-    input[, options$xplot] <- log10(input[options$xplot])
-    input[, options$yplot] <- log10(input[options$yplot])
-}else if(options$transform == "log10plus1"){
-    input[, options$xplot] <- log10(input[options$xplot]+1)
-    input[, options$yplot] <- log10(input[options$yplot]+1)
-    }else{
-}
-
-
-#axis label custization
-if(options$axistitlecust == "Default"){
-    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))
-} else {
-    gg_axistitle = theme(axis.title = element_text(color = options$axistitlecolor, size = options$axistitlesize, face = options$axistitleface))
-}
-
-
-#axis text(tick) custization
-if(options$axistextcust == "Default"){
-    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))
-} else {
-    gg_axistext = theme(axis.text = element_text(color = options$axistextcolor, size = options$axistextsize, face = options$axistextface))
-}
-
-
-#plot title custimization
-if(options$plottitlecust == "Default"){
-    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))
-} else {
-    gg_plottitle = theme(plot.title = element_text(color = options$plottitlecolor, size = options$plottitlesize, face = options$plottitleface))
-}
-
-#grid line customization
-if(options$gridlinecust == "Default"){
-    gg_gridline = NULL
-} else if(options$gridlinecust == "hidemajor"){
-    gg_gridline = theme(panel.grid.major = element_blank())
-} else if(options$gridlinecust == "hideminor"){
-    gg_gridline = theme(panel.grid.minor = element_blank())
-} else if(options$gridlinecust == "hideboth"){
-    gg_gridline = theme(panel.grid.minor = element_blank(), panel.grid.major = element_blank())
-} else {
-}
-
-
-#this is the actual ggplot command to make the final plot(s)
-ggplot(input, aes(xcol,ycol))+gg_point+gg_facet+
-gg_theme+gg_scalex+gg_scaley+color_scale+ggtitle(options$title)+xlab(options$xlab)+ylab(options$ylab)+
-gg_axistitle+gg_axistext+gg_plottitle+gg_gridline
-
-ggsave(file=options$output, width=gg_width, height=gg_height)
--- a/tool_dependency.xml	Wed Jan 11 10:34:22 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="R" version="3.2.1">
-        <repository name="package_r_3_2_1" owner="iuc" />
-        <repository name="package_r_3_2_1_getopt_1_20_0" owner="bebatut" />
-        <repository name="package_r_ggplot2_2_2_0" owner="moheydarian" />
-    </package>
-</tool_dependency>
\ No newline at end of file