Mercurial > repos > moheydarian > ggplot_scatterplot
changeset 12:8df1c60db1c4 draft
Deleted selected files
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(-) [+] |
line wrap: on
line diff
--- 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 @@ -1,719 +0,0 @@ - - - - -<!DOCTYPE html> -<html lang="en" class=""> - <head prefix="og: http://ogp.me/ns# fb: http://ogp.me/ns/fb# object: http://ogp.me/ns/object# article: http://ogp.me/ns/article# profile: http://ogp.me/ns/profile#"> - <meta charset='utf-8'> - - - <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/frameworks-b431521ec2343144c1229e0d67b03f2806422759f2de314fc592fa70e320750b.css" media="all" rel="stylesheet" /> - <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/github-4cecee2389c0651faf755b4519c9e5940a15760e2378e77ec6c51eece20ce2fc.css" media="all" rel="stylesheet" /> - - - <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/site-293f92180d0a619a750fa2b5eae9e36740f5723a59c0ec308972c70d24e834fc.css" media="all" rel="stylesheet" /> - - - <meta http-equiv="X-UA-Compatible" content="IE=edge"> - <meta http-equiv="Content-Language" content="en"> - <meta name="viewport" content="width=device-width"> - - <title>GitHub - MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot</title> - <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub"> - <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub"> - <link rel="apple-touch-icon" href="/apple-touch-icon.png"> - <link rel="apple-touch-icon" sizes="57x57" href="/apple-touch-icon-57x57.png"> - <link rel="apple-touch-icon" sizes="60x60" href="/apple-touch-icon-60x60.png"> - <link rel="apple-touch-icon" sizes="72x72" href="/apple-touch-icon-72x72.png"> - <link rel="apple-touch-icon" sizes="76x76" href="/apple-touch-icon-76x76.png"> - <link rel="apple-touch-icon" sizes="114x114" href="/apple-touch-icon-114x114.png"> - <link rel="apple-touch-icon" sizes="120x120" href="/apple-touch-icon-120x120.png"> - <link rel="apple-touch-icon" sizes="144x144" href="/apple-touch-icon-144x144.png"> - <link rel="apple-touch-icon" sizes="152x152" href="/apple-touch-icon-152x152.png"> - <link rel="apple-touch-icon" sizes="180x180" href="/apple-touch-icon-180x180.png"> - <meta property="fb:app_id" content="1401488693436528"> - - <meta content="https://avatars1.githubusercontent.com/u/18484759?v=3&s=400" name="twitter:image:src" /><meta content="@github" name="twitter:site" /><meta content="summary" name="twitter:card" /><meta content="MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot" name="twitter:title" /><meta content="Contribute to Galaxy-wrapper-for-ggplot2-scatterplot development by creating an account on GitHub." name="twitter:description" /> - <meta content="https://avatars1.githubusercontent.com/u/18484759?v=3&s=400" property="og:image" /><meta content="GitHub" property="og:site_name" /><meta content="object" property="og:type" /><meta content="MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot" property="og:title" /><meta content="https://github.com/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot" property="og:url" /><meta content="Contribute to Galaxy-wrapper-for-ggplot2-scatterplot development by creating an account on GitHub." property="og:description" /> - <meta name="browser-stats-url" content="https://api.github.com/_private/browser/stats"> - <meta name="browser-errors-url" content="https://api.github.com/_private/browser/errors"> - <link rel="assets" href="https://assets-cdn.github.com/"> - - <meta name="pjax-timeout" content="1000"> - - <meta name="request-id" content="8076FA05:7429:DDD0E5F:5876507E" data-pjax-transient> - - <meta name="msapplication-TileImage" content="/windows-tile.png"> - <meta name="msapplication-TileColor" content="#ffffff"> - <meta name="selected-link" value="repo_source" data-pjax-transient> - - <meta name="google-site-verification" content="KT5gs8h0wvaagLKAVWq8bbeNwnZZK1r1XQysX3xurLU"> -<meta name="google-site-verification" content="ZzhVyEFwb7w3e0-uOTltm8Jsck2F5StVihD0exw2fsA"> - <meta name="google-analytics" content="UA-3769691-2"> - -<meta content="collector.githubapp.com" name="octolytics-host" /><meta content="github" name="octolytics-app-id" /><meta content="8076FA05:7429:DDD0E5F:5876507E" name="octolytics-dimension-request_id" /> -<meta content="/<user-name>/<repo-name>" data-pjax-transient="true" name="analytics-location" /> - - - - <meta class="js-ga-set" name="dimension1" content="Logged Out"> - - - - <meta name="hostname" content="github.com"> - <meta name="user-login" content=""> - - <meta name="expected-hostname" content="github.com"> - <meta name="js-proxy-site-detection-payload" content="NjNiNDQ0YzRjMDdlMzk2ZWQ1YjA1NjZiNDNjODVkZjdjYjRlMTlhZDllOGFjOTJhOWYyZThlNTZlODY0NWJjMnx7InJlbW90ZV9hZGRyZXNzIjoiMTI4LjExOC4yNTAuNSIsInJlcXVlc3RfaWQiOiI4MDc2RkEwNTo3NDI5OkRERDBFNUY6NTg3NjUwN0UiLCJ0aW1lc3RhbXAiOjE0ODQxNDg4NjIsImhvc3QiOiJnaXRodWIuY29tIn0="> - - - <link rel="mask-icon" href="https://assets-cdn.github.com/pinned-octocat.svg" color="#000000"> - <link rel="icon" type="image/x-icon" href="https://assets-cdn.github.com/favicon.ico"> - - <meta name="html-safe-nonce" content="848f3a07ee80f0f8860aee40afb687ae5e65b5eb"> - - <meta http-equiv="x-pjax-version" content="eb2dee35b7132688a62f9b42e689312a"> - - - - <meta name="description" content="Contribute to Galaxy-wrapper-for-ggplot2-scatterplot development by creating an account on GitHub."> - <meta name="go-import" content="github.com/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot git https://github.com/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot.git"> - - <meta content="18484759" name="octolytics-dimension-user_id" /><meta content="MoHeydarian" name="octolytics-dimension-user_login" /><meta content="65494201" name="octolytics-dimension-repository_id" /><meta content="MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot" name="octolytics-dimension-repository_nwo" /><meta content="true" name="octolytics-dimension-repository_public" /><meta content="false" name="octolytics-dimension-repository_is_fork" /><meta content="65494201" name="octolytics-dimension-repository_network_root_id" /><meta content="MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot" name="octolytics-dimension-repository_network_root_nwo" /> - <link href="https://github.com/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/commits/master.atom" rel="alternate" title="Recent Commits to Galaxy-wrapper-for-ggplot2-scatterplot:master" type="application/atom+xml"> - - - <link rel="canonical" href="https://github.com/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot" data-pjax-transient> - </head> - - - <body class="logged-out env-production vis-public"> - <div id="js-pjax-loader-bar" class="pjax-loader-bar"><div class="progress"></div></div> - <a href="#start-of-content" tabindex="1" class="accessibility-aid js-skip-to-content">Skip to content</a> - - - - - - - - <header class="site-header js-details-container alt-body-font" role="banner"> - <div class="container-responsive"> - <a class="header-logo-invertocat" href="https://github.com/" aria-label="Homepage" data-ga-click="(Logged out) Header, go to homepage, icon:logo-wordmark"> - <svg aria-hidden="true" class="octicon octicon-mark-github" height="32" version="1.1" viewBox="0 0 16 16" width="32"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg> - </a> - - <button class="btn-link float-right site-header-toggle js-details-target" type="button" aria-label="Toggle navigation"> - <svg aria-hidden="true" class="octicon octicon-three-bars" height="24" version="1.1" viewBox="0 0 12 16" width="18"><path fill-rule="evenodd" d="M11.41 9H.59C0 9 0 8.59 0 8c0-.59 0-1 .59-1H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1h.01zm0-4H.59C0 5 0 4.59 0 4c0-.59 0-1 .59-1H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1h.01zM.59 11H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1H.59C0 13 0 12.59 0 12c0-.59 0-1 .59-1z"/></svg> - </button> - - <div class="site-header-menu"> - <nav class="site-header-nav site-header-nav-main"> - <a href="/personal" class="js-selected-navigation-item nav-item nav-item-personal" data-ga-click="Header, click, Nav menu - item:personal" data-selected-links="/personal /personal"> - Personal -</a> <a href="/open-source" class="js-selected-navigation-item nav-item nav-item-opensource" data-ga-click="Header, click, Nav menu - item:opensource" data-selected-links="/open-source /open-source"> - Open source -</a> <a href="/business" class="js-selected-navigation-item nav-item nav-item-business" data-ga-click="Header, click, Nav menu - item:business" data-selected-links="/business /business/partners /business/features /business/customers /business"> - Business -</a> <a href="/explore" class="js-selected-navigation-item nav-item nav-item-explore" data-ga-click="Header, click, Nav menu - item:explore" data-selected-links="/explore /trending /trending/developers /integrations /integrations/feature/code /integrations/feature/collaborate /integrations/feature/ship /showcases /explore"> - Explore -</a> </nav> - - <div class="site-header-actions"> - <a class="btn btn-primary site-header-actions-btn" href="/join?source=header-repo" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up">Sign up</a> - <a class="btn site-header-actions-btn mr-1" href="/login?return_to=%2FMoHeydarian%2FGalaxy-wrapper-for-ggplot2-scatterplot" data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in">Sign in</a> - </div> - - <nav class="site-header-nav site-header-nav-secondary mr-md-3"> - <a class="nav-item" href="/pricing">Pricing</a> - <a class="nav-item" href="/blog">Blog</a> - <a class="nav-item" href="https://help.github.com">Support</a> - <a class="nav-item header-search-link" href="https://github.com/search">Search GitHub</a> - <div class="header-search scoped-search site-scoped-search js-site-search" role="search"> - <!-- '"` --><!-- </textarea></xmp> --></option></form><form accept-charset="UTF-8" action="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/search" class="js-site-search-form" data-scoped-search-url="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/search" data-unscoped-search-url="/search" method="get"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /></div> - <label class="form-control header-search-wrapper js-chromeless-input-container"> - <div class="header-search-scope">This repository</div> - <input type="text" - class="form-control header-search-input js-site-search-focus js-site-search-field is-clearable" - data-hotkey="s" - name="q" - placeholder="Search" - aria-label="Search this repository" - data-unscoped-placeholder="Search GitHub" - data-scoped-placeholder="Search" - autocapitalize="off"> - </label> -</form></div> - - </nav> - </div> - </div> -</header> - - - - <div id="start-of-content" class="accessibility-aid"></div> - - <div id="js-flash-container"> -</div> - - - <div role="main"> - <div itemscope itemtype="http://schema.org/SoftwareSourceCode"> - <div id="js-repo-pjax-container" data-pjax-container> - -<div class="pagehead repohead instapaper_ignore readability-menu experiment-repo-nav"> - <div class="container repohead-details-container"> - - - -<ul class="pagehead-actions"> - - <li> - <a href="/login?return_to=%2FMoHeydarian%2FGalaxy-wrapper-for-ggplot2-scatterplot" - class="btn btn-sm btn-with-count tooltipped tooltipped-n" - aria-label="You must be signed in to watch a repository" rel="nofollow"> - <svg aria-hidden="true" class="octicon octicon-eye" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M8.06 2C3 2 0 8 0 8s3 6 8.06 6C13 14 16 8 16 8s-3-6-7.94-6zM8 12c-2.2 0-4-1.78-4-4 0-2.2 1.8-4 4-4 2.22 0 4 1.8 4 4 0 2.22-1.78 4-4 4zm2-4c0 1.11-.89 2-2 2-1.11 0-2-.89-2-2 0-1.11.89-2 2-2 1.11 0 2 .89 2 2z"/></svg> - Watch - </a> - <a class="social-count" href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/watchers" - aria-label="1 user is watching this repository"> - 1 - </a> - - </li> - - <li> - <a href="/login?return_to=%2FMoHeydarian%2FGalaxy-wrapper-for-ggplot2-scatterplot" - class="btn btn-sm btn-with-count tooltipped tooltipped-n" - aria-label="You must be signed in to star a repository" rel="nofollow"> - <svg aria-hidden="true" class="octicon octicon-star" height="16" version="1.1" viewBox="0 0 14 16" width="14"><path fill-rule="evenodd" d="M14 6l-4.9-.64L7 1 4.9 5.36 0 6l3.6 3.26L2.67 14 7 11.67 11.33 14l-.93-4.74z"/></svg> - Star - </a> - - <a class="social-count js-social-count" href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/stargazers" - aria-label="0 users starred this repository"> - 0 - </a> - - </li> - - <li> - <a href="/login?return_to=%2FMoHeydarian%2FGalaxy-wrapper-for-ggplot2-scatterplot" - class="btn btn-sm btn-with-count tooltipped tooltipped-n" - aria-label="You must be signed in to fork a repository" rel="nofollow"> - <svg aria-hidden="true" class="octicon octicon-repo-forked" height="16" version="1.1" viewBox="0 0 10 16" width="10"><path fill-rule="evenodd" d="M8 1a1.993 1.993 0 0 0-1 3.72V6L5 8 3 6V4.72A1.993 1.993 0 0 0 2 1a1.993 1.993 0 0 0-1 3.72V6.5l3 3v1.78A1.993 1.993 0 0 0 5 15a1.993 1.993 0 0 0 1-3.72V9.5l3-3V4.72A1.993 1.993 0 0 0 8 1zM2 4.2C1.34 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm3 10c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm3-10c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg> - Fork - </a> - - <a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/network" class="social-count" - aria-label="0 users forked this repository"> - 0 - </a> - </li> -</ul> - - <h1 class="public "> - <svg aria-hidden="true" class="octicon octicon-repo" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> - <span class="author" itemprop="author"><a href="/MoHeydarian" class="url fn" rel="author">MoHeydarian</a></span><!-- ---><span class="path-divider">/</span><!-- ---><strong itemprop="name"><a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot" data-pjax="#js-repo-pjax-container">Galaxy-wrapper-for-ggplot2-scatterplot</a></strong> - -</h1> - - </div> - <div class="container"> - -<nav class="reponav js-repo-nav js-sidenav-container-pjax" - itemscope - itemtype="http://schema.org/BreadcrumbList" - role="navigation" - data-pjax="#js-repo-pjax-container"> - - <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement"> - <a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot" class="js-selected-navigation-item selected reponav-item" data-hotkey="g c" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches /MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot" itemprop="url"> - <svg aria-hidden="true" class="octicon octicon-code" height="16" version="1.1" viewBox="0 0 14 16" width="14"><path fill-rule="evenodd" d="M9.5 3L8 4.5 11.5 8 8 11.5 9.5 13 14 8 9.5 3zm-5 0L0 8l4.5 5L6 11.5 2.5 8 6 4.5 4.5 3z"/></svg> - <span itemprop="name">Code</span> - <meta itemprop="position" content="1"> -</a> </span> - - <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement"> - <a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/issues" class="js-selected-navigation-item reponav-item" data-hotkey="g i" data-selected-links="repo_issues repo_labels repo_milestones /MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/issues" itemprop="url"> - <svg aria-hidden="true" class="octicon octicon-issue-opened" height="16" version="1.1" viewBox="0 0 14 16" width="14"><path fill-rule="evenodd" d="M7 2.3c3.14 0 5.7 2.56 5.7 5.7s-2.56 5.7-5.7 5.7A5.71 5.71 0 0 1 1.3 8c0-3.14 2.56-5.7 5.7-5.7zM7 1C3.14 1 0 4.14 0 8s3.14 7 7 7 7-3.14 7-7-3.14-7-7-7zm1 3H6v5h2V4zm0 6H6v2h2v-2z"/></svg> - <span itemprop="name">Issues</span> - <span class="counter">0</span> - <meta itemprop="position" content="2"> -</a> </span> - - <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement"> - <a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/pulls" class="js-selected-navigation-item reponav-item" data-hotkey="g p" data-selected-links="repo_pulls /MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/pulls" itemprop="url"> - <svg aria-hidden="true" class="octicon octicon-git-pull-request" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path fill-rule="evenodd" d="M11 11.28V5c-.03-.78-.34-1.47-.94-2.06C9.46 2.35 8.78 2.03 8 2H7V0L4 3l3 3V4h1c.27.02.48.11.69.31.21.2.3.42.31.69v6.28A1.993 1.993 0 0 0 10 15a1.993 1.993 0 0 0 1-3.72zm-1 2.92c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zM4 3c0-1.11-.89-2-2-2a1.993 1.993 0 0 0-1 3.72v6.56A1.993 1.993 0 0 0 2 15a1.993 1.993 0 0 0 1-3.72V4.72c.59-.34 1-.98 1-1.72zm-.8 10c0 .66-.55 1.2-1.2 1.2-.65 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2zM2 4.2C1.34 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg> - <span itemprop="name">Pull requests</span> - <span class="counter">0</span> - <meta itemprop="position" content="3"> -</a> </span> - - <a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/projects" class="js-selected-navigation-item reponav-item" data-selected-links="repo_projects new_repo_project repo_project /MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/projects"> - <svg aria-hidden="true" class="octicon octicon-project" height="16" version="1.1" viewBox="0 0 15 16" width="15"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> - Projects - <span class="counter">0</span> -</a> - - - <a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/pulse" class="js-selected-navigation-item reponav-item" data-selected-links="pulse /MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/pulse"> - <svg aria-hidden="true" class="octicon octicon-pulse" height="16" version="1.1" viewBox="0 0 14 16" width="14"><path fill-rule="evenodd" d="M11.5 8L8.8 5.4 6.6 8.5 5.5 1.6 2.38 8H0v2h3.6l.9-1.8.9 5.4L9 8.5l1.6 1.5H14V8z"/></svg> - Pulse -</a> - <a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/graphs" class="js-selected-navigation-item reponav-item" data-selected-links="repo_graphs repo_contributors /MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/graphs"> - <svg aria-hidden="true" class="octicon octicon-graph" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M16 14v1H0V0h1v14h15zM5 13H3V8h2v5zm4 0H7V3h2v10zm4 0h-2V6h2v7z"/></svg> - Graphs -</a> - -</nav> - - </div> -</div> - -<div class="container new-discussion-timeline experiment-repo-nav"> - <div class="repository-content"> - - -<div class="repository-meta js-details-container"> - <div class="repository-meta-content col-11"> - <em class="d-inline-block text-gray mb-1"> - No description or website provided. - </em> - - </div> - -</div> - - - -<div class="overall-summary overall-summary-bottomless"> - <div class="stats-switcher-viewport js-stats-switcher-viewport"> - <div class="stats-switcher-wrapper"> - <ul class="numbers-summary"> - <li class="commits"> - <a data-pjax href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/commits/master"> - <svg aria-hidden="true" class="octicon octicon-history" height="16" version="1.1" viewBox="0 0 14 16" width="14"><path fill-rule="evenodd" d="M8 13H6V6h5v2H8v5zM7 1C4.81 1 2.87 2.02 1.59 3.59L0 2v4h4L2.5 4.5C3.55 3.17 5.17 2.3 7 2.3c3.14 0 5.7 2.56 5.7 5.7s-2.56 5.7-5.7 5.7A5.71 5.71 0 0 1 1.3 8c0-.34.03-.67.09-1H.08C.03 7.33 0 7.66 0 8c0 3.86 3.14 7 7 7s7-3.14 7-7-3.14-7-7-7z"/></svg> - <span class="num text-emphasized"> - 12 - </span> - commits - </a> - </li> - <li> - <a data-pjax href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/branches"> - <svg aria-hidden="true" class="octicon octicon-git-branch" height="16" version="1.1" viewBox="0 0 10 16" width="10"><path fill-rule="evenodd" d="M10 5c0-1.11-.89-2-2-2a1.993 1.993 0 0 0-1 3.72v.3c-.02.52-.23.98-.63 1.38-.4.4-.86.61-1.38.63-.83.02-1.48.16-2 .45V4.72a1.993 1.993 0 0 0-1-3.72C.88 1 0 1.89 0 3a2 2 0 0 0 1 1.72v6.56c-.59.35-1 .99-1 1.72 0 1.11.89 2 2 2 1.11 0 2-.89 2-2 0-.53-.2-1-.53-1.36.09-.06.48-.41.59-.47.25-.11.56-.17.94-.17 1.05-.05 1.95-.45 2.75-1.25S8.95 7.77 9 6.73h-.02C9.59 6.37 10 5.73 10 5zM2 1.8c.66 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2C1.35 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2zm0 12.41c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm6-8c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg> - <span class="num text-emphasized"> - 3 - </span> - branches - </a> - </li> - - <li> - <a data-pjax href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/releases"> - <svg aria-hidden="true" class="octicon octicon-tag" height="16" version="1.1" viewBox="0 0 14 16" width="14"><path fill-rule="evenodd" d="M7.73 1.73C7.26 1.26 6.62 1 5.96 1H3.5C2.13 1 1 2.13 1 3.5v2.47c0 .66.27 1.3.73 1.77l6.06 6.06c.39.39 1.02.39 1.41 0l4.59-4.59a.996.996 0 0 0 0-1.41L7.73 1.73zM2.38 7.09c-.31-.3-.47-.7-.47-1.13V3.5c0-.88.72-1.59 1.59-1.59h2.47c.42 0 .83.16 1.13.47l6.14 6.13-4.73 4.73-6.13-6.15zM3.01 3h2v2H3V3h.01z"/></svg> - <span class="num text-emphasized"> - 0 - </span> - releases - </a> - </li> - - <li> - <a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/graphs/contributors"> - <svg aria-hidden="true" class="octicon octicon-organization" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M16 12.999c0 .439-.45 1-1 1H7.995c-.539 0-.994-.447-.995-.999H1c-.54 0-1-.561-1-1 0-2.634 3-4 3-4s.229-.409 0-1c-.841-.621-1.058-.59-1-3 .058-2.419 1.367-3 2.5-3s2.442.58 2.5 3c.058 2.41-.159 2.379-1 3-.229.59 0 1 0 1s1.549.711 2.42 2.088C9.196 9.369 10 8.999 10 8.999s.229-.409 0-1c-.841-.62-1.058-.59-1-3 .058-2.419 1.367-3 2.5-3s2.437.581 2.495 3c.059 2.41-.158 2.38-1 3-.229.59 0 1 0 1s3.005 1.366 3.005 4"/></svg> - <span class="num text-emphasized"> - 1 - </span> - contributor -</a> - - </li> - </ul> - - <div class="repository-lang-stats"> - <ol class="repository-lang-stats-numbers"> - <li> - <a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/search?l=r" data-ga-click="Repository, language stats search click, location:repo overview"> - <span class="color-block language-color" style="background-color:#198CE7;"></span> - <span class="lang">R</span> - <span class="percent">100.0%</span> - </a> - </li> - </ol> - </div> - </div> - </div> -</div> - - <div class="repository-lang-stats-graph js-toggle-lang-stats" title="Click for language details" data-ga-click="Repository, language bar stats toggle, location:repo overview"> - <span class="language-color" aria-label="R 100.0%" style="width:100.0%; background-color:#198CE7;" itemprop="keywords">R</span> - </div> - - -<div class="file-navigation in-mid-page"> - - <div class="select-menu get-repo-select-menu js-menu-container float-right select-menu-modal-right"> - <button class="btn btn-sm btn-primary select-menu-button js-menu-target" - title="Clone or download this repository" - type="button" aria-label="Clone or download this repository" tabindex="0" aria-haspopup="true"> - <span>Clone or download</span> - </button> - - <div class="select-menu-modal-holder dropdown-menu-content js-menu-content" aria-hidden="true"> - <div class="get-repo-modal dropdown-menu dropdown-menu-sw pb-0 js-toggler-container "> - <div class="clone-options https-clone-options"> - - <h4 class="mb-1"> - Clone with HTTPS - <a class="muted-link" href="https://help.github.com/articles/which-remote-url-should-i-use" target="_blank"> - <svg aria-hidden="true" class="octicon octicon-question" height="16" version="1.1" viewBox="0 0 14 16" width="14"><path fill-rule="evenodd" d="M6 10h2v2H6v-2zm4-3.5C10 8.64 8 9 8 9H6c0-.55.45-1 1-1h.5c.28 0 .5-.22.5-.5v-1c0-.28-.22-.5-.5-.5h-1c-.28 0-.5.22-.5.5V7H4c0-1.5 1.5-3 3-3s3 1 3 2.5zM7 2.3c3.14 0 5.7 2.56 5.7 5.7s-2.56 5.7-5.7 5.7A5.71 5.71 0 0 1 1.3 8c0-3.14 2.56-5.7 5.7-5.7zM7 1C3.14 1 0 4.14 0 8s3.14 7 7 7 7-3.14 7-7-3.14-7-7-7z"/></svg> - </a> - </h4> - <p class="mb-2 get-repo-decription-text"> - Use Git or checkout with SVN using the web URL. - </p> - - <div class="input-group js-zeroclipboard-container"> - <input type="text" class="form-control input-monospace input-sm js-zeroclipboard-target js-url-field" value="https://github.com/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot.git" aria-label="Clone this repository at https://github.com/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot.git" readonly> - <div class="input-group-button"> - <button aria-label="Copy to clipboard" class="js-zeroclipboard btn btn-sm zeroclipboard-button tooltipped tooltipped-s" data-copied-hint="Copied!" type="button"><svg aria-hidden="true" class="octicon octicon-clippy" height="16" version="1.1" viewBox="0 0 14 16" width="14"><path fill-rule="evenodd" d="M2 13h4v1H2v-1zm5-6H2v1h5V7zm2 3V8l-3 3 3 3v-2h5v-2H9zM4.5 9H2v1h2.5V9zM2 12h2.5v-1H2v1zm9 1h1v2c-.02.28-.11.52-.3.7-.19.18-.42.28-.7.3H1c-.55 0-1-.45-1-1V4c0-.55.45-1 1-1h3c0-1.11.89-2 2-2 1.11 0 2 .89 2 2h3c.55 0 1 .45 1 1v5h-1V6H1v9h10v-2zM2 5h8c0-.55-.45-1-1-1H8c-.55 0-1-.45-1-1s-.45-1-1-1-1 .45-1 1-.45 1-1 1H3c-.55 0-1 .45-1 1z"/></svg></button> - </div> -</div> - - </div> - - - <div class="mt-2"> - -<a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/archive/master.zip" - class="btn btn-outline get-repo-btn -" - rel="nofollow" - data-ga-click="Repository, download zip, location:repo overview"> - Download ZIP -</a> - - </div> - </div> - </div> -</div> - - - <div class="BtnGroup float-right"> - - <a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/find/master" - class="btn btn-sm empty-icon float-right BtnGroup-item" - data-pjax - data-hotkey="t" - data-ga-click="Repository, find file, location:repo overview"> - Find file - </a> - </div> - - -<div class="select-menu branch-select-menu js-menu-container js-select-menu float-left"> - <button class="btn btn-sm select-menu-button js-menu-target css-truncate" data-hotkey="w" - - type="button" aria-label="Switch branches or tags" tabindex="0" aria-haspopup="true"> - <i>Branch:</i> - <span class="js-select-button css-truncate-target">master</span> - </button> - - <div class="select-menu-modal-holder js-menu-content js-navigation-container" data-pjax aria-hidden="true"> - - <div class="select-menu-modal"> - <div class="select-menu-header"> - <svg aria-label="Close" class="octicon octicon-x js-menu-close" height="16" role="img" version="1.1" viewBox="0 0 12 16" width="12"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48z"/></svg> - <span class="select-menu-title">Switch branches/tags</span> - </div> - - <div class="select-menu-filters"> - <div class="select-menu-text-filter"> - <input type="text" aria-label="Filter branches/tags" id="context-commitish-filter-field" class="form-control js-filterable-field js-navigation-enable" placeholder="Filter branches/tags"> - </div> - <div class="select-menu-tabs"> - <ul> - <li class="select-menu-tab"> - <a href="#" data-tab-filter="branches" data-filter-placeholder="Filter branches/tags" class="js-select-menu-tab" role="tab">Branches</a> - </li> - <li class="select-menu-tab"> - <a href="#" data-tab-filter="tags" data-filter-placeholder="Find a tag…" class="js-select-menu-tab" role="tab">Tags</a> - </li> - </ul> - </div> - </div> - - <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="branches" role="menu"> - - <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring"> - - - <a class="select-menu-item js-navigation-item js-navigation-open " - href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/tree/MoHeydarian-preplanemo" - data-name="MoHeydarian-preplanemo" - data-skip-pjax="true" - rel="nofollow"> - <svg aria-hidden="true" class="octicon octicon-check select-menu-item-icon" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path fill-rule="evenodd" d="M12 5l-8 8-4-4 1.5-1.5L4 10l6.5-6.5z"/></svg> - <span class="select-menu-item-text css-truncate-target js-select-menu-filter-text"> - MoHeydarian-preplanemo - </span> - </a> - <a class="select-menu-item js-navigation-item js-navigation-open " - href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/tree/adding-dependencies" - data-name="adding-dependencies" - data-skip-pjax="true" - rel="nofollow"> - <svg aria-hidden="true" class="octicon octicon-check select-menu-item-icon" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path fill-rule="evenodd" d="M12 5l-8 8-4-4 1.5-1.5L4 10l6.5-6.5z"/></svg> - <span class="select-menu-item-text css-truncate-target js-select-menu-filter-text"> - adding-dependencies - </span> - </a> - <a class="select-menu-item js-navigation-item js-navigation-open selected" - href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/tree/master" - data-name="master" - data-skip-pjax="true" - rel="nofollow"> - <svg aria-hidden="true" class="octicon octicon-check select-menu-item-icon" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path fill-rule="evenodd" d="M12 5l-8 8-4-4 1.5-1.5L4 10l6.5-6.5z"/></svg> - <span class="select-menu-item-text css-truncate-target js-select-menu-filter-text"> - master - </span> - </a> - </div> - - <div class="select-menu-no-results">Nothing to show</div> - </div> - - <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="tags"> - <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring"> - - - </div> - - <div class="select-menu-no-results">Nothing to show</div> - </div> - - </div> - </div> -</div> - - - <button type="button" class="btn btn-sm disabled tooltipped tooltipped-n new-pull-request-btn" aria-label="You must be signed in to create a pull request"> - New pull request - </button> - - <div class="breadcrumb"> - - </div> -</div> - - - - - - <div class="commit-tease js-details-container"> - <span class="float-right"> - Latest commit - <a class="commit-tease-sha" href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/commit/ce9dd112e88e7fb52ef50a0c1ae68311573f9399" data-pjax> - ce9dd11 - </a> - <span itemprop="dateModified"><relative-time datetime="2017-01-11T15:32:51Z">Jan 11, 2017</relative-time></span> - </span> - - - <span class="commit-author-section"> - <img alt="@MoHeydarian" class="avatar" height="20" src="https://avatars2.githubusercontent.com/u/18484759?v=3&s=40" width="20" /> - <a href="/MoHeydarian" class="user-mention" rel="author">MoHeydarian</a> - committed on <strong>GitHub</strong> - </span> - - <a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/commit/ce9dd112e88e7fb52ef50a0c1ae68311573f9399" class="message" data-pjax="true" title="v1-removing dir address of Rscript">v1-removing dir address of Rscript</a> - </span> - - </div> - - -<div class="file-wrap"> - - <a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/tree/ce9dd112e88e7fb52ef50a0c1ae68311573f9399" class="d-none js-permalink-shortcut" data-hotkey="y">Permalink</a> - - <table class="files js-navigation-container js-active-navigation-container" data-pjax> - - - <tbody> - <tr class="warning include-fragment-error"> - <td class="icon"><svg aria-hidden="true" class="octicon octicon-alert" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M8.865 1.52c-.18-.31-.51-.5-.87-.5s-.69.19-.87.5L.275 13.5c-.18.31-.18.69 0 1 .19.31.52.5.87.5h13.7c.36 0 .69-.19.86-.5.17-.31.18-.69.01-1L8.865 1.52zM8.995 13h-2v-2h2v2zm0-3h-2V6h2v4z"/></svg></td> - <td class="content" colspan="3">Failed to load latest commit information.</td> - </tr> - - <tr class="js-navigation-item"> - <td class="icon"> - <svg aria-hidden="true" class="octicon octicon-file-text" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg> - <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> - </td> - <td class="content"> - <span class="css-truncate css-truncate-target"><a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/blob/master/README.md" class="js-navigation-open" id="04c6e90faac2675aa89e2176d2eec7d8-16639d975635dabfb26aa3748c1eba88ba4c3656" title="README.md">README.md</a></span> - </td> - <td class="message"> - <span class="css-truncate css-truncate-target"> - <a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/commit/8c483a9ddf04e05f19018851e0ca7bc6e77b109d" class="message" data-pjax="true" title="Update README.md">Update README.md</a> - </span> - </td> - <td class="age"> - <span class="css-truncate css-truncate-target"><time-ago datetime="2016-12-01T04:48:19Z">Dec 1, 2016</time-ago></span> - </td> - </tr> - <tr class="js-navigation-item"> - <td class="icon"> - <svg aria-hidden="true" class="octicon octicon-file-text" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg> - <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> - </td> - <td class="content"> - <span class="css-truncate css-truncate-target"><a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/blob/master/cDiff_test_data_from_GSE37703_(chr_in_c4)" class="js-navigation-open" id="e649b8e62a2e0c34291bca79e6917a9c-98138e975c8c879eeb9a2f45cad5c938bafe5525" title="cDiff_test_data_from_GSE37703_(chr_in_c4)">cDiff_test_data_from_GSE37703_(chr_in_c4)</a></span> - </td> - <td class="message"> - <span class="css-truncate css-truncate-target"> - <a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/commit/17a1b4bb3f9cab60d133931bdf7275cdc8ec79e8" class="message" data-pjax="true" title="first commit to the repo - -Three files uploaded: an xml file, a Rscript file, and a test data file.">first commit to the repo</a> - </span> - </td> - <td class="age"> - <span class="css-truncate css-truncate-target"><time-ago datetime="2016-08-11T19:10:23Z">Aug 11, 2016</time-ago></span> - </td> - </tr> - <tr class="js-navigation-item"> - <td class="icon"> - <svg aria-hidden="true" class="octicon octicon-file-text" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg> - <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> - </td> - <td class="content"> - <span class="css-truncate css-truncate-target"><a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/blob/master/ggplot_point.xml" class="js-navigation-open" id="9bc36e9decb8e37316fe53ca336601af-e4a1509b67b66570744b0e16c58a7375fb80cc46" title="ggplot_point.xml">ggplot_point.xml</a></span> - </td> - <td class="message"> - <span class="css-truncate css-truncate-target"> - <a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/commit/ce9dd112e88e7fb52ef50a0c1ae68311573f9399" class="message" data-pjax="true" title="v1-removing dir address of Rscript">v1-removing dir address of Rscript</a> - </span> - </td> - <td class="age"> - <span class="css-truncate css-truncate-target"><time-ago datetime="2017-01-11T15:32:51Z">Jan 11, 2017</time-ago></span> - </td> - </tr> - <tr class="js-navigation-item"> - <td class="icon"> - <svg aria-hidden="true" class="octicon octicon-file-text" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg> - <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> - </td> - <td class="content"> - <span class="css-truncate css-truncate-target"><a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/blob/master/ggplotpointscript.R" class="js-navigation-open" id="192f33a55225e1a82f08d1547bcd7ea7-8c6f150b668944cf1fe0c09dc20b6a1acfe06939" title="ggplotpointscript.R">ggplotpointscript.R</a></span> - </td> - <td class="message"> - <span class="css-truncate css-truncate-target"> - <a href="/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot/commit/f89c2128bfda2274de8fc16a9afad85c68059e15" class="message" data-pjax="true" title="cleaned up R script file name">cleaned up R script file name</a> - </span> - </td> - <td class="age"> - <span class="css-truncate css-truncate-target"><time-ago datetime="2016-12-01T18:20:46Z">Dec 1, 2016</time-ago></span> - </td> - </tr> - </tbody> - </table> - -</div> - - - - <div id="readme" class="readme boxed-group clearfix announce instapaper_body md"> - <h3> - <svg aria-hidden="true" class="octicon octicon-book" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M3 5h4v1H3V5zm0 3h4V7H3v1zm0 2h4V9H3v1zm11-5h-4v1h4V5zm0 2h-4v1h4V7zm0 2h-4v1h4V9zm2-6v9c0 .55-.45 1-1 1H9.5l-1 1-1-1H2c-.55 0-1-.45-1-1V3c0-.55.45-1 1-1h5.5l1 1 1-1H15c.55 0 1 .45 1 1zm-8 .5L7.5 3H2v9h6V3.5zm7-.5H9.5l-.5.5V12h6V3z"/></svg> - 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> - </div> - - - </div> - <div class="modal-backdrop js-touch-events"></div> -</div> - - - </div> - </div> - - </div> - - <div class="container site-footer-container"> - <div class="site-footer" role="contentinfo"> - <ul class="site-footer-links float-right"> - <li><a href="https://github.com/contact" data-ga-click="Footer, go to contact, text:contact">Contact GitHub</a></li> - <li><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li> - <li><a href="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li> - <li><a href="https://shop.github.com" data-ga-click="Footer, go to shop, text:shop">Shop</a></li> - <li><a href="https://github.com/blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li> - <li><a href="https://github.com/about" data-ga-click="Footer, go to about, text:about">About</a></li> - - </ul> - - <a href="https://github.com" aria-label="Homepage" class="site-footer-mark" title="GitHub"> - <svg aria-hidden="true" class="octicon octicon-mark-github" height="24" version="1.1" viewBox="0 0 16 16" width="24"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg> -</a> - <ul class="site-footer-links"> - <li>© 2017 <span title="0.09355s from github-fe149-cp1-prd.iad.github.net">GitHub</span>, Inc.</li> - <li><a href="https://github.com/site/terms" data-ga-click="Footer, go to terms, text:terms">Terms</a></li> - <li><a href="https://github.com/site/privacy" data-ga-click="Footer, go to privacy, text:privacy">Privacy</a></li> - <li><a href="https://github.com/security" data-ga-click="Footer, go to security, text:security">Security</a></li> - <li><a href="https://status.github.com/" data-ga-click="Footer, go to status, text:status">Status</a></li> - <li><a href="https://help.github.com" data-ga-click="Footer, go to help, text:help">Help</a></li> - </ul> - </div> -</div> - - - - - - <div id="ajax-error-message" class="ajax-error-message flash flash-error"> - <svg aria-hidden="true" class="octicon octicon-alert" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M8.865 1.52c-.18-.31-.51-.5-.87-.5s-.69.19-.87.5L.275 13.5c-.18.31-.18.69 0 1 .19.31.52.5.87.5h13.7c.36 0 .69-.19.86-.5.17-.31.18-.69.01-1L8.865 1.52zM8.995 13h-2v-2h2v2zm0-3h-2V6h2v4z"/></svg> - <button type="button" class="flash-close js-flash-close js-ajax-error-dismiss" aria-label="Dismiss error"> - <svg aria-hidden="true" class="octicon octicon-x" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48z"/></svg> - </button> - You can't perform that action at this time. - </div> - - - <script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/compat-30ce4c86c27f88c3d1b4eb03efda59b45d8d7c871880dee0b8f73d5ef1b25fdf.js"></script> - <script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/frameworks-66b48990d363eebc8bae53cbe192b1e96621f21bcf65b8682858aacf03bff522.js"></script> - <script async="async" crossorigin="anonymous" src="https://assets-cdn.github.com/assets/github-9528568888dd7325437f280e2b4150b7117219f92b0e57c44af176957085d0b9.js"></script> - - - - - <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner d-none"> - <svg aria-hidden="true" class="octicon octicon-alert" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M8.865 1.52c-.18-.31-.51-.5-.87-.5s-.69.19-.87.5L.275 13.5c-.18.31-.18.69 0 1 .19.31.52.5.87.5h13.7c.36 0 .69-.19.86-.5.17-.31.18-.69.01-1L8.865 1.52zM8.995 13h-2v-2h2v2zm0-3h-2V6h2v4z"/></svg> - <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span> - <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span> - </div> - <div class="facebox" id="facebox" style="display:none;"> - <div class="facebox-popup"> - <div class="facebox-content" role="dialog" aria-labelledby="facebox-header" aria-describedby="facebox-description"> - </div> - <button type="button" class="facebox-close js-facebox-close" aria-label="Close modal"> - <svg aria-hidden="true" class="octicon octicon-x" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48z"/></svg> - </button> - </div> -</div> - - </body> -</html> -
--- 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