Mercurial > repos > moheydarian > heatmap2
changeset 3:f4e9535003ad draft
Uploaded
| author | moheydarian |
|---|---|
| date | Tue, 14 Mar 2017 14:20:35 -0400 |
| parents | ca138397d628 |
| children | d61d62699e5c |
| files | heatmap2.R |
| diffstat | 1 files changed, 49 insertions(+), 785 deletions(-) [+] |
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--- a/heatmap2.R Tue Mar 14 14:20:18 2017 -0400 +++ b/heatmap2.R Tue Mar 14 14:20:35 2017 -0400 @@ -1,802 +1,66 @@ - - - - - - -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> - - - - <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/frameworks-19e26a1cefb5f1e92203a9468134dbf46b5a5308aeeeee09c96b32fec8c8b044.css" media="all" rel="stylesheet" /> - <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/github-f886e4c2d166bd2750de4f941f1f14b0658f60e7cf5a680a5926b1c2fb1f5252.css" media="all" rel="stylesheet" /> - - - <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/site-c47804daf40159016fecc8d259abd34792c6e416b16d84c5268895fbdfbefd5e.css" media="all" rel="stylesheet" /> - - - <meta name="viewport" content="width=device-width"> - - <title>Galaxy-heatmap.2-wrapper/heatmap2.R at master · MoHeydarian/Galaxy-heatmap.2-wrapper · GitHub</title> - <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub"> - 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<link href="https://github.com/MoHeydarian/Galaxy-heatmap.2-wrapper/commits/master.atom" rel="alternate" title="Recent Commits to Galaxy-heatmap.2-wrapper:master" type="application/atom+xml"> - - - <link rel="canonical" href="https://github.com/MoHeydarian/Galaxy-heatmap.2-wrapper/blob/master/heatmap2.R" data-pjax-transient> +# We need to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") - <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="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="theme-color" content="#1e2327"> - - - - </head> - - <body class="logged-out env-production page-blob"> - - - <div class="position-relative js-header-wrapper "> - <a href="#start-of-content" tabindex="1" class="accessibility-aid js-skip-to-content">Skip to content</a> - <div id="js-pjax-loader-bar" class="pjax-loader-bar"><div class="progress"></div></div> - - - - - +# Import library +library("getopt") +library("RColorBrewer") +library("gplots") +options(stringAsfactors = FALSE, useFancyQuotes = FALSE) +# Take in trailing command line arguments +args <- commandArgs(trailingOnly = TRUE) - <header class="site-header js-details-container Details" 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> - 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Explore -</a> <a href="/pricing" class="js-selected-navigation-item nav-item" data-ga-click="Header, click, Nav menu - item:pricing" data-selected-links="/pricing /pricing"> - Pricing -</a> </nav> +# 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', + 'transform', 'c', 2, 'character', + 'keylabel', 'k',2, 'character', + 'output', 'o', 2, 'character' + ), byrow=TRUE, ncol=4); - <div class="site-header-actions"> - <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-heatmap.2-wrapper/search" class="js-site-search-form" data-scoped-search-url="/MoHeydarian/Galaxy-heatmap.2-wrapper/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> - - - <a class="text-bold site-header-link" href="/login?return_to=%2FMoHeydarian%2FGalaxy-heatmap.2-wrapper%2Fblob%2Fmaster%2Fheatmap2.R" data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in">Sign in</a> - <span class="text-gray">or</span> - <a class="text-bold site-header-link" href="/join?source=header-repo" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up">Sign up</a> - </div> - </div> - </div> -</header> - - - </div> - - <div id="start-of-content" class="accessibility-aid"></div> - - <div id="js-flash-container"> -</div> +# Parse options +options = getopt(option_specification); - 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Pulse -</a> - <a href="/MoHeydarian/Galaxy-heatmap.2-wrapper/graphs" class="js-selected-navigation-item reponav-item" data-selected-links="repo_graphs repo_contributors /MoHeydarian/Galaxy-heatmap.2-wrapper/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"> - - - -<a href="/MoHeydarian/Galaxy-heatmap.2-wrapper/blob/7db399461c28cd9a107403cfb0947605428fd5c5/heatmap2.R" class="d-none js-permalink-shortcut" data-hotkey="y">Permalink</a> - -<!-- blob contrib key: blob_contributors:v21:67686cee77ff3d961e240bf79b13ab0e --> +# Print options to see what is going on +cat("\n input: ",options$input) +cat("\n title: ",options$title) +cat("\n output: ",options$output) -<div class="file-navigation js-zeroclipboard-container"> - -<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 selected" - href="/MoHeydarian/Galaxy-heatmap.2-wrapper/blob/master/heatmap2.R" - 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> +input <- read.delim(options$input,sep='\t',header=TRUE) - <div class="select-menu-no-results">Nothing to show</div> - </div> - - </div> - </div> -</div> - - <div class="BtnGroup float-right"> - <a href="/MoHeydarian/Galaxy-heatmap.2-wrapper/find/master" - class="js-pjax-capture-input btn btn-sm BtnGroup-item" - data-pjax - data-hotkey="t"> - Find file - </a> - <button aria-label="Copy file path to clipboard" class="js-zeroclipboard btn btn-sm BtnGroup-item tooltipped tooltipped-s" data-copied-hint="Copied!" type="button">Copy path</button> - </div> - <div class="breadcrumb js-zeroclipboard-target"> - <span class="repo-root js-repo-root"><span class="js-path-segment"><a href="/MoHeydarian/Galaxy-heatmap.2-wrapper"><span>Galaxy-heatmap.2-wrapper</span></a></span></span><span class="separator">/</span><strong class="final-path">heatmap2.R</strong> - </div> -</div> - - - <div class="commit-tease"> - <span class="float-right"> - <a class="commit-tease-sha" href="/MoHeydarian/Galaxy-heatmap.2-wrapper/commit/7db399461c28cd9a107403cfb0947605428fd5c5" data-pjax> - 7db3994 - </a> - <relative-time datetime="2017-03-14T18:18:21Z">Mar 14, 2017</relative-time> - </span> - <div> - <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> - <a href="/MoHeydarian/Galaxy-heatmap.2-wrapper/commit/7db399461c28cd9a107403cfb0947605428fd5c5" class="message" data-pjax="true" title="Update heatmap2.R">Update heatmap2.R</a> - </div> - - <div class="commit-tease-contributors"> - <button type="button" class="btn-link muted-link contributors-toggle" data-facebox="#blob_contributors_box"> - <strong>1</strong> - contributor - </button> - - </div> - - <div id="blob_contributors_box" style="display:none"> - <h2 class="facebox-header" data-facebox-id="facebox-header">Users who have contributed to this file</h2> - <ul class="facebox-user-list" data-facebox-id="facebox-description"> - <li class="facebox-user-list-item"> - <img alt="@MoHeydarian" height="24" src="https://avatars0.githubusercontent.com/u/18484759?v=3&s=48" width="24" /> - <a href="/MoHeydarian">MoHeydarian</a> - </li> - </ul> - </div> - </div> - - -<div class="file"> - <div class="file-header"> - <div class="file-actions"> - - <div class="BtnGroup"> - <a href="/MoHeydarian/Galaxy-heatmap.2-wrapper/raw/master/heatmap2.R" class="btn btn-sm BtnGroup-item" id="raw-url">Raw</a> - <a href="/MoHeydarian/Galaxy-heatmap.2-wrapper/blame/master/heatmap2.R" class="btn btn-sm js-update-url-with-hash BtnGroup-item" data-hotkey="b">Blame</a> - <a href="/MoHeydarian/Galaxy-heatmap.2-wrapper/commits/master/heatmap2.R" class="btn btn-sm BtnGroup-item" rel="nofollow">History</a> - </div> +mat_input <- data.matrix(input[,2:ncol(input)]) - <button type="button" class="btn-octicon disabled tooltipped tooltipped-nw" - aria-label="You must be signed in to make or propose changes"> - <svg aria-hidden="true" class="octicon octicon-pencil" height="16" version="1.1" viewBox="0 0 14 16" width="14"><path fill-rule="evenodd" d="M0 12v3h3l8-8-3-3-8 8zm3 2H1v-2h1v1h1v1zm10.3-9.3L12 6 9 3l1.3-1.3a.996.996 0 0 1 1.41 0l1.59 1.59c.39.39.39 1.02 0 1.41z"/></svg> - </button> - <button type="button" class="btn-octicon btn-octicon-danger disabled tooltipped tooltipped-nw" - aria-label="You must be signed in to make or propose changes"> - <svg aria-hidden="true" class="octicon octicon-trashcan" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path fill-rule="evenodd" d="M11 2H9c0-.55-.45-1-1-1H5c-.55 0-1 .45-1 1H2c-.55 0-1 .45-1 1v1c0 .55.45 1 1 1v9c0 .55.45 1 1 1h7c.55 0 1-.45 1-1V5c.55 0 1-.45 1-1V3c0-.55-.45-1-1-1zm-1 12H3V5h1v8h1V5h1v8h1V5h1v8h1V5h1v9zm1-10H2V3h9v1z"/></svg> - </button> - </div> - - <div class="file-info"> - 67 lines (49 sloc) - <span class="file-info-divider"></span> - 1.89 KB - </div> -</div> - - - - <div itemprop="text" class="blob-wrapper data type-r"> - <table class="highlight tab-size js-file-line-container" data-tab-size="8"> - <tr> - <td id="L1" class="blob-num js-line-number" data-line-number="1"></td> - <td id="LC1" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> Setup R error handling to go to stderr</span></td> - </tr> - <tr> - <td id="L2" class="blob-num js-line-number" data-line-number="2"></td> - <td id="LC2" class="blob-code blob-code-inner js-file-line">options(<span class="pl-v">show.error.messages</span><span class="pl-k">=</span><span class="pl-c1">F</span>, <span class="pl-v">error</span><span class="pl-k">=</span><span class="pl-k">function</span>(){cat(geterrmessage(),<span class="pl-v">file</span><span class="pl-k">=</span>stderr());q(<span class="pl-s"><span class="pl-pds">"</span>no<span class="pl-pds">"</span></span>,<span class="pl-c1">1</span>,<span class="pl-c1">F</span>)})</td> - </tr> - <tr> - <td id="L3" class="blob-num js-line-number" data-line-number="3"></td> - <td id="LC3" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L4" class="blob-num js-line-number" data-line-number="4"></td> - <td id="LC4" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> We need to not crash galaxy with an UTF8 error on German LC settings.</span></td> - </tr> - <tr> - <td id="L5" class="blob-num js-line-number" data-line-number="5"></td> - <td id="LC5" class="blob-code blob-code-inner js-file-line"><span class="pl-smi">loc</span> <span class="pl-k"><-</span> Sys.setlocale(<span class="pl-s"><span class="pl-pds">"</span>LC_MESSAGES<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>en_US.UTF-8<span class="pl-pds">"</span></span>)</td> - </tr> - <tr> - <td id="L6" class="blob-num js-line-number" data-line-number="6"></td> - <td id="LC6" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L7" class="blob-num js-line-number" data-line-number="7"></td> - <td id="LC7" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L8" class="blob-num js-line-number" data-line-number="8"></td> - <td id="LC8" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> Import library</span></td> - </tr> - <tr> - <td id="L9" class="blob-num js-line-number" data-line-number="9"></td> - <td id="LC9" class="blob-code blob-code-inner js-file-line">library(<span class="pl-s"><span class="pl-pds">"</span>getopt<span class="pl-pds">"</span></span>)</td> - </tr> - <tr> - <td id="L10" class="blob-num js-line-number" data-line-number="10"></td> - <td id="LC10" class="blob-code blob-code-inner js-file-line">library(<span class="pl-s"><span class="pl-pds">"</span>RColorBrewer<span class="pl-pds">"</span></span>)</td> - </tr> - <tr> - <td id="L11" class="blob-num js-line-number" data-line-number="11"></td> - <td id="LC11" class="blob-code blob-code-inner js-file-line">library(<span class="pl-s"><span class="pl-pds">"</span>gplots<span class="pl-pds">"</span></span>)</td> - </tr> - <tr> - <td id="L12" class="blob-num js-line-number" data-line-number="12"></td> - <td id="LC12" class="blob-code blob-code-inner js-file-line">options(<span class="pl-v">stringAsfactors</span> <span class="pl-k">=</span> <span class="pl-c1">FALSE</span>, <span class="pl-v">useFancyQuotes</span> <span class="pl-k">=</span> <span class="pl-c1">FALSE</span>)</td> - </tr> - <tr> - <td id="L13" class="blob-num js-line-number" data-line-number="13"></td> - <td id="LC13" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> Take in trailing command line arguments</span></td> - </tr> - <tr> - <td id="L14" class="blob-num js-line-number" data-line-number="14"></td> - <td id="LC14" class="blob-code blob-code-inner js-file-line"><span class="pl-smi">args</span> <span class="pl-k"><-</span> commandArgs(<span class="pl-v">trailingOnly</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</td> - </tr> - <tr> - <td id="L15" class="blob-num js-line-number" data-line-number="15"></td> - <td id="LC15" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L16" class="blob-num js-line-number" data-line-number="16"></td> - <td id="LC16" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L17" class="blob-num js-line-number" data-line-number="17"></td> - <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> get options, using the spec as defined by the enclosed list.</span></td> - </tr> - <tr> - <td id="L18" class="blob-num js-line-number" data-line-number="18"></td> - <td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> we read the options from the default: commandArgs(TRUE).</span></td> - </tr> - <tr> - <td id="L19" class="blob-num js-line-number" data-line-number="19"></td> - <td id="LC19" class="blob-code blob-code-inner js-file-line"><span class="pl-v">option_specification</span> <span class="pl-k">=</span> <span class="pl-k">matrix</span>(c(</td> - </tr> - <tr> - <td id="L20" class="blob-num js-line-number" data-line-number="20"></td> - <td id="LC20" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">'</span>input<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>i<span class="pl-pds">'</span></span>, <span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>character<span class="pl-pds">'</span></span>,</td> - </tr> - <tr> - <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> - <td id="LC21" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">'</span>title<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>t<span class="pl-pds">'</span></span>,<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>character<span class="pl-pds">'</span></span>,</td> - </tr> - <tr> - <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> - <td id="LC22" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">'</span>transform<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>c<span class="pl-pds">'</span></span>, <span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>character<span class="pl-pds">'</span></span>,</td> - </tr> - <tr> - <td id="L23" class="blob-num js-line-number" data-line-number="23"></td> - <td id="LC23" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">'</span>keylabel<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>k<span class="pl-pds">'</span></span>,<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>character<span class="pl-pds">'</span></span>,</td> - </tr> - <tr> - <td id="L24" class="blob-num js-line-number" data-line-number="24"></td> - <td id="LC24" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">'</span>output<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>o<span class="pl-pds">'</span></span>, <span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>character<span class="pl-pds">'</span></span></td> - </tr> - <tr> - <td id="L25" class="blob-num js-line-number" data-line-number="25"></td> - <td id="LC25" class="blob-code blob-code-inner js-file-line"> ), <span class="pl-v">byrow</span><span class="pl-k">=</span><span class="pl-c1">TRUE</span>, <span class="pl-v">ncol</span><span class="pl-k">=</span><span class="pl-c1">4</span>);</td> - </tr> - <tr> - <td id="L26" class="blob-num js-line-number" data-line-number="26"></td> - <td id="LC26" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L27" class="blob-num js-line-number" data-line-number="27"></td> - <td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> Parse options</span></td> - </tr> - <tr> - <td id="L28" class="blob-num js-line-number" data-line-number="28"></td> - <td id="LC28" class="blob-code blob-code-inner js-file-line"><span class="pl-v">options</span> <span class="pl-k">=</span> getopt(<span class="pl-smi">option_specification</span>);</td> - </tr> - <tr> - <td id="L29" class="blob-num js-line-number" data-line-number="29"></td> - <td id="LC29" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L30" class="blob-num js-line-number" data-line-number="30"></td> - <td id="LC30" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L31" class="blob-num js-line-number" data-line-number="31"></td> - <td id="LC31" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L32" class="blob-num js-line-number" data-line-number="32"></td> - <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> Print options to see what is going on</span></td> - </tr> - <tr> - <td id="L33" class="blob-num js-line-number" data-line-number="33"></td> - <td id="LC33" class="blob-code blob-code-inner js-file-line">cat(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span> input: <span class="pl-pds">"</span></span>,<span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">input</span>)</td> - </tr> - <tr> - <td id="L34" class="blob-num js-line-number" data-line-number="34"></td> - <td id="LC34" class="blob-code blob-code-inner js-file-line">cat(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span> title: <span class="pl-pds">"</span></span>,<span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">title</span>)</td> - </tr> - <tr> - <td id="L35" class="blob-num js-line-number" data-line-number="35"></td> - <td id="LC35" class="blob-code blob-code-inner js-file-line">cat(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span> output: <span class="pl-pds">"</span></span>,<span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">output</span>)</td> - </tr> - <tr> - <td id="L36" class="blob-num js-line-number" data-line-number="36"></td> - <td id="LC36" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L37" class="blob-num js-line-number" data-line-number="37"></td> - <td id="LC37" class="blob-code blob-code-inner js-file-line"><span class="pl-smi">input</span> <span class="pl-k"><-</span> read.delim(<span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">input</span>,<span class="pl-v">sep</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\t</span><span class="pl-pds">'</span></span>,<span class="pl-v">header</span><span class="pl-k">=</span><span class="pl-c1">TRUE</span>)</td> - </tr> - <tr> - <td id="L38" class="blob-num js-line-number" data-line-number="38"></td> - <td id="LC38" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L39" class="blob-num js-line-number" data-line-number="39"></td> - <td id="LC39" class="blob-code blob-code-inner js-file-line"><span class="pl-smi">mat_input</span> <span class="pl-k"><-</span> data.matrix(<span class="pl-smi">input</span>[,<span class="pl-c1">2</span><span class="pl-k">:</span>ncol(<span class="pl-smi">input</span>)]) </td> - </tr> - <tr> - <td id="L40" class="blob-num js-line-number" data-line-number="40"></td> - <td id="LC40" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L41" class="blob-num js-line-number" data-line-number="41"></td> - <td id="LC41" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L42" class="blob-num js-line-number" data-line-number="42"></td> - <td id="LC42" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span>(<span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">transform</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>none<span class="pl-pds">"</span></span>){</td> - </tr> - <tr> - <td id="L43" class="blob-num js-line-number" data-line-number="43"></td> - <td id="LC43" class="blob-code blob-code-inner js-file-line"> <span class="pl-smi">linput</span> <span class="pl-k"><-</span> <span class="pl-smi">mat_input</span></td> - </tr> - <tr> - <td id="L44" class="blob-num js-line-number" data-line-number="44"></td> - <td id="LC44" class="blob-code blob-code-inner js-file-line">}<span class="pl-k">else</span> <span class="pl-k">if</span>(<span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">transform</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>log2<span class="pl-pds">"</span></span>){</td> - </tr> - <tr> - <td id="L45" class="blob-num js-line-number" data-line-number="45"></td> - <td id="LC45" class="blob-code blob-code-inner js-file-line"> <span class="pl-smi">linput</span> <span class="pl-k"><-</span> log2(<span class="pl-smi">mat_input</span>)</td> - </tr> - <tr> - <td id="L46" class="blob-num js-line-number" data-line-number="46"></td> - <td id="LC46" class="blob-code blob-code-inner js-file-line">}<span class="pl-k">else</span> <span class="pl-k">if</span>(<span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">transform</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>log2plus1<span class="pl-pds">"</span></span>){</td> - </tr> - <tr> - <td id="L47" class="blob-num js-line-number" data-line-number="47"></td> - <td id="LC47" class="blob-code blob-code-inner js-file-line"> <span class="pl-smi">linput</span> <span class="pl-k"><-</span> log2(<span class="pl-smi">mat_input</span><span class="pl-k">+</span><span class="pl-c1">1</span>)</td> - </tr> - <tr> - <td id="L48" class="blob-num js-line-number" data-line-number="48"></td> - <td id="LC48" class="blob-code blob-code-inner js-file-line">}<span class="pl-k">else</span> <span class="pl-k">if</span>(<span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">transform</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>log10<span class="pl-pds">"</span></span>){</td> - </tr> - <tr> - <td id="L49" class="blob-num js-line-number" data-line-number="49"></td> - <td id="LC49" class="blob-code blob-code-inner js-file-line"> <span class="pl-smi">linput</span> <span class="pl-k"><-</span> log10(<span class="pl-smi">mat_input</span>)</td> - </tr> - <tr> - <td id="L50" class="blob-num js-line-number" data-line-number="50"></td> - <td id="LC50" class="blob-code blob-code-inner js-file-line">}<span class="pl-k">else</span> <span class="pl-k">if</span>(<span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">transform</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>log10plus1<span class="pl-pds">"</span></span>){</td> - </tr> - <tr> - <td id="L51" class="blob-num js-line-number" data-line-number="51"></td> - <td id="LC51" class="blob-code blob-code-inner js-file-line"> <span class="pl-smi">linput</span> <span class="pl-k"><-</span> log10(<span class="pl-smi">mat_input</span><span class="pl-k">+</span><span class="pl-c1">1</span>)</td> - </tr> - <tr> - <td id="L52" class="blob-num js-line-number" data-line-number="52"></td> - <td id="LC52" class="blob-code blob-code-inner js-file-line"> }<span class="pl-k">else</span>{</td> - </tr> - <tr> - <td id="L53" class="blob-num js-line-number" data-line-number="53"></td> - <td id="LC53" class="blob-code blob-code-inner js-file-line">}</td> - </tr> - <tr> - <td id="L54" class="blob-num js-line-number" data-line-number="54"></td> - <td id="LC54" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L55" class="blob-num js-line-number" data-line-number="55"></td> - <td id="LC55" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L56" class="blob-num js-line-number" data-line-number="56"></td> - <td id="LC56" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L57" class="blob-num js-line-number" data-line-number="57"></td> - <td id="LC57" class="blob-code blob-code-inner js-file-line"><span class="pl-v">hclust_fun</span> <span class="pl-k">=</span> <span class="pl-k">function</span>(<span class="pl-smi">x</span>) hclust(<span class="pl-smi">x</span>, <span class="pl-v">method</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">"</span>complete<span class="pl-pds">"</span></span>)</td> - </tr> - <tr> - <td id="L58" class="blob-num js-line-number" data-line-number="58"></td> - <td id="LC58" class="blob-code blob-code-inner js-file-line"><span class="pl-v">dist_fun</span> <span class="pl-k">=</span> <span class="pl-k">function</span>(<span class="pl-smi">x</span>) dist(<span class="pl-smi">x</span>, <span class="pl-v">method</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">"</span>maximum<span class="pl-pds">"</span></span>)</td> - </tr> - <tr> - <td id="L59" class="blob-num js-line-number" data-line-number="59"></td> - <td id="LC59" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L60" class="blob-num js-line-number" data-line-number="60"></td> - <td id="LC60" class="blob-code blob-code-inner js-file-line">pdf(<span class="pl-v">file</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">"</span>Rplot.pdf<span class="pl-pds">"</span></span>)</td> - </tr> - <tr> - <td id="L61" class="blob-num js-line-number" data-line-number="61"></td> - <td id="LC61" class="blob-code blob-code-inner js-file-line"><span class="pl-smi">colfunc</span> <span class="pl-k"><-</span> colorRampPalette(c(<span class="pl-s"><span class="pl-pds">"</span>white<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>red<span class="pl-pds">"</span></span>))</td> - </tr> - <tr> - <td id="L62" class="blob-num js-line-number" data-line-number="62"></td> - <td id="LC62" class="blob-code blob-code-inner js-file-line">heatmap.2(<span class="pl-smi">linput</span>,</td> - </tr> - <tr> - <td id="L63" class="blob-num js-line-number" data-line-number="63"></td> - <td id="LC63" class="blob-code blob-code-inner js-file-line"> <span class="pl-v">distfun</span><span class="pl-k">=</span><span class="pl-smi">dist_fun</span>, <span class="pl-v">hclustfun</span><span class="pl-k">=</span><span class="pl-smi">hclust_fun</span>, <span class="pl-v">scale</span> <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>none<span class="pl-pds">"</span></span>,</td> - </tr> - <tr> - <td id="L64" class="blob-num js-line-number" data-line-number="64"></td> - <td id="LC64" class="blob-code blob-code-inner js-file-line"> <span class="pl-v">col</span><span class="pl-k">=</span>colfunc(<span class="pl-c1">50</span>), <span class="pl-v">trace</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">"</span>none<span class="pl-pds">"</span></span>, <span class="pl-v">density.info</span> <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>none<span class="pl-pds">"</span></span>,<span class="pl-v">labRow</span><span class="pl-k">=</span><span class="pl-c1">FALSE</span>, <span class="pl-v">margins</span><span class="pl-k">=</span>c(<span class="pl-c1">8</span>,<span class="pl-c1">2</span>),</td> - </tr> - <tr> - <td id="L65" class="blob-num js-line-number" data-line-number="65"></td> - <td id="LC65" class="blob-code blob-code-inner js-file-line"> <span class="pl-v">main</span> <span class="pl-k">=</span> <span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">title</span>, <span class="pl-v">key.xlab</span><span class="pl-k">=</span> <span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">keylabel</span>, <span class="pl-v">keysize</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td> - </tr> - <tr> - <td id="L66" class="blob-num js-line-number" data-line-number="66"></td> - <td id="LC66" class="blob-code blob-code-inner js-file-line">dev.off()</td> - </tr> -</table> - - </div> - -</div> - -<button type="button" data-facebox="#jump-to-line" data-facebox-class="linejump" data-hotkey="l" class="d-none">Jump to Line</button> -<div id="jump-to-line" style="display:none"> - <!-- '"` --><!-- </textarea></xmp> --></option></form><form accept-charset="UTF-8" action="" class="js-jump-to-line-form" method="get"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /></div> - <input class="form-control linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" aria-label="Jump to line" autofocus> - <button type="submit" class="btn">Go</button> -</form></div> - - </div> - <div class="modal-backdrop js-touch-events"></div> -</div> +if(options$transform == "none"){ + linput <- mat_input +}else if(options$transform == "log2"){ + linput <- log2(mat_input) +}else if(options$transform == "log2plus1"){ + linput <- log2(mat_input+1) +}else if(options$transform == "log10"){ + linput <- log10(mat_input) +}else if(options$transform == "log10plus1"){ + linput <- log10(mat_input+1) + }else{ +} - 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<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> - +pdf(file="Rplot.pdf") +colfunc <- colorRampPalette(c("white", "red")) +heatmap.2(linput, + distfun=dist_fun, hclustfun=hclust_fun, scale = "none", + col=colfunc(50), trace="none", density.info = "none",labRow=FALSE, margins=c(8,2), + main = options$title, key.xlab= options$keylabel, keysize=1) +dev.off()