<!DOCTYPE html> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <meta charset="utf-8" /> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <meta name="generator" content="pandoc" /> <meta name="author" content="Lei Sun" /> <meta name="date" content="2017-05-12" /> <title>plot_diagnostic in ashr</title> <script src="site_libs/jquery-1.11.3/jquery.min.js"></script> <meta name="viewport" content="width=device-width, initial-scale=1" /> <link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" /> <script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script> <script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script> <script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script> <script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script> <link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" /> <script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script> <script src="site_libs/navigation-1.1/tabsets.js"></script> <link href="site_libs/highlightjs-9.12.0/textmate.css" rel="stylesheet" /> <script src="site_libs/highlightjs-9.12.0/highlight.js"></script> <link href="site_libs/font-awesome-4.5.0/css/font-awesome.min.css" rel="stylesheet" /> <style type="text/css">code{white-space: pre;}</style> <style type="text/css"> pre:not([class]) { background-color: white; } </style> <script type="text/javascript"> if (window.hljs) { hljs.configure({languages: []}); hljs.initHighlightingOnLoad(); if (document.readyState && document.readyState === "complete") { window.setTimeout(function() { hljs.initHighlighting(); }, 0); } } </script> <style type="text/css"> h1 { font-size: 34px; } h1.title { font-size: 38px; } h2 { font-size: 30px; } h3 { font-size: 24px; } h4 { font-size: 18px; } h5 { font-size: 16px; } h6 { font-size: 12px; } .table th:not([align]) { text-align: left; } </style> </head> <body> <style type = "text/css"> .main-container { max-width: 940px; margin-left: auto; margin-right: auto; } code { color: inherit; background-color: rgba(0, 0, 0, 0.04); } img { max-width:100%; height: auto; } .tabbed-pane { padding-top: 12px; } button.code-folding-btn:focus { outline: none; } </style> <style type="text/css"> /* padding for bootstrap navbar */ body { padding-top: 51px; padding-bottom: 40px; } /* offset scroll position for anchor links (for fixed navbar) */ .section h1 { padding-top: 56px; margin-top: -56px; } .section h2 { padding-top: 56px; margin-top: -56px; } .section h3 { padding-top: 56px; margin-top: -56px; } .section h4 { padding-top: 56px; margin-top: -56px; } .section h5 { padding-top: 56px; margin-top: -56px; } .section h6 { padding-top: 56px; margin-top: -56px; } </style> <script> // manage active state of menu based on current page $(document).ready(function () { // active menu anchor href = window.location.pathname href = href.substr(href.lastIndexOf('/') + 1) if (href === "") href = "index.html"; var menuAnchor = $('a[href="' + href + '"]'); // mark it active menuAnchor.parent().addClass('active'); // if it's got a parent navbar menu mark it active as well menuAnchor.closest('li.dropdown').addClass('active'); }); </script> <div class="container-fluid main-container"> <!-- tabsets --> <script> $(document).ready(function () { window.buildTabsets("TOC"); }); </script> <!-- code folding --> <script> $(document).ready(function () { // move toc-ignore selectors from section div to header $('div.section.toc-ignore') .removeClass('toc-ignore') .children('h1,h2,h3,h4,h5').addClass('toc-ignore'); // establish options var options = { selectors: "h1,h2,h3", theme: "bootstrap3", context: '.toc-content', hashGenerator: function (text) { return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase(); }, ignoreSelector: ".toc-ignore", scrollTo: 0 }; options.showAndHide = true; options.smoothScroll = true; // tocify var toc = $("#TOC").tocify(options).data("toc-tocify"); }); </script> <style type="text/css"> #TOC { margin: 25px 0px 20px 0px; } @media (max-width: 768px) { #TOC { position: relative; width: 100%; } } .toc-content { padding-left: 30px; padding-right: 40px; } div.main-container { max-width: 1200px; } div.tocify { width: 20%; max-width: 260px; max-height: 85%; } @media (min-width: 768px) and (max-width: 991px) { div.tocify { width: 25%; } } @media (max-width: 767px) { div.tocify { width: 100%; max-width: none; } } .tocify ul, .tocify li { line-height: 20px; } .tocify-subheader .tocify-item { font-size: 0.90em; padding-left: 25px; text-indent: 0; } .tocify .list-group-item { border-radius: 0px; } </style> <!-- setup 3col/9col grid for toc_float and main content --> <div class="row-fluid"> <div class="col-xs-12 col-sm-4 col-md-3"> <div id="TOC" class="tocify"> </div> </div> <div class="toc-content col-xs-12 col-sm-8 col-md-9"> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <a class="navbar-brand" href="index.html">truncash</a> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> <a href="index.html">Home</a> </li> <li> <a href="about.html">About</a> </li> <li> <a href="license.html">License</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/LSun/truncash"> <span class="fa fa-github"></span> </a> </li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> <div class="fluid-row" id="header"> <h1 class="title toc-ignore"><code>plot_diagnostic</code> in <code>ashr</code></h1> <h4 class="author"><em>Lei Sun</em></h4> <h4 class="date"><em>2017-05-12</em></h4> </div> <!-- The file analysis/chunks.R contains chunks that define default settings shared across the workflowr files. --> <!-- Update knitr chunk options --> <!-- Insert the date the file was last updated --> <p><strong>Last updated:</strong> 2017-12-21</p> <!-- Insert the code version (Git commit SHA1) if Git repository exists and R package git2r is installed --> <p><strong>Code version:</strong> 6e42447</p> <!-- Add your analysis here --> <section id="introduction" class="level2"> <h2>Introduction</h2> <p>This file documents some simulations done for a May 12, 2017, NHS presentation on the diagnostic plots for ASH implemented by <code>ashr::plot_diagnostic()</code>.</p> <pre class="r"><code>library(ashr) library(qvalue)</code></pre> </section> <section id="the-concept-of-a-q-q-plot" class="level2"> <h2>The concept of a Q-Q plot</h2> <pre class="r"><code>set.seed(777) x = rnorm(100) qqnorm(x) qqline(x)</code></pre> <p><img src="figure/plot_diagnostic.rmd/unnamed-chunk-2-1.png" width="672" style="display: block; margin: auto;" /></p> <pre class="r"><code>y = runif(100) qqnorm(y) qqline(y)</code></pre> <p><img src="figure/plot_diagnostic.rmd/unnamed-chunk-2-2.png" width="672" style="display: block; margin: auto;" /></p> </section> <section id="diagnostic-plots-for-ash-applied-to-different-data-sets" class="level2"> <h2>Diagnostic plots for <code>ASH</code> applied to different data sets</h2> <pre class="r"><code>beta = runif(10000) betahat = beta + rnorm(10000) fit = ash(betahat, 1, mixcompdist = "normal", method = "fdr") plot_diagnostic(fit)</code></pre> <p><img src="figure/plot_diagnostic.rmd/unnamed-chunk-3-1.png" width="672" style="display: block; margin: auto;" /></p> <pre><code>Press [enter] to see next plot</code></pre> <p><img src="figure/plot_diagnostic.rmd/unnamed-chunk-3-2.png" width="672" style="display: block; margin: auto;" /></p> <pre><code>Press [enter] to see next plot</code></pre> <p><img src="figure/plot_diagnostic.rmd/unnamed-chunk-3-3.png" width="672" style="display: block; margin: auto;" /></p> <pre><code>Press [enter] to see next plot</code></pre> <p><img src="figure/plot_diagnostic.rmd/unnamed-chunk-3-4.png" width="672" style="display: block; margin: auto;" /></p> <pre class="r"><code>par(mfrow = c(2, 2)) fit = ash(rnorm(10000), 1, mixcompdist = "normal", method = "fdr") plot_diagnostic(fit, breaks = 100)</code></pre> <pre><code>Press [enter] to see next plot</code></pre> <pre><code>Press [enter] to see next plot</code></pre> <pre><code>Press [enter] to see next plot</code></pre> <p><img src="figure/plot_diagnostic.rmd/unnamed-chunk-3-5.png" width="672" style="display: block; margin: auto;" /></p> <pre class="r"><code>beta = sample(c(rnorm(5000, 1.5, 1), rnorm(5000, -1.5, 1))) betahat = beta + rnorm(10000) fit = ash(betahat, 1, mixcompdist = "normal", method = "fdr") plot_diagnostic(fit, breaks = 100)</code></pre> <pre><code>Press [enter] to see next plot</code></pre> <pre><code>Press [enter] to see next plot</code></pre> <pre><code>Press [enter] to see next plot</code></pre> <p><img src="figure/plot_diagnostic.rmd/unnamed-chunk-3-6.png" width="672" style="display: block; margin: auto;" /></p> </section> <section id="the-peculiarities-of-the-correlated-null" class="level2"> <h2>The peculiarities of the correlated null</h2> <pre class="r"><code>z = readRDS("../output/z_null_liver_777_select.RDS") z = z$typical[[5]] hist(z, breaks = 100, prob = TRUE, xlab = "Correlated N(0, 1) Z Scores", ylim = c(0, dnorm(0)), main = "Histogram of Correlated Z Scores") lines(seq(-6, 6, 0.01), dnorm(seq(-6, 6, 0.01)), col = "red")</code></pre> <p><img src="figure/plot_diagnostic.rmd/unnamed-chunk-4-1.png" width="672" style="display: block; margin: auto;" /></p> <pre class="r"><code>hist(z, breaks = 100, prob = TRUE, xlab = "Correlated N(0, 1) Z Scores", ylim = c(0, 0.1), main = "Histogram of Correlated Z Scores: Left Tail", xlim = c(-5, -2.5)) lines(seq(-6, 6, 0.01), dnorm(seq(-6, 6, 0.01)), col = "red")</code></pre> <p><img src="figure/plot_diagnostic.rmd/unnamed-chunk-4-2.png" width="672" style="display: block; margin: auto;" /></p> <pre class="r"><code>pval = (1 - pnorm(abs(z))) * 2 q = qvalue(pval) hist(pval, breaks = 100, main = "Histogram of Correlated Z Scores' p-values", xlab = "p-values", prob = TRUE) abline(h = q$pi0, col = "red", lty = 2) legend("topright", lty = 2, col = "red", expression(paste(hat(pi)[0], " by qvalue")))</code></pre> <p><img src="figure/plot_diagnostic.rmd/unnamed-chunk-4-3.png" width="672" style="display: block; margin: auto;" /></p> </section> <section id="diagnostic-plots-for-ash-applied-to-the-correlated-null." class="level2"> <h2>Diagnostic plots for <code>ASH</code> applied to the correlated null.</h2> <pre class="r"><code>library(ashr) fit = ashr::ash(z, 1, mixcompdist = "normal", method = "fdr") par(mfrow = c(2, 2)) plot_diagnostic(fit, breaks = 100)</code></pre> <pre><code>Press [enter] to see next plot</code></pre> <pre><code>Press [enter] to see next plot</code></pre> <pre><code>Press [enter] to see next plot</code></pre> <p><img src="figure/plot_diagnostic.rmd/unnamed-chunk-5-1.png" width="672" style="display: block; margin: auto;" /></p> </section> <section id="session-information" class="level2"> <h2>Session information</h2> <!-- Insert the session information into the document --> <pre class="r"><code>sessionInfo()</code></pre> <pre><code>R version 3.4.3 (2017-11-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.2 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] qvalue_2.10.0 ashr_2.2-2 loaded via a namespace (and not attached): [1] Rcpp_0.12.14 compiler_3.4.3 git2r_0.20.0 [4] plyr_1.8.4 iterators_1.0.9 tools_3.4.3 [7] digest_0.6.13 evaluate_0.10.1 tibble_1.3.4 [10] gtable_0.2.0 lattice_0.20-35 rlang_0.1.4 [13] Matrix_1.2-12 foreach_1.4.4 yaml_2.1.16 [16] parallel_3.4.3 stringr_1.2.0 knitr_1.17 [19] REBayes_1.2 rprojroot_1.3-1 grid_3.4.3 [22] rmarkdown_1.8 ggplot2_2.2.1 reshape2_1.4.3 [25] magrittr_1.5 backports_1.1.2 scales_0.5.0 [28] codetools_0.2-15 htmltools_0.3.6 MASS_7.3-47 [31] splines_3.4.3 assertthat_0.2.0 colorspace_1.3-2 [34] stringi_1.1.6 Rmosek_8.0.69 lazyeval_0.2.1 [37] pscl_1.5.2 doParallel_1.0.11 munsell_0.4.3 [40] truncnorm_1.0-7 SQUAREM_2017.10-1</code></pre> </section> <hr> <p> This <a href="http://rmarkdown.rstudio.com">R Markdown</a> site was created with <a href="https://github.com/jdblischak/workflowr">workflowr</a> </p> <hr> <!-- To enable disqus, uncomment the section below and provide your disqus_shortname --> <!-- disqus <div id="disqus_thread"></div> <script type="text/javascript"> /* * * CONFIGURATION VARIABLES: EDIT BEFORE PASTING INTO YOUR WEBPAGE * * */ var disqus_shortname = 'rmarkdown'; // required: replace example with your forum shortname /* * * DON'T EDIT BELOW THIS LINE * * */ (function() { var dsq = document.createElement('script'); dsq.type = 'text/javascript'; dsq.async = true; dsq.src = '//' + disqus_shortname + '.disqus.com/embed.js'; (document.getElementsByTagName('head')[0] || document.getElementsByTagName('body')[0]).appendChild(dsq); })(); </script> <noscript>Please enable JavaScript to view the <a href="http://disqus.com/?ref_noscript">comments powered by Disqus.</a></noscript> <a href="http://disqus.com" class="dsq-brlink">comments powered by <span class="logo-disqus">Disqus</span></a> --> </div> </div> </div> <script> // add bootstrap table styles to pandoc tables function bootstrapStylePandocTables() { $('tr.header').parent('thead').parent('table').addClass('table table-condensed'); } $(document).ready(function () { bootstrapStylePandocTables(); }); </script> <!-- dynamically load mathjax for compatibility with self-contained --> <script> (function () { var script = document.createElement("script"); script.type = "text/javascript"; script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"; document.getElementsByTagName("head")[0].appendChild(script); })(); </script> </body> </html>