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re-work pairs a bit
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kylebaron committed Jun 23, 2022
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25 changes: 13 additions & 12 deletions docs/eta.html
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Expand Up @@ -295,10 +295,10 @@ <h2 id="toc-title">Table of contents</h2>
<ul>
<li><a href="#setup" id="toc-setup" class="nav-link active" data-scroll-target="#setup"> <span class="header-section-number">8.1</span> Setup</a></li>
<li><a href="#data-used-on-this-page" id="toc-data-used-on-this-page" class="nav-link" data-scroll-target="#data-used-on-this-page"> <span class="header-section-number">8.2</span> Data used on this page</a></li>
<li><a href="#eta-versus-continuous-eta_cont" id="toc-eta-versus-continuous-eta_cont" class="nav-link" data-scroll-target="#eta-versus-continuous-eta_cont"> <span class="header-section-number">8.3</span> ETA versus continuous <code>[eta_cont]</code></a></li>
<li><a href="#eta-by-categorical-eta_cat" id="toc-eta-by-categorical-eta_cat" class="nav-link" data-scroll-target="#eta-by-categorical-eta_cat"> <span class="header-section-number">8.4</span> ETA by categorical <code>[eta_cat]</code></a></li>
<li><a href="#eta-histograms-eta_hist" id="toc-eta-histograms-eta_hist" class="nav-link" data-scroll-target="#eta-histograms-eta_hist"> <span class="header-section-number">8.5</span> ETA histograms <code>[eta_hist]</code></a></li>
<li><a href="#eta-pairs-eta_pairs" id="toc-eta-pairs-eta_pairs" class="nav-link" data-scroll-target="#eta-pairs-eta_pairs"> <span class="header-section-number">8.6</span> ETA pairs <code>[eta_pairs]</code></a></li>
<li><a href="#versus-continuous-eta_cont" id="toc-versus-continuous-eta_cont" class="nav-link" data-scroll-target="#versus-continuous-eta_cont"> <span class="header-section-number">8.3</span> Versus continuous <code>[eta_cont]</code></a></li>
<li><a href="#by-categorical-eta_cat" id="toc-by-categorical-eta_cat" class="nav-link" data-scroll-target="#by-categorical-eta_cat"> <span class="header-section-number">8.4</span> By categorical <code>[eta_cat]</code></a></li>
<li><a href="#histograms-eta_hist" id="toc-histograms-eta_hist" class="nav-link" data-scroll-target="#histograms-eta_hist"> <span class="header-section-number">8.5</span> Histograms <code>[eta_hist]</code></a></li>
<li><a href="#pairs-eta_pairs" id="toc-pairs-eta_pairs" class="nav-link" data-scroll-target="#pairs-eta_pairs"> <span class="header-section-number">8.6</span> Pairs <code>[eta_pairs]</code></a></li>
</ul>
<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/metrumresearchgroup/pmp-book/blob/main/book/eta.qmd" class="toc-action">View source</a></p><p><a href="https://github.com/metrumresearchgroup/pmp-book/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
</div>
Expand Down Expand Up @@ -367,8 +367,8 @@ <h2 data-number="8.2" class="anchored" data-anchor-id="data-used-on-this-page"><
</div>
</div>
</section>
<section id="eta-versus-continuous-eta_cont" class="level2" data-number="8.3">
<h2 data-number="8.3" class="anchored" data-anchor-id="eta-versus-continuous-eta_cont"><span class="header-section-number">8.3</span> ETA versus continuous <code>[eta_cont]</code></h2>
<section id="versus-continuous-eta_cont" class="level2" data-number="8.3">
<h2 data-number="8.3" class="anchored" data-anchor-id="versus-continuous-eta_cont"><span class="header-section-number">8.3</span> Versus continuous <code>[eta_cont]</code></h2>
<p>Grouped by eta</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="fu">eta_cont</span>(id, <span class="at">x =</span> covs, <span class="at">y =</span> etas[<span class="dv">2</span>]) <span class="sc">%&gt;%</span> </span>
Expand Down Expand Up @@ -396,8 +396,8 @@ <h2 data-number="8.3" class="anchored" data-anchor-id="eta-versus-continuous-eta
</div>
</div>
</section>
<section id="eta-by-categorical-eta_cat" class="level2" data-number="8.4">
<h2 data-number="8.4" class="anchored" data-anchor-id="eta-by-categorical-eta_cat"><span class="header-section-number">8.4</span> ETA by categorical <code>[eta_cat]</code></h2>
<section id="by-categorical-eta_cat" class="level2" data-number="8.4">
<h2 data-number="8.4" class="anchored" data-anchor-id="by-categorical-eta_cat"><span class="header-section-number">8.4</span> By categorical <code>[eta_cat]</code></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb7"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="fu">eta_cat</span>(id, <span class="at">x =</span> <span class="st">"STUDYc//Study type"</span>, <span class="at">y =</span> etas) <span class="sc">%&gt;%</span> </span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">pm_grid</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
Expand All @@ -411,8 +411,8 @@ <h2 data-number="8.4" class="anchored" data-anchor-id="eta-by-categorical-eta_ca
</div>
</div>
</section>
<section id="eta-histograms-eta_hist" class="level2" data-number="8.5">
<h2 data-number="8.5" class="anchored" data-anchor-id="eta-histograms-eta_hist"><span class="header-section-number">8.5</span> ETA histograms <code>[eta_hist]</code></h2>
<section id="histograms-eta_hist" class="level2" data-number="8.5">
<h2 data-number="8.5" class="anchored" data-anchor-id="histograms-eta_hist"><span class="header-section-number">8.5</span> Histograms <code>[eta_hist]</code></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb8"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="fu">eta_hist</span>(id, etas, <span class="at">bins =</span> <span class="dv">10</span>) <span class="sc">%&gt;%</span> </span>
<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">pm_grid</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
Expand All @@ -426,8 +426,9 @@ <h2 data-number="8.5" class="anchored" data-anchor-id="eta-histograms-eta_hist">
</div>
</div>
</section>
<section id="eta-pairs-eta_pairs" class="level2" data-number="8.6">
<h2 data-number="8.6" class="anchored" data-anchor-id="eta-pairs-eta_pairs"><span class="header-section-number">8.6</span> ETA pairs <code>[eta_pairs]</code></h2>
<section id="pairs-eta_pairs" class="level2" data-number="8.6">
<h2 data-number="8.6" class="anchored" data-anchor-id="pairs-eta_pairs"><span class="header-section-number">8.6</span> Pairs <code>[eta_pairs]</code></h2>
<p>See also <a href="pairs.html">Chapter&nbsp;<span>10</span></a> on making pairs plots.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb9"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="fu">eta_pairs</span>(id, etas) </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
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2 changes: 1 addition & 1 deletion docs/index.html
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Expand Up @@ -215,7 +215,7 @@ <h1 class="title d-none d-lg-block">The pmplots Gallery</h1>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">Jun 16, 2022</p>
<p class="date">Jun 23, 2022</p>
</div>
</div>

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32 changes: 21 additions & 11 deletions docs/pairs.html
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Expand Up @@ -197,7 +197,7 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">10</span>&nb
<header id="title-block-header" class="quarto-title-block default page-columns page-full">
<div class="quarto-title-banner page-columns page-full">
<div class="quarto-title column-body">
<h1 class="title d-none d-lg-block"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Pairs plots</span></h1>
<h1 class="title"><span id="sec-pairs" class="quarto-section-identifier d-none d-lg-block"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Pairs plots</span></span></h1>
</div>
</div>

Expand Down Expand Up @@ -294,7 +294,8 @@ <h2 id="toc-title">Table of contents</h2>

<ul>
<li><a href="#general-pairs-plot" id="toc-general-pairs-plot" class="nav-link active" data-scroll-target="#general-pairs-plot"> <span class="header-section-number">10.1</span> General pairs plot</a></li>
<li><a href="#customized-lower-triangle" id="toc-customized-lower-triangle" class="nav-link" data-scroll-target="#customized-lower-triangle"> <span class="header-section-number">10.2</span> Customized lower triangle</a></li>
<li><a href="#eta-pairs-plots" id="toc-eta-pairs-plots" class="nav-link" data-scroll-target="#eta-pairs-plots"> <span class="header-section-number">10.2</span> ETA pairs plots</a></li>
<li><a href="#customized-lower-triangle" id="toc-customized-lower-triangle" class="nav-link" data-scroll-target="#customized-lower-triangle"> <span class="header-section-number">10.3</span> Customized lower triangle</a></li>
</ul>
<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/metrumresearchgroup/pmp-book/blob/main/book/pairs.qmd" class="toc-action">View source</a></p><p><a href="https://github.com/metrumresearchgroup/pmp-book/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
</div>
Expand All @@ -306,22 +307,29 @@ <h2 id="toc-title">Table of contents</h2>

<section id="general-pairs-plot" class="level2" data-number="10.1">
<h2 data-number="10.1" class="anchored" data-anchor-id="general-pairs-plot"><span class="header-section-number">10.1</span> General pairs plot</h2>
<p>This is a simple wrapper around <code>GGally::ggpairs</code> with some customizations that have been developed internally at Metrum over the years.</p>
<p>This is a simple wrapper around <code>GGally::ggpairs</code> with some customizations that have been developed internally at MetrumRG over the years.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>cols <span class="ot">&lt;-</span> <span class="fu">c</span>(<span class="st">"WT//Weight"</span>, <span class="st">"ALB//Albumin"</span>, <span class="st">"SCR//Serum creat"</span>)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">pairs_plot</span>(id, cols)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<div id="fig-pairs" class="quarto-figure quarto-figure-center anchored">
<figure class="figure">
<p><img src="pairs_files/figure-html/unnamed-chunk-1-1.png" class="img-fluid figure-img" width="576"></p>
<p></p><figcaption aria-hidden="true" class="figure-caption"></figcaption><p></p>
<figure class="figure">
<img src="pairs_files/figure-html/fig-pairs-1.png" class="img-fluid figure-img" width="480">
</figure>
<p></p><figcaption aria-hidden="true" class="figure-caption">Figure 10.1: General pairs plot.</figcaption><p></p>
</figure>
</div>
</div>
</div>
<p>One customization we’ve added is the annotation on the upper triangle, which is the <code>complete.obs</code> correlation between <code>x</code> and <code>y</code> along with the number of observations.</p>
</section>
<section id="eta-pairs-plots" class="level2" data-number="10.2">
<h2 data-number="10.2" class="anchored" data-anchor-id="eta-pairs-plots"><span class="header-section-number">10.2</span> ETA pairs plots</h2>
<p>There is also a function called <code>eta_pairs()</code> that is identical to the <code>pairs_plot()</code> function. This might be helpful to remember the function name but there is no difference in functionality between <code>eta_pairs()</code> and <code>pairs_plot()</code>.</p>
</section>
<section id="customized-lower-triangle" class="level2" data-number="10.2">
<h2 data-number="10.2" class="anchored" data-anchor-id="customized-lower-triangle"><span class="header-section-number">10.2</span> Customized lower triangle</h2>
<section id="customized-lower-triangle" class="level2" data-number="10.3">
<h2 data-number="10.3" class="anchored" data-anchor-id="customized-lower-triangle"><span class="header-section-number">10.3</span> Customized lower triangle</h2>
<p>Pass a function that customizes the scatter plots on the lower triangle. This function should accept a gg object and add a geom to it</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb2"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>my_lower <span class="ot">&lt;-</span> <span class="cf">function</span>(p) {</span>
Expand All @@ -332,10 +340,12 @@ <h2 data-number="10.2" class="anchored" data-anchor-id="customized-lower-triangl
<div class="cell">
<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">pairs_plot</span>(id, <span class="fu">c</span>(<span class="st">"WT"</span>, <span class="st">"ALB"</span>), <span class="at">lower_plot =</span> my_lower)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<div id="fig-pairs-custom-lower" class="quarto-figure quarto-figure-center anchored">
<figure class="figure">
<p><img src="pairs_files/figure-html/unnamed-chunk-3-1.png" class="img-fluid figure-img" width="576"></p>
<p></p><figcaption aria-hidden="true" class="figure-caption"></figcaption><p></p>
<figure class="figure">
<img src="pairs_files/figure-html/fig-pairs-custom-lower-1.png" class="img-fluid figure-img" width="480">
</figure>
<p></p><figcaption aria-hidden="true" class="figure-caption">Figure 10.2: Pairs plot with customized lower triangle.</figcaption><p></p>
</figure>
</div>
</div>
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45 changes: 26 additions & 19 deletions docs/search.json
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Expand Up @@ -175,32 +175,32 @@
"text": "8.2 Data used on this page\nWe are exclusively using a data set that is one row per individual\n\n\n\n\n\n\nPreview the data used on this page\n\n\n\n\n\n\nhead(as.data.frame(id), n=3)\n\n C NUM ID SUBJ TIME SEQ CMT EVID AMT DV AGE WT CRCL ALB BMI AAG\n1 NA 1 1 1 0 0 1 1 5 0 28.03 55.16 114.45 4.40 21.67 106.36\n2 NA 17 2 2 0 0 1 1 5 0 34.67 51.74 100.54 3.88 23.85 61.79\n3 NA 33 3 3 0 0 1 1 5 0 26.24 54.84 99.05 3.84 19.43 50.10\n SCR AST ALT HT CP TAFD TAD LDOS MDV BLQ PHASE STUDY RF 102 IPRED\n1 1.14 11.88 12.66 159.55 0 0 0 5 1 0 1 1 norm 1 0\n2 0.98 15.09 27.44 147.27 0 0 0 5 1 0 1 1 norm 1 0\n3 1.05 35.85 31.26 168.02 0 0 0 5 1 0 1 1 norm 1 0\n CWRESI NPDE PRED RES WRES CL V2 KA ETA1 ETA2 ETA3\n1 0 0 0 0 0 2.5927 40.287 1.4520 -0.075300 -0.184030 -0.095308\n2 0 0 0 0 0 1.9339 32.925 1.6044 0.024467 -0.321810 -0.340470\n3 0 0 0 0 0 3.2407 50.967 1.4195 -0.097942 0.056922 0.132150\n DOSE STUDYc CPc\n1 5 SAD normal\n2 5 SAD normal\n3 5 SAD normal"
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"objectID": "eta.html#versus-continuous-eta_cont",
"href": "eta.html#versus-continuous-eta_cont",
"title": "8  ETA plots",
"section": "8.3 ETA versus continuous [eta_cont]",
"text": "8.3 ETA versus continuous [eta_cont]\nGrouped by eta\n\neta_cont(id, x = covs, y = etas[2]) %>% \n pm_grid()\n\n\n\n\n\n\n\n\n\nGrouped by covariate\n\neta_cont(id, x = covs[1], y = etas) %>% \n pm_grid(ncol = 2)"
"section": "8.3 Versus continuous [eta_cont]",
"text": "8.3 Versus continuous [eta_cont]\nGrouped by eta\n\neta_cont(id, x = covs, y = etas[2]) %>% \n pm_grid()\n\n\n\n\n\n\n\n\n\nGrouped by covariate\n\neta_cont(id, x = covs[1], y = etas) %>% \n pm_grid(ncol = 2)"
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"title": "8  ETA plots",
"section": "8.4 ETA by categorical [eta_cat]",
"text": "8.4 ETA by categorical [eta_cat]\n\neta_cat(id, x = \"STUDYc//Study type\", y = etas) %>% \n pm_grid()"
"section": "8.4 By categorical [eta_cat]",
"text": "8.4 By categorical [eta_cat]\n\neta_cat(id, x = \"STUDYc//Study type\", y = etas) %>% \n pm_grid()"
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"title": "8  ETA plots",
"section": "8.5 ETA histograms [eta_hist]",
"text": "8.5 ETA histograms [eta_hist]\n\neta_hist(id, etas, bins = 10) %>% \n pm_grid()"
"section": "8.5 Histograms [eta_hist]",
"text": "8.5 Histograms [eta_hist]\n\neta_hist(id, etas, bins = 10) %>% \n pm_grid()"
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"title": "8  ETA plots",
"section": "8.6 ETA pairs [eta_pairs]",
"text": "8.6 ETA pairs [eta_pairs]\n\neta_pairs(id, etas)"
"section": "8.6 Pairs [eta_pairs]",
"text": "8.6 Pairs [eta_pairs]\nSee also Chapter 10 on making pairs plots.\n\neta_pairs(id, etas)"
},
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"objectID": "wrap.html",
Expand Down Expand Up @@ -263,14 +263,21 @@
"href": "pairs.html",
"title": "10  Pairs plots",
"section": "",
"text": "This is a simple wrapper around GGally::ggpairs with some customizations that have been developed internally at Metrum over the years.\n\ncols <- c(\"WT//Weight\", \"ALB//Albumin\", \"SCR//Serum creat\")\npairs_plot(id, cols)"
"text": "This is a simple wrapper around GGally::ggpairs with some customizations that have been developed internally at MetrumRG over the years.\n\ncols <- c(\"WT//Weight\", \"ALB//Albumin\", \"SCR//Serum creat\")\npairs_plot(id, cols)\n\n\n\n\n\n\nFigure 10.1: General pairs plot.\n\n\n\n\nOne customization we’ve added is the annotation on the upper triangle, which is the complete.obs correlation between x and y along with the number of observations."
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"section": "10.2 ETA pairs plots",
"text": "10.2 ETA pairs plots\nThere is also a function called eta_pairs() that is identical to the pairs_plot() function. This might be helpful to remember the function name but there is no difference in functionality between eta_pairs() and pairs_plot()."
},
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"href": "pairs.html#customized-lower-triangle",
"title": "10  Pairs plots",
"section": "10.2 Customized lower triangle",
"text": "10.2 Customized lower triangle\nPass a function that customizes the scatter plots on the lower triangle. This function should accept a gg object and add a geom to it\n\nmy_lower <- function(p) {\n p + geom_point(aes(color = STUDYc)) + \n geom_smooth(se = FALSE, color = \"black\")\n}\n\n\npairs_plot(id, c(\"WT\", \"ALB\"), lower_plot = my_lower)"
"section": "10.3 Customized lower triangle",
"text": "10.3 Customized lower triangle\nPass a function that customizes the scatter plots on the lower triangle. This function should accept a gg object and add a geom to it\n\nmy_lower <- function(p) {\n p + geom_point(aes(color = STUDYc)) + \n geom_smooth(se = FALSE, color = \"black\")\n}\n\n\npairs_plot(id, c(\"WT\", \"ALB\"), lower_plot = my_lower)\n\n\n\n\n\n\nFigure 10.2: Pairs plot with customized lower triangle."
},
{
"objectID": "vectorized.html",
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