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index.html
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<!DOCTYPE html>
<html lang="en"><head>
<script src="index_files/libs/clipboard/clipboard.min.js"></script>
<script src="index_files/libs/quarto-html/tabby.min.js"></script>
<script src="index_files/libs/quarto-html/popper.min.js"></script>
<script src="index_files/libs/quarto-html/tippy.umd.min.js"></script>
<link href="index_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="index_files/libs/quarto-html/quarto-html.min.css" rel="stylesheet" data-mode="light">
<link href="index_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles"><meta charset="utf-8">
<meta name="generator" content="quarto-1.0.36">
<title>index</title>
<meta name="apple-mobile-web-app-capable" content="yes">
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no, minimal-ui">
<link rel="stylesheet" href="index_files/libs/revealjs/dist/reset.css">
<link rel="stylesheet" href="index_files/libs/revealjs/dist/reveal.css">
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
span.underline{text-decoration: underline;}
div.column{display: inline-block; vertical-align: top; width: 50%;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
pre > code.sourceCode > span:empty { height: 1.2em; }
.sourceCode { overflow: visible; }
code.sourceCode > span { color: inherit; text-decoration: inherit; }
div.sourceCode { margin: 1em 0; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
pre > code.sourceCode { white-space: pre-wrap; }
pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
}
pre.numberSource code
{ counter-reset: source-line 0; }
pre.numberSource code > span
{ position: relative; left: -4em; counter-increment: source-line; }
pre.numberSource code > span > a:first-child::before
{ content: counter(source-line);
position: relative; left: -1em; text-align: right; vertical-align: baseline;
border: none; display: inline-block;
-webkit-touch-callout: none; -webkit-user-select: none;
-khtml-user-select: none; -moz-user-select: none;
-ms-user-select: none; user-select: none;
padding: 0 4px; width: 4em;
color: #767676;
}
pre.numberSource { margin-left: 3em; border-left: 1px solid #767676; padding-left: 4px; }
div.sourceCode
{ color: #545454; background-color: #fefefe; }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span { color: #545454; } /* Normal */
code span.al { color: #7928a1; } /* Alert */
code span.an { color: #696969; } /* Annotation */
code span.at { color: #aa5d00; } /* Attribute */
code span.bn { color: #7928a1; } /* BaseN */
code span.bu { } /* BuiltIn */
code span.cf { color: #d91e18; } /* ControlFlow */
code span.ch { color: #008000; } /* Char */
code span.cn { color: #d91e18; } /* Constant */
code span.co { color: #696969; } /* Comment */
code span.cv { color: #696969; font-style: italic; } /* CommentVar */
code span.do { color: #696969; font-style: italic; } /* Documentation */
code span.dt { color: #7928a1; } /* DataType */
code span.dv { color: #7928a1; } /* DecVal */
code span.er { color: #7928a1; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #aa5d00; } /* Float */
code span.fu { color: #06287e; } /* Function */
code span.im { } /* Import */
code span.in { color: #696969; } /* Information */
code span.kw { color: #d91e18; } /* Keyword */
code span.op { color: #007faa; } /* Operator */
code span.ot { color: #d91e18; } /* Other */
code span.pp { color: #7928a1; } /* Preprocessor */
code span.sc { color: #007faa; } /* SpecialChar */
code span.ss { color: #008000; } /* SpecialString */
code span.st { color: #008000; } /* String */
code span.va { color: #aa5d00; } /* Variable */
code span.vs { color: #008000; } /* VerbatimString */
code span.wa { color: #696969; font-style: italic; } /* Warning */
</style>
<link rel="stylesheet" href="index_files/libs/revealjs/dist/theme/quarto.css" id="theme">
<link href="index_files/libs/revealjs/plugin/quarto-line-highlight/line-highlight.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/reveal-menu/menu.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/reveal-menu/quarto-menu.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/reveal-chalkboard/font-awesome/css/all.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/reveal-chalkboard/style.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/quarto-support/footer.css" rel="stylesheet">
<style type="text/css">
.callout {
margin-top: 1em;
margin-bottom: 1em;
border-radius: .25rem;
}
.callout.callout-style-simple {
padding: 0em 0.5em;
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
display: flex;
}
.callout.callout-style-default {
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
}
.callout .callout-body-container {
flex-grow: 1;
}
.callout.callout-style-simple .callout-body {
font-size: 1rem;
font-weight: 400;
}
.callout.callout-style-default .callout-body {
font-size: 0.9rem;
font-weight: 400;
}
.callout.callout-captioned.callout-style-simple .callout-body {
margin-top: 0.2em;
}
.callout:not(.callout-captioned) .callout-body {
display: flex;
}
.callout:not(.no-icon).callout-captioned.callout-style-simple .callout-content {
padding-left: 1.6em;
}
.callout.callout-captioned .callout-header {
padding-top: 0.2em;
margin-bottom: -0.2em;
}
.callout.callout-captioned .callout-caption p {
margin-top: 0.5em;
margin-bottom: 0.5em;
}
.callout.callout-captioned.callout-style-simple .callout-content p {
margin-top: 0;
}
.callout.callout-captioned.callout-style-default .callout-content p {
margin-top: 0.7em;
}
.callout.callout-style-simple div.callout-caption {
border-bottom: none;
font-size: .9rem;
font-weight: 600;
opacity: 75%;
}
.callout.callout-style-default div.callout-caption {
border-bottom: none;
font-weight: 600;
opacity: 85%;
font-size: 0.9rem;
padding-left: 0.5em;
padding-right: 0.5em;
}
.callout.callout-style-default div.callout-content {
padding-left: 0.5em;
padding-right: 0.5em;
}
.callout.callout-style-simple .callout-icon::before {
height: 1rem;
width: 1rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 1rem 1rem;
}
.callout.callout-style-default .callout-icon::before {
height: 0.9rem;
width: 0.9rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 0.9rem 0.9rem;
}
.callout-caption {
display: flex
}
.callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
.callout.no-icon::before {
display: none !important;
}
.callout.callout-captioned .callout-body > .callout-content > :last-child {
margin-bottom: 0.5rem;
}
.callout.callout-captioned .callout-icon::before {
margin-top: .5rem;
padding-right: .5rem;
}
.callout:not(.callout-captioned) .callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
/* Callout Types */
div.callout-note {
border-left-color: #4582ec !important;
}
div.callout-note .callout-icon::before {
background-image: url('data:image/png;base64,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');
}
div.callout-note.callout-style-default .callout-caption {
background-color: #dae6fb
}
div.callout-important {
border-left-color: #d9534f !important;
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<section class="slide level2">
<br> <br> <br> <br> <br>
<h1>
How to plot general scientific figures in <code>R</code>
</h1>
<hr>
<h3>
Li Zhiwei <br>Capital Medical University
</h3>
<h3>
2022-09-19
</h3>
<p><br></p>
<h3>
<p><svg aria-hidden="true" role="img" viewbox="0 0 496 512" style="height:1em;width:0.97em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:black;overflow:visible;position:relative;"><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"></path></svg> <a href="https://github.com/lizhiwei1994/How-to-plot-in-R">github.com/lizhiwei1994/How-to-plot-in-R</a></p>
<p><svg aria-hidden="true" role="img" viewbox="0 0 576 512" style="height:1em;width:1.12em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:black;overflow:visible;position:relative;"><path d="M160 448c-25.6 0-51.2-22.4-64-32-64-44.8-83.2-60.8-96-70.4V480c0 17.67 14.33 32 32 32h256c17.67 0 32-14.33 32-32V345.6c-12.8 9.6-32 25.6-96 70.4-12.8 9.6-38.4 32-64 32zm128-192H32c-17.67 0-32 14.33-32 32v16c25.6 19.2 22.4 19.2 115.2 86.4 9.6 6.4 28.8 25.6 44.8 25.6s35.2-19.2 44.8-22.4c92.8-67.2 89.6-67.2 115.2-86.4V288c0-17.67-14.33-32-32-32zm256-96H224c-17.67 0-32 14.33-32 32v32h96c33.21 0 60.59 25.42 63.71 57.82l.29-.22V416h192c17.67 0 32-14.33 32-32V192c0-17.67-14.33-32-32-32zm-32 128h-64v-64h64v64zm-352-96c0-35.29 28.71-64 64-64h224V32c0-17.67-14.33-32-32-32H96C78.33 0 64 14.33 64 32v192h96v-32z"></path></svg> <a href="[email protected]">[email protected]</a></p>
</h3></section>
<section id="content" class="slide level2">
<h2>Content</h2>
<p><br> <br></p>
<ul>
<li class="fragment">Table 1 <br> <br></li>
<li class="fragment">Forestplot <br> <br></li>
<li class="fragment">A combined plot</li>
</ul>
</section>
<section>
<section id="table-1" class="title-slide slide level1 center">
<h1>Table 1</h1>
</section>
<section id="what-is-table-1" class="slide level2">
<h2>What is <code>Table-1</code>?</h2>
<div class="columns">
<div class="column" style="width:35%;">
<p>It is standard practice in epidemiology and related fields that the first table of any journal article, referred to as “Table 1”, is a table that presents descriptive statistics of <strong>baseline characteristics</strong> of the study population <strong>stratified by exposure</strong>.</p>
</div><div class="column" style="width:31%;">
<p><img data-src="images/paper_table1.png"></p>
</div><div class="column" style="width:31%;">
<p><img data-src="images/paper_table2.png"></p>
</div>
</div>
</section>
<section id="creat-table-1-using-tableone-package" class="slide level2">
<h2>Creat table 1 using <code>tableone</code> package</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb1" data-code-line-numbers="1|2"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a><span class="fu">library</span>(tableone) <span class="co"># main package</span></span>
<span id="cb1-2"><a href="#cb1-2"></a>dat <span class="ot">=</span> <span class="fu">read.csv</span>(<span class="st">'examples/data/table1_data.csv'</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="fragment">
<p><img data-src="images/data_tableone.png"></p>
</div>
</section>
<section id="creat-table-1-using-tableone-package-1" class="slide level2">
<h2>Creat table 1 using <code>tableone</code> package</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb2" data-code-line-numbers="|1-2|3|4-7|8-9|10"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a>listVars <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"Age"</span>, <span class="st">"Gender"</span>, <span class="st">"Cholesterol"</span>, <span class="st">"SystolicBP"</span>, </span>
<span id="cb2-2"><a href="#cb2-2"></a> <span class="st">"BMI"</span>, <span class="st">"Smoking"</span>, <span class="st">"Education"</span>)</span>
<span id="cb2-3"><a href="#cb2-3"></a>catVars <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"Smoking"</span>,<span class="st">"Education"</span>)</span>
<span id="cb2-4"><a href="#cb2-4"></a>table1 <span class="ot"><-</span> <span class="fu">CreateTableOne</span>(<span class="at">vars =</span> listVars, </span>
<span id="cb2-5"><a href="#cb2-5"></a> <span class="at">data =</span> dat, </span>
<span id="cb2-6"><a href="#cb2-6"></a> <span class="at">factorVars =</span> catVars, </span>
<span id="cb2-7"><a href="#cb2-7"></a> <span class="at">strata =</span> <span class="fu">c</span>(<span class="st">"Gender"</span>))</span>
<span id="cb2-8"><a href="#cb2-8"></a>a <span class="ot"><-</span> <span class="fu">print</span>(table1, <span class="at">quote =</span> <span class="cn">TRUE</span>, <span class="at">noSpaces =</span> <span class="cn">TRUE</span>)</span>
<span id="cb2-9"><a href="#cb2-9"></a>a <span class="ot"><-</span> <span class="fu">as.data.frame</span>(a)</span>
<span id="cb2-10"><a href="#cb2-10"></a><span class="fu">write.csv</span>(a, <span class="st">'result_tableone.csv'</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="fragment">
<p><img data-src="images/result_tableone.png"></p>
</div>
</section>
<section id="creat-table-1-using-arsenal-package" class="slide level2">
<h2>Creat table 1 using <code>arsenal</code> package</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb3" data-code-line-numbers="1|2-3|4-5"><pre class="sourceCode numberSource r code-overflow-wrap number-lines code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a><span class="fu">library</span>(arsenal)</span>
<span id="cb3-2"><a href="#cb3-2"></a>tab1 <span class="ot"><-</span> <span class="fu">tableby</span>(Gender <span class="sc">~</span> Age <span class="sc">+</span> Cholesterol <span class="sc">+</span> SystolicBP <span class="sc">+</span> </span>
<span id="cb3-3"><a href="#cb3-3"></a> BMI <span class="sc">+</span> Smoking<span class="sc">+</span> Education, <span class="at">data =</span> dat)</span>
<span id="cb3-4"><a href="#cb3-4"></a>sum_tab1 <span class="ot"><-</span> <span class="fu">summary</span>(tab1, <span class="at">text=</span><span class="cn">TRUE</span>)</span>
<span id="cb3-5"><a href="#cb3-5"></a>sum_tab1</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="cell fragment">
<div class="cell-output cell-output-stdout">
<pre><code>
| | Female (N=143) | Male (N=107) | Total (N=250) | p value|
|:------------|:-----------------:|:-----------------:|:-----------------:|-------:|
|Age | | | | 0.191|
|- Mean (SD) | 56.938 (8.055) | 58.253 (7.550) | 57.501 (7.854) | |
|- Range | 33.700 - 77.500 | 45.700 - 79.300 | 33.700 - 79.300 | |
|Cholesterol | | | | 0.637|
|- N-Miss | 1 | 1 | 2 | |
|- Mean (SD) | 224.929 (25.104) | 223.414 (24.808) | 224.281 (24.939) | |
|- Range | 157.500 - 288.700 | 170.300 - 303.000 | 157.500 - 303.000 | |
|SystolicBP | | | | 0.305|
|- Mean (SD) | 144.946 (10.995) | 146.272 (8.710) | 145.514 (10.083) | |
|- Range | 117.500 - 175.400 | 124.600 - 165.200 | 117.500 - 175.400 | |
|BMI | | | | 0.864|
|- N-Miss | 1 | 0 | 1 | |
|- Mean (SD) | 26.746 (4.592) | 26.842 (4.088) | 26.787 (4.374) | |
|- Range | 13.800 - 38.700 | 14.500 - 35.900 | 13.800 - 38.700 | |
|Smoking | | | | 0.572|
|- | 2 (1.4%) | 1 (0.9%) | 3 (1.2%) | |
|- No | 104 (72.7%) | 72 (67.3%) | 176 (70.4%) | |
|- Yes | 37 (25.9%) | 34 (31.8%) | 71 (28.4%) | |
|Education | | | | 0.289|
|- High | 56 (39.2%) | 52 (48.6%) | 108 (43.2%) | |
|- Low | 45 (31.5%) | 26 (24.3%) | 71 (28.4%) | |
|- Medium | 42 (29.4%) | 29 (27.1%) | 71 (28.4%) | |</code></pre>
</div>
</div>
</section>
<section id="creat-table-1-using-arsenal-package-1" class="slide level2">
<h2>Creat table 1 using <code>arsenal</code> package</h2>
<div class="sourceCode" id="cb5"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1"></a>sum_tab1_out <span class="ot"><-</span> <span class="fu">summary</span>(tab1, <span class="at">text=</span><span class="cn">NULL</span>) <span class="sc">%>%</span> <span class="fu">as.data.frame</span>()</span>
<span id="cb5-2"><a href="#cb5-2"></a><span class="fu">write.csv</span>(sum_tab1_out, <span class="st">'code/table1/result_arsenal_table1.csv'</span>, <span class="at">row.names =</span> F)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<img data-src="images/result_tableby.png" class="r-stretch"></section>
<section id="creat-table-1-using-arsenal-package-2" class="slide level2">
<h2>Creat table 1 using <code>arsenal</code> package</h2>
<h4 id="tableby.control-function">tableby.control() function</h4>
<p>Control test and summary settings for the <em>tableby()</em> function.</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1"></a><span class="fu">tableby.control</span>(</span>
<span id="cb6-2"><a href="#cb6-2"></a> <span class="at">test =</span> <span class="cn">TRUE</span>,</span>
<span id="cb6-3"><a href="#cb6-3"></a> <span class="at">total =</span> <span class="cn">TRUE</span>,</span>
<span id="cb6-4"><a href="#cb6-4"></a> <span class="at">total.pos =</span> <span class="fu">c</span>(<span class="st">"after"</span>, <span class="st">"before"</span>),</span>
<span id="cb6-5"><a href="#cb6-5"></a> <span class="at">test.pname =</span> <span class="cn">NULL</span>,</span>
<span id="cb6-6"><a href="#cb6-6"></a> <span class="at">numeric.simplify =</span> <span class="cn">FALSE</span>,</span>
<span id="cb6-7"><a href="#cb6-7"></a> <span class="at">cat.simplify =</span> <span class="cn">FALSE</span>,</span>
<span id="cb6-8"><a href="#cb6-8"></a> <span class="at">cat.droplevels =</span> <span class="cn">FALSE</span>,</span>
<span id="cb6-9"><a href="#cb6-9"></a> <span class="at">ordered.simplify =</span> <span class="cn">FALSE</span>,</span>
<span id="cb6-10"><a href="#cb6-10"></a> <span class="at">date.simplify =</span> <span class="cn">FALSE</span>,</span>
<span id="cb6-11"><a href="#cb6-11"></a> <span class="at">numeric.test =</span> <span class="st">"anova"</span>,</span>
<span id="cb6-12"><a href="#cb6-12"></a> <span class="at">cat.test =</span> <span class="st">"chisq"</span>,</span>
<span id="cb6-13"><a href="#cb6-13"></a> <span class="at">ordered.test =</span> <span class="st">"trend"</span>,</span>
<span id="cb6-14"><a href="#cb6-14"></a> <span class="at">surv.test =</span> <span class="st">"logrank"</span>,</span>
<span id="cb6-15"><a href="#cb6-15"></a> <span class="at">date.test =</span> <span class="st">"kwt"</span>,</span>
<span id="cb6-16"><a href="#cb6-16"></a> <span class="at">selectall.test =</span> <span class="st">"notest"</span>,</span>
<span id="cb6-17"><a href="#cb6-17"></a> <span class="at">test.always =</span> <span class="cn">FALSE</span>,</span>
<span id="cb6-18"><a href="#cb6-18"></a> <span class="at">numeric.stats =</span> <span class="fu">c</span>(<span class="st">"Nmiss"</span>, <span class="st">"meansd"</span>, <span class="st">"range"</span>),</span>
<span id="cb6-19"><a href="#cb6-19"></a> <span class="at">cat.stats =</span> <span class="fu">c</span>(<span class="st">"Nmiss"</span>, <span class="st">"countpct"</span>),</span>
<span id="cb6-20"><a href="#cb6-20"></a> <span class="at">ordered.stats =</span> <span class="fu">c</span>(<span class="st">"Nmiss"</span>, <span class="st">"countpct"</span>),</span>
<span id="cb6-21"><a href="#cb6-21"></a> <span class="at">surv.stats =</span> <span class="fu">c</span>(<span class="st">"Nmiss"</span>, <span class="st">"Nevents"</span>, <span class="st">"medSurv"</span>),</span>
<span id="cb6-22"><a href="#cb6-22"></a> <span class="at">date.stats =</span> <span class="fu">c</span>(<span class="st">"Nmiss"</span>, <span class="st">"median"</span>, <span class="st">"range"</span>),</span>
<span id="cb6-23"><a href="#cb6-23"></a> <span class="at">selectall.stats =</span> <span class="fu">c</span>(<span class="st">"Nmiss"</span>, <span class="st">"countpct"</span>),</span>
<span id="cb6-24"><a href="#cb6-24"></a> <span class="at">stats.labels =</span> <span class="fu">list</span>(),</span>
<span id="cb6-25"><a href="#cb6-25"></a> <span class="at">digits =</span> 3L,</span>
<span id="cb6-26"><a href="#cb6-26"></a> <span class="at">digits.count =</span> 0L,</span>
<span id="cb6-27"><a href="#cb6-27"></a> <span class="at">digits.pct =</span> 1L,</span>
<span id="cb6-28"><a href="#cb6-28"></a> <span class="at">digits.p =</span> 3L,</span>
<span id="cb6-29"><a href="#cb6-29"></a> <span class="at">format.p =</span> <span class="cn">TRUE</span>,</span>
<span id="cb6-30"><a href="#cb6-30"></a> <span class="at">digits.n =</span> 0L,</span>
<span id="cb6-31"><a href="#cb6-31"></a> <span class="at">conf.level =</span> <span class="fl">0.95</span>,</span>
<span id="cb6-32"><a href="#cb6-32"></a> <span class="at">wilcox.correct =</span> <span class="cn">FALSE</span>,</span>
<span id="cb6-33"><a href="#cb6-33"></a> <span class="at">wilcox.exact =</span> <span class="cn">NULL</span>,</span>
<span id="cb6-34"><a href="#cb6-34"></a> <span class="at">chisq.correct =</span> <span class="cn">FALSE</span>,</span>
<span id="cb6-35"><a href="#cb6-35"></a> <span class="at">simulate.p.value =</span> <span class="cn">FALSE</span>,</span>
<span id="cb6-36"><a href="#cb6-36"></a> <span class="at">B =</span> <span class="dv">2000</span>,</span>
<span id="cb6-37"><a href="#cb6-37"></a> <span class="at">times =</span> <span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>,</span>
<span id="cb6-38"><a href="#cb6-38"></a> ...</span>
<span id="cb6-39"><a href="#cb6-39"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</section>
<section id="creat-table-1-using-arsenal-package-3" class="slide level2">
<h2>Creat table 1 using <code>arsenal</code> package</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb7" data-code-line-numbers="|1|4"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1"></a>mycontrols <span class="ot"><-</span> <span class="fu">tableby.control</span>(<span class="at">numeric.stats =</span> <span class="fu">c</span>(<span class="st">"meansd"</span>))</span>
<span id="cb7-2"><a href="#cb7-2"></a>tab1 <span class="ot"><-</span> <span class="fu">tableby</span>(Gender <span class="sc">~</span> Age <span class="sc">+</span> Cholesterol <span class="sc">+</span> SystolicBP <span class="sc">+</span> </span>
<span id="cb7-3"><a href="#cb7-3"></a> BMI <span class="sc">+</span> Smoking<span class="sc">+</span> Education, <span class="at">data =</span> dat,</span>
<span id="cb7-4"><a href="#cb7-4"></a> <span class="at">control =</span> mycontrols)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="fragment">
<p><img data-src="images/result_tableby_control.png" style="width:60.0%"></p>
</div>
</section>
<section id="application-tableby-in-our-paper" class="slide level2">
<h2>Application <code>tableby()</code> in our paper</h2>
<div class="sourceCode" id="cb8"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1"></a>tab1 <span class="ot"><-</span> <span class="fu">tableby</span>(disease_type_en<span class="sc">~</span>sex<span class="sc">+</span>age_group2<span class="sc">+</span>continent<span class="sc">+</span>defi_year,<span class="at">data=</span>data2)</span>
<span id="cb8-2"><a href="#cb8-2"></a>sum_tab1_out <span class="ot"><-</span> <span class="fu">summary</span>(tab1, <span class="at">text=</span><span class="cn">NULL</span>) <span class="sc">%>%</span> <span class="fu">as.data.frame</span>()</span>
<span id="cb8-3"><a href="#cb8-3"></a>writexl<span class="sc">::</span><span class="fu">write_xlsx</span>(sum_tab1_out, <span class="st">'table_1.new.xlsx'</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p><img data-src="images/application_table1.png" width="1400" height="800"></p>
</section>
<section id="application-tableby-in-our-paper-1" class="slide level2">
<h2>Application <code>tableby()</code> in our paper</h2>
<img data-src="images/application_table1-2.png" class="r-stretch"></section>
<section id="resources" class="slide level2">
<h2>Resources</h2>
<p><br> <br> 1. <a href="https://cran.r-project.org/web/packages/table1/vignettes/table1-examples.html">Using the table1 Package to Create HTML Tables of Descriptive Statistics</a> <br> <br> <br> 2. <a href="https://cran.r-project.org/web/packages/tableone/vignettes/introduction.html">Introduction to tableone</a> <br> <br> <br> 3. <a href="https://cran.r-project.org/web/packages/arsenal/vignettes/tableby.html">The tableby function</a></p>
</section></section>
<section>
<section id="forestplot" class="title-slide slide level1 center">
<h1>Forestplot</h1>
</section>
<section id="what-is-forestplot" class="slide level2">
<h2>What is <code>forestplot</code>?</h2>
<div class="columns">
<div class="column" style="width:55%;">
<p>A <strong>forest plot</strong>, also known as a blobbogram, is a graphical display of <strong>estimated results from a number of scientific studies addressing the same question</strong>, along with the overall results.</p>
<p><img data-src="images/paper_fp.png"></p>
</div><div class="column" style="width:5%;">
</div><div class="column" style="width:40%;">
<p><img data-src="images/paper_fp2.png" style="width:120.0%"></p>
</div>
</div>
</section>
<section id="data-preparation" class="slide level2">
<h2>Data Preparation</h2>
<div class="columns">
<div class="column" style="width:60%;">
<div class="cell">
<div class="sourceCode cell-code" id="cb9" data-code-line-numbers="|1|3"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1"></a><span class="fu">library</span>(forestplot) <span class="co"># main package</span></span>
<span id="cb9-2"><a href="#cb9-2"></a>fp <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"examples/data/forestplot.csv"</span>,</span>
<span id="cb9-3"><a href="#cb9-3"></a> <span class="at">header =</span> F)</span>
<span id="cb9-4"><a href="#cb9-4"></a>fp</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code> V1 V2 V3 V4 V5
1 Disease Percentage Changes (95% CI) NA NA NA
2 Arrhythmia NA NA NA
3 Age NA NA NA
4 <65 -2.14(-4.02 to -0.27) -2.14 -4.02 -0.27
5 >=65 -0.31(-1.8 to 1.19) -0.31 -1.80 1.19
6 Sex NA NA NA
7 Male -1.22(-3.1 to 0.65) -1.22 -3.10 0.65
8 Female -0.55(-2.23 to 1.12) -0.55 -2.23 1.12
9 NA NA NA
10 Cerebrovascular NA NA NA
11 Age NA NA NA
12 <65 -0.11(-0.62 to 0.4) -0.11 -0.62 0.40
13 >=65 -0.05(-0.51 to 0.41) -0.05 -0.51 0.41
14 Sex NA NA NA
15 Male 0.12(-0.36 to 0.59) 0.12 -0.36 0.59
16 Female -0.3(-0.86 to 0.25) -0.30 -0.86 0.25
17 NA NA NA
18 CHD NA NA NA
19 Age NA NA NA
20 <65 1.67(0.68 to 2.67) 1.67 0.68 2.67
21 >=65 0.84(0.09 to 1.58) 0.84 0.09 1.58
22 Sex NA NA NA
23 Male 1.28(0.42 to 2.15) 1.28 0.42 2.15
24 Female 1.01(0.18 to 1.83) 1.01 0.18 1.83
25 NA NA NA
26 Heart failure NA NA NA
27 Age NA NA NA
28 <65 1.23(-2.65 to 5.11) 1.23 -2.65 5.11
29 >=65 -0.67(-2.65 to 1.32) -0.67 -2.65 1.32
30 Sex NA NA NA
31 Male 0.54(-1.95 to 3.03) 0.54 -1.95 3.03
32 Female -1.09(-3.6 to 1.42) -1.09 -3.60 1.42</code></pre>
</div>
</div>
</div><div class="column" style="width:40%;">
<p><img data-src="images/data.png" style="width:140.0%"></p>
</div>
</div>
</section>
<section id="a-simple-forestplot" class="slide level2">
<h2>A <code>simple</code> forestplot</h2>
<div class="cell columns column-output-location">
<div class="column">
<div class="sourceCode cell-code" id="cb11" data-code-line-numbers="|2|3|4|5"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1"></a><span class="fu">forestplot</span>(</span>
<span id="cb11-2"><a href="#cb11-2"></a> <span class="at">labeltext =</span> <span class="fu">as.matrix</span>(fp[,<span class="dv">1</span><span class="sc">:</span><span class="dv">2</span>]),<span class="co">#设置文本列</span></span>
<span id="cb11-3"><a href="#cb11-3"></a> <span class="at">mean =</span> fp<span class="sc">$</span>V3, <span class="co">#均值</span></span>
<span id="cb11-4"><a href="#cb11-4"></a> <span class="at">lower =</span> fp<span class="sc">$</span>V4,<span class="co">#95%下限</span></span>
<span id="cb11-5"><a href="#cb11-5"></a> <span class="at">upper =</span> fp<span class="sc">$</span>V5 <span class="co">#95%上限</span></span>
<span id="cb11-6"><a href="#cb11-6"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column">
<div class="cell-output-display">
<p><img data-src="index_files/figure-revealjs/simple%20fp-1.png" width="960"></p>
</div>
</div>
</div>
</section>
<section id="a-complex-forestplot" class="slide level2">
<h2>A <code>complex</code> forestplot</h2>
<div class="cell columns column-output-location">
<div class="column">
<div class="sourceCode cell-code" id="cb12" data-code-line-numbers="2-5|6|7|8-11|12-22|23|24-27|28-39"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb12-1"><a href="#cb12-1"></a><span class="fu">forestplot</span>(</span>
<span id="cb12-2"><a href="#cb12-2"></a> <span class="at">labeltext =</span> <span class="fu">as.matrix</span>(fp[,<span class="dv">1</span><span class="sc">:</span><span class="dv">2</span>]),<span class="co">#设置文本列#</span></span>
<span id="cb12-3"><a href="#cb12-3"></a> <span class="at">mean =</span> fp<span class="sc">$</span>V3, <span class="co">#绘图用的均值#</span></span>
<span id="cb12-4"><a href="#cb12-4"></a> <span class="at">lower =</span> fp<span class="sc">$</span>V4,</span>
<span id="cb12-5"><a href="#cb12-5"></a> <span class="at">upper =</span> fp<span class="sc">$</span>V5,</span>
<span id="cb12-6"><a href="#cb12-6"></a> <span class="at">is.summary =</span> <span class="fu">c</span>(T,<span class="fu">rep</span>(<span class="fu">c</span>(T,F,F,F,F,F,F,F),<span class="dv">3</span>),T,F,F,F,F,F,F), <span class="co">#某行是否加粗显示#</span></span>
<span id="cb12-7"><a href="#cb12-7"></a> <span class="at">zero =</span> <span class="dv">0</span>, </span>
<span id="cb12-8"><a href="#cb12-8"></a> <span class="at">col =</span> <span class="fu">fpColors</span>(<span class="at">box=</span><span class="st">'blue'</span>, <span class="co">#均值点的颜色#</span></span>
<span id="cb12-9"><a href="#cb12-9"></a> <span class="at">summary=</span><span class="st">'#8B008B'</span>, <span class="co">#加粗行的颜色#</span></span>
<span id="cb12-10"><a href="#cb12-10"></a> <span class="at">lines =</span> <span class="st">'black'</span>, <span class="co">#95%CI线的颜色#</span></span>
<span id="cb12-11"><a href="#cb12-11"></a> <span class="at">zero =</span> <span class="st">'skyblue'</span>), <span class="co">#无效线的颜色#</span></span>
<span id="cb12-12"><a href="#cb12-12"></a> <span class="at">boxsize =</span> <span class="fl">0.5</span>, <span class="co">#均值点图形的大小#</span></span>
<span id="cb12-13"><a href="#cb12-13"></a> <span class="at">lineheight =</span> <span class="fu">unit</span>(<span class="dv">8</span>,<span class="st">'mm'</span>), <span class="co">#行距#</span></span>
<span id="cb12-14"><a href="#cb12-14"></a> <span class="at">colgap =</span> <span class="fu">unit</span>(<span class="dv">2</span>,<span class="st">'mm'</span>), <span class="co">#列宽#</span></span>
<span id="cb12-15"><a href="#cb12-15"></a> <span class="at">lwd.zero =</span> <span class="dv">1</span>,<span class="co"># 无效线宽度</span></span>
<span id="cb12-16"><a href="#cb12-16"></a> <span class="at">lwd.ci =</span> <span class="dv">1</span>, <span class="co"># 95%CI线宽度</span></span>
<span id="cb12-17"><a href="#cb12-17"></a> <span class="at">xlab =</span> <span class="st">'The estimate'</span>, <span class="co">#x轴的标题#</span></span>
<span id="cb12-18"><a href="#cb12-18"></a> <span class="at">lwd.xaxis =</span> <span class="dv">1</span>, <span class="co">#x 轴的刻度#</span></span>
<span id="cb12-19"><a href="#cb12-19"></a> <span class="at">lty.ci =</span> <span class="dv">1</span>,<span class="co"># 95%CI线类型</span></span>
<span id="cb12-20"><a href="#cb12-20"></a> <span class="at">ci.vertices =</span> T, <span class="co">#是否在95%CI两头添加箭头#</span></span>
<span id="cb12-21"><a href="#cb12-21"></a> <span class="at">ci.vertices.height =</span> <span class="fl">0.15</span>, <span class="co">#箭头的长短#</span></span>
<span id="cb12-22"><a href="#cb12-22"></a> <span class="at">graph.pos =</span> <span class="dv">2</span>, <span class="co">#森林图画在第几列#</span></span>
<span id="cb12-23"><a href="#cb12-23"></a> <span class="at">fn.ci_norm =</span> fpDrawNormalCI, <span class="co">#均值点的形状，Normal是方形，Circel是圆形，Diamod是菱形，Ponit是点#</span></span>
<span id="cb12-24"><a href="#cb12-24"></a> <span class="at">txt_gp =</span> <span class="fu">fpTxtGp</span>(</span>
<span id="cb12-25"><a href="#cb12-25"></a> <span class="at">ticks =</span> <span class="fu">gpar</span>(<span class="at">cex =</span> <span class="dv">1</span>), <span class="co">#坐标轴上刻度的大小#</span></span>
<span id="cb12-26"><a href="#cb12-26"></a> <span class="at">xlab =</span> <span class="fu">gpar</span>(<span class="at">cex =</span> <span class="dv">1</span>), <span class="co">#x轴名称的大小#</span></span>
<span id="cb12-27"><a href="#cb12-27"></a> <span class="at">label =</span> <span class="fu">gpar</span>(<span class="at">cex =</span> <span class="dv">1</span>)), <span class="co">#开始用labeltext（）函数设置的文本字体的大小#</span></span>
<span id="cb12-28"><a href="#cb12-28"></a> <span class="at">hrzl_lines=</span><span class="fu">list</span>( <span class="st">"1"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">1</span>, <span class="at">col=</span><span class="st">"black"</span>,<span class="at">fill=</span><span class="st">"black"</span>), <span class="co">#在表的第1行上边加一条黑线#</span></span>
<span id="cb12-29"><a href="#cb12-29"></a> <span class="st">"2"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">1</span>, <span class="at">col=</span><span class="st">"black"</span>,<span class="at">fill=</span><span class="st">"black"</span>),<span class="co">#在表的第2行上边加一条黑线#</span></span>
<span id="cb12-30"><a href="#cb12-30"></a> <span class="st">"33"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">1</span>, <span class="at">col=</span><span class="st">"black"</span>,<span class="at">fill=</span><span class="st">"black"</span>),<span class="co">#在表的第33行上边加一条黑线</span></span>
<span id="cb12-31"><a href="#cb12-31"></a> <span class="co">#在表的第5行上边加一条宽度为60，线型两端为butt，颜色为#898988，透明度为55的线段，线段分布在表格的2-3列</span></span>
<span id="cb12-32"><a href="#cb12-32"></a> <span class="st">"5"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">60</span>,<span class="at">lineend=</span><span class="st">"butt"</span>,<span class="at">columns=</span><span class="fu">c</span>(<span class="dv">2</span><span class="sc">:</span><span class="dv">3</span>),<span class="at">col=</span><span class="st">"#89898855"</span>),</span>
<span id="cb12-33"><a href="#cb12-33"></a> <span class="st">"8"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">60</span>,<span class="at">lineend=</span><span class="st">"butt"</span>,<span class="at">columns=</span><span class="fu">c</span>(<span class="dv">2</span><span class="sc">:</span><span class="dv">3</span>),<span class="at">col=</span><span class="st">"#89898855"</span>),</span>
<span id="cb12-34"><a href="#cb12-34"></a> <span class="st">"13"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">60</span>,<span class="at">lineend=</span><span class="st">"butt"</span>,<span class="at">columns=</span><span class="fu">c</span>(<span class="dv">2</span><span class="sc">:</span><span class="dv">3</span>),<span class="at">col=</span><span class="st">"#89898855"</span>),</span>
<span id="cb12-35"><a href="#cb12-35"></a> <span class="st">"16"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">60</span>,<span class="at">lineend=</span><span class="st">"butt"</span>,<span class="at">columns=</span><span class="fu">c</span>(<span class="dv">2</span><span class="sc">:</span><span class="dv">3</span>),<span class="at">col=</span><span class="st">"#89898855"</span>),</span>
<span id="cb12-36"><a href="#cb12-36"></a> <span class="st">"21"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">60</span>,<span class="at">lineend=</span><span class="st">"butt"</span>,<span class="at">columns=</span><span class="fu">c</span>(<span class="dv">2</span><span class="sc">:</span><span class="dv">3</span>),<span class="at">col=</span><span class="st">"#89898855"</span>),</span>
<span id="cb12-37"><a href="#cb12-37"></a> <span class="st">"24"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">60</span>,<span class="at">lineend=</span><span class="st">"butt"</span>,<span class="at">columns=</span><span class="fu">c</span>(<span class="dv">2</span><span class="sc">:</span><span class="dv">3</span>),<span class="at">col=</span><span class="st">"#89898855"</span>),</span>
<span id="cb12-38"><a href="#cb12-38"></a> <span class="st">"29"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">60</span>,<span class="at">lineend=</span><span class="st">"butt"</span>,<span class="at">columns=</span><span class="fu">c</span>(<span class="dv">2</span><span class="sc">:</span><span class="dv">3</span>),<span class="at">col=</span><span class="st">"#89898855"</span>),</span>
<span id="cb12-39"><a href="#cb12-39"></a> <span class="st">"32"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">60</span>,<span class="at">lineend=</span><span class="st">"butt"</span>,<span class="at">columns=</span><span class="fu">c</span>(<span class="dv">2</span><span class="sc">:</span><span class="dv">3</span>),<span class="at">col=</span><span class="st">"#89898855"</span>)</span>
<span id="cb12-40"><a href="#cb12-40"></a> )</span>
<span id="cb12-41"><a href="#cb12-41"></a> </span>
<span id="cb12-42"><a href="#cb12-42"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column">
<div class="cell-output-display">
<p><img data-src="index_files/figure-revealjs/complex%20fp-1.png" width="960"></p>
</div>
</div>
</div>
</section>
<section id="forestplot-with-different-color" class="slide level2">
<h2>Forestplot with <code>different color</code></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb13" data-code-line-numbers="|4-5"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1"></a>fn <span class="ot"><-</span> <span class="fu">local</span>({</span>
<span id="cb13-2"><a href="#cb13-2"></a> i <span class="ot">=</span> <span class="dv">0</span></span>
<span id="cb13-3"><a href="#cb13-3"></a> no_lines <span class="ot"><-</span> <span class="fu">sum</span>(<span class="sc">!</span><span class="fu">is.na</span>(fp<span class="sc">$</span>V3))</span>
<span id="cb13-4"><a href="#cb13-4"></a> b_clrs <span class="ot">=</span> <span class="fu">colorRampPalette</span>(<span class="at">colors=</span><span class="fu">c</span>(<span class="fu">rep</span>(<span class="st">'blue'</span>, <span class="dv">8</span>), <span class="fu">rep</span>(<span class="st">'red'</span>, <span class="dv">4</span>), <span class="fu">rep</span>(<span class="st">'blue'</span>, <span class="dv">4</span>)))(no_lines)</span>
<span id="cb13-5"><a href="#cb13-5"></a> l_clrs <span class="ot">=</span> <span class="fu">colorRampPalette</span>(<span class="at">colors=</span><span class="fu">c</span>(<span class="fu">rep</span>(<span class="st">'blue'</span>, <span class="dv">8</span>), <span class="fu">rep</span>(<span class="st">'red'</span>, <span class="dv">4</span>), <span class="fu">rep</span>(<span class="st">'blue'</span>, <span class="dv">4</span>)))(no_lines)</span>
<span id="cb13-6"><a href="#cb13-6"></a> </span>
<span id="cb13-7"><a href="#cb13-7"></a> <span class="cf">function</span>(..., clr.line, clr.marker){</span>
<span id="cb13-8"><a href="#cb13-8"></a> i <span class="ot"><<-</span> i <span class="sc">+</span> <span class="dv">1</span></span>
<span id="cb13-9"><a href="#cb13-9"></a> <span class="fu">fpDrawNormalCI</span>(..., <span class="at">clr.line =</span> l_clrs[i], <span class="at">clr.marker =</span> b_clrs[i])</span>
<span id="cb13-10"><a href="#cb13-10"></a> }</span>
<span id="cb13-11"><a href="#cb13-11"></a>})</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p><br></p>
<div class="cell" data-layout-align="center">
<div class="sourceCode cell-code" id="cb14" data-code-line-numbers="23"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb14-1"><a href="#cb14-1"></a><span class="fu">forestplot</span>(</span>
<span id="cb14-2"><a href="#cb14-2"></a> <span class="at">labeltext =</span> <span class="fu">as.matrix</span>(fp[,<span class="dv">1</span><span class="sc">:</span><span class="dv">2</span>]),<span class="co">#设置文本列#</span></span>
<span id="cb14-3"><a href="#cb14-3"></a> <span class="at">mean =</span> fp<span class="sc">$</span>V3, <span class="co">#绘图用的均值#</span></span>
<span id="cb14-4"><a href="#cb14-4"></a> <span class="at">lower =</span> fp<span class="sc">$</span>V4,</span>
<span id="cb14-5"><a href="#cb14-5"></a> <span class="at">upper =</span> fp<span class="sc">$</span>V5,</span>
<span id="cb14-6"><a href="#cb14-6"></a> <span class="at">is.summary =</span> <span class="fu">c</span>(T,<span class="fu">rep</span>(<span class="fu">c</span>(T,F,F,F,F,F,F,F),<span class="dv">3</span>),T,F,F,F,F,F,F), <span class="co">#某行是否加粗显示#</span></span>
<span id="cb14-7"><a href="#cb14-7"></a> <span class="at">zero =</span> <span class="dv">0</span>, </span>
<span id="cb14-8"><a href="#cb14-8"></a> <span class="at">col =</span> <span class="fu">fpColors</span>(<span class="at">box=</span><span class="st">'blue'</span>, <span class="co">#均值点的颜色#</span></span>
<span id="cb14-9"><a href="#cb14-9"></a> <span class="at">summary=</span><span class="st">'#8B008B'</span>, <span class="co">#加粗行的颜色#</span></span>
<span id="cb14-10"><a href="#cb14-10"></a> <span class="at">lines =</span> <span class="st">'black'</span>, <span class="co">#95%CI线的颜色#</span></span>
<span id="cb14-11"><a href="#cb14-11"></a> <span class="at">zero =</span> <span class="st">'skyblue'</span>), <span class="co">#无效线的颜色#</span></span>
<span id="cb14-12"><a href="#cb14-12"></a> <span class="at">boxsize =</span> <span class="fl">0.5</span>, <span class="co">#均值点图形的大小#</span></span>
<span id="cb14-13"><a href="#cb14-13"></a> <span class="at">lineheight =</span> <span class="fu">unit</span>(<span class="dv">8</span>,<span class="st">'mm'</span>), <span class="co">#行距#</span></span>
<span id="cb14-14"><a href="#cb14-14"></a> <span class="at">colgap =</span> <span class="fu">unit</span>(<span class="dv">2</span>,<span class="st">'mm'</span>), <span class="co">#列宽#</span></span>
<span id="cb14-15"><a href="#cb14-15"></a> <span class="at">lwd.zero =</span> <span class="dv">1</span>,<span class="co"># 无效线宽度</span></span>
<span id="cb14-16"><a href="#cb14-16"></a> <span class="at">lwd.ci =</span> <span class="dv">1</span>, <span class="co"># 95%CI线宽度</span></span>
<span id="cb14-17"><a href="#cb14-17"></a> <span class="at">xlab =</span> <span class="st">'The estimate'</span>, <span class="co">#x轴的标题#</span></span>
<span id="cb14-18"><a href="#cb14-18"></a> <span class="at">lwd.xaxis =</span> <span class="dv">1</span>, <span class="co">#x 轴的刻度#</span></span>
<span id="cb14-19"><a href="#cb14-19"></a> <span class="at">lty.ci =</span> <span class="dv">1</span>,<span class="co"># 95%CI线类型</span></span>
<span id="cb14-20"><a href="#cb14-20"></a> <span class="at">ci.vertices =</span> T, <span class="co">#是否在95%CI两头添加箭头#</span></span>
<span id="cb14-21"><a href="#cb14-21"></a> <span class="at">ci.vertices.height =</span> <span class="fl">0.15</span>, <span class="co">#箭头的长短#</span></span>
<span id="cb14-22"><a href="#cb14-22"></a> <span class="at">graph.pos =</span> <span class="dv">2</span>, <span class="co">#森林图画在第几列#</span></span>
<span id="cb14-23"><a href="#cb14-23"></a> <span class="at">fn.ci_norm =</span> fn, <span class="co">#均值点的形状，Normal是方形，Circel是圆形，Diamod是菱形，Ponit是点#</span></span>
<span id="cb14-24"><a href="#cb14-24"></a> <span class="at">txt_gp =</span> <span class="fu">fpTxtGp</span>(</span>
<span id="cb14-25"><a href="#cb14-25"></a> <span class="at">ticks =</span> <span class="fu">gpar</span>(<span class="at">cex =</span> <span class="dv">1</span>), <span class="co">#坐标轴上刻度的大小#</span></span>
<span id="cb14-26"><a href="#cb14-26"></a> <span class="at">xlab =</span> <span class="fu">gpar</span>(<span class="at">cex =</span> <span class="dv">1</span>), <span class="co">#x轴名称的大小#</span></span>
<span id="cb14-27"><a href="#cb14-27"></a> <span class="at">label =</span> <span class="fu">gpar</span>(<span class="at">cex =</span> <span class="dv">1</span>)), <span class="co">#开始用labeltext（）函数设置的文本字体的大小#</span></span>
<span id="cb14-28"><a href="#cb14-28"></a> <span class="at">hrzl_lines=</span><span class="fu">list</span>( <span class="st">"1"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">1</span>, <span class="at">col=</span><span class="st">"black"</span>,<span class="at">fill=</span><span class="st">"black"</span>), <span class="co">#在表的第1行上边加一条黑线#</span></span>
<span id="cb14-29"><a href="#cb14-29"></a> <span class="st">"2"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">1</span>, <span class="at">col=</span><span class="st">"black"</span>,<span class="at">fill=</span><span class="st">"black"</span>),<span class="co">#在表的第2行上边加一条黑线#</span></span>
<span id="cb14-30"><a href="#cb14-30"></a> <span class="st">"33"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">1</span>, <span class="at">col=</span><span class="st">"black"</span>,<span class="at">fill=</span><span class="st">"black"</span>),<span class="co">#在表的第33行上边加一条黑线</span></span>
<span id="cb14-31"><a href="#cb14-31"></a> <span class="co">#在表的第5行上边加一条宽度为60，线型两端为butt，颜色为#898988，透明度为55的线段，线段分布在表格的2-3列</span></span>
<span id="cb14-32"><a href="#cb14-32"></a> <span class="st">"5"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">60</span>,<span class="at">lineend=</span><span class="st">"butt"</span>,<span class="at">columns=</span><span class="fu">c</span>(<span class="dv">2</span><span class="sc">:</span><span class="dv">3</span>),<span class="at">col=</span><span class="st">"#89898855"</span>),</span>
<span id="cb14-33"><a href="#cb14-33"></a> <span class="st">"8"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">60</span>,<span class="at">lineend=</span><span class="st">"butt"</span>,<span class="at">columns=</span><span class="fu">c</span>(<span class="dv">2</span><span class="sc">:</span><span class="dv">3</span>),<span class="at">col=</span><span class="st">"#89898855"</span>),</span>
<span id="cb14-34"><a href="#cb14-34"></a> <span class="st">"13"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">60</span>,<span class="at">lineend=</span><span class="st">"butt"</span>,<span class="at">columns=</span><span class="fu">c</span>(<span class="dv">2</span><span class="sc">:</span><span class="dv">3</span>),<span class="at">col=</span><span class="st">"#89898855"</span>),</span>
<span id="cb14-35"><a href="#cb14-35"></a> <span class="st">"16"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">60</span>,<span class="at">lineend=</span><span class="st">"butt"</span>,<span class="at">columns=</span><span class="fu">c</span>(<span class="dv">2</span><span class="sc">:</span><span class="dv">3</span>),<span class="at">col=</span><span class="st">"#89898855"</span>),</span>
<span id="cb14-36"><a href="#cb14-36"></a> <span class="st">"21"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">60</span>,<span class="at">lineend=</span><span class="st">"butt"</span>,<span class="at">columns=</span><span class="fu">c</span>(<span class="dv">2</span><span class="sc">:</span><span class="dv">3</span>),<span class="at">col=</span><span class="st">"#89898855"</span>),</span>
<span id="cb14-37"><a href="#cb14-37"></a> <span class="st">"24"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">60</span>,<span class="at">lineend=</span><span class="st">"butt"</span>,<span class="at">columns=</span><span class="fu">c</span>(<span class="dv">2</span><span class="sc">:</span><span class="dv">3</span>),<span class="at">col=</span><span class="st">"#89898855"</span>),</span>
<span id="cb14-38"><a href="#cb14-38"></a> <span class="st">"29"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">60</span>,<span class="at">lineend=</span><span class="st">"butt"</span>,<span class="at">columns=</span><span class="fu">c</span>(<span class="dv">2</span><span class="sc">:</span><span class="dv">3</span>),<span class="at">col=</span><span class="st">"#89898855"</span>),</span>
<span id="cb14-39"><a href="#cb14-39"></a> <span class="st">"32"</span> <span class="ot">=</span> <span class="fu">gpar</span>(<span class="at">lty=</span><span class="dv">1</span>,<span class="at">lwd=</span><span class="dv">60</span>,<span class="at">lineend=</span><span class="st">"butt"</span>,<span class="at">columns=</span><span class="fu">c</span>(<span class="dv">2</span><span class="sc">:</span><span class="dv">3</span>),<span class="at">col=</span><span class="st">"#89898855"</span>)</span>
<span id="cb14-40"><a href="#cb14-40"></a> )</span>
<span id="cb14-41"><a href="#cb14-41"></a> </span>
<span id="cb14-42"><a href="#cb14-42"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="forestplot-with-different-color-output" class="slide level2 output-location-slide"><h2>Forestplot with <code>different color</code></h2><div class="cell output-location-slide" data-layout-align="center">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="index_files/figure-revealjs/colored%20fp-1.png" width="960"></p>
</figure>
</div>
</div>
</div></section><section id="creat-forestplot-using-ggplot2-package" class="slide level2">
<h2>Creat forestplot using <code>ggplot2</code> package</h2>
<img data-src="images/ggfp9.png" class="r-stretch"></section>
<section id="step-0-data-preparation" class="slide level2">
<h2>Step 0: <code>Data Preparation</code></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb15"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb15-1"><a href="#cb15-1"></a><span class="fu">library</span>(ggplot2)</span>
<span id="cb15-2"><a href="#cb15-2"></a>dat <span class="ot">=</span> <span class="fu">read.csv</span>(<span class="st">"examples/data/forestplot_ggplot.csv"</span>)</span>
<span id="cb15-3"><a href="#cb15-3"></a>dat</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code> Disease group PC PC_95_LOW PC_95_UP
1 Arrhythmia <65 -2.14 -4.02 -0.27
2 Arrhythmia >=65 -0.31 -1.80 1.19
3 Arrhythmia Male -1.22 -3.10 0.65
4 Arrhythmia Female -0.55 -2.23 1.12
5 Cerebrovascular <65 -0.11 -0.62 0.40
6 Cerebrovascular >=65 -0.05 -0.51 0.41
7 Cerebrovascular Male 0.12 -0.36 0.59
8 Cerebrovascular Female -0.30 -0.86 0.25
9 CHD <65 1.67 0.68 2.67
10 CHD >=65 0.84 0.09 1.58
11 CHD Male 1.28 0.42 2.15
12 CHD Female 1.01 0.18 1.83
13 Heart failure <65 1.23 -2.65 5.11
14 Heart failure >=65 -0.67 -2.65 1.32
15 Heart failure Male 0.54 -1.95 3.03
16 Heart failure Female -1.09 -3.60 1.42</code></pre>
</div>
</div>
</section>
<section id="step-1-mapping-data" class="slide level2">
<h2>Step 1: <code>Mapping data</code></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb17" data-code-line-numbers="1"><pre class="sourceCode numberSource r fourlinesish number-lines code-with-copy"><code class="sourceCode r"><span id="cb17-1"><a href="#cb17-1"></a><span class="fu">ggplot</span>(dat, <span class="fu">aes</span>(<span class="at">x =</span> Disease, <span class="at">y =</span> PC, <span class="at">shape =</span> group, <span class="at">fill =</span> group, <span class="at">colour =</span> group, <span class="at">group =</span> group)) </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<img data-src="index_files/figure-revealjs/ggplot%20Step%201%20blank-1.png" width="960" class="r-stretch"></section>
<section id="step-2-add-point" class="slide level2">
<h2>Step 2: <code>Add point</code></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb18" data-code-line-numbers="2"><pre class="sourceCode numberSource r fourlinesish number-lines code-with-copy"><code class="sourceCode r"><span id="cb18-1"><a href="#cb18-1"></a><span class="fu">ggplot</span>(dat, <span class="fu">aes</span>(<span class="at">x =</span> Disease, <span class="at">y =</span> PC, <span class="at">shape =</span> group, <span class="at">fill =</span> group, <span class="at">colour =</span> group, <span class="at">group =</span> group)) <span class="sc">+</span></span>
<span id="cb18-2"><a href="#cb18-2"></a><span class="fu">geom_point</span>(<span class="at">position =</span> <span class="fu">position_dodge</span>(.<span class="dv">7</span>), <span class="at">size =</span> <span class="dv">2</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<img data-src="index_files/figure-revealjs/ggplot%20Step%202%20point-1.png" width="960" class="r-stretch"></section>
<section id="step-3-add-errorbar" class="slide level2">
<h2>Step 3: <code>Add errorbar</code></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb19" data-code-line-numbers="3"><pre class="sourceCode numberSource r fourlinesish number-lines code-with-copy"><code class="sourceCode r"><span id="cb19-1"><a href="#cb19-1"></a><span class="fu">ggplot</span>(dat, <span class="fu">aes</span>(<span class="at">x =</span> Disease, <span class="at">y =</span> PC, <span class="at">shape =</span> group, <span class="at">fill =</span> group, <span class="at">colour =</span> group, <span class="at">group =</span> group)) <span class="sc">+</span></span>
<span id="cb19-2"><a href="#cb19-2"></a><span class="fu">geom_point</span>(<span class="at">position =</span> <span class="fu">position_dodge</span>(.<span class="dv">7</span>), <span class="at">size =</span> <span class="dv">2</span>)<span class="sc">+</span></span>
<span id="cb19-3"><a href="#cb19-3"></a><span class="fu">geom_errorbar</span>(<span class="fu">aes</span>(<span class="at">ymin =</span> PC_95_LOW, <span class="at">ymax =</span> PC_95_UP), <span class="at">position =</span> <span class="fu">position_dodge</span>(.<span class="dv">7</span>), <span class="at">width =</span> <span class="fl">0.3</span>, <span class="at">size =</span> <span class="fl">0.6</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<img data-src="index_files/figure-revealjs/ggplot%20Step%203%20errorbar-1.png" width="960" class="r-stretch"></section>
<section id="step-4-add-horizontal-line" class="slide level2">
<h2>Step 4: <code>Add horizontal line</code></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb20" data-code-line-numbers="4"><pre class="sourceCode numberSource r fourlinesish number-lines code-with-copy"><code class="sourceCode r"><span id="cb20-1"><a href="#cb20-1"></a><span class="fu">ggplot</span>(dat, <span class="fu">aes</span>(<span class="at">x =</span> Disease, <span class="at">y =</span> PC, <span class="at">shape =</span> group, <span class="at">fill =</span> group, <span class="at">colour =</span> group, <span class="at">group =</span> group)) <span class="sc">+</span></span>
<span id="cb20-2"><a href="#cb20-2"></a><span class="fu">geom_point</span>(<span class="at">position =</span> <span class="fu">position_dodge</span>(.<span class="dv">7</span>), <span class="at">size =</span> <span class="dv">2</span>) <span class="sc">+</span></span>
<span id="cb20-3"><a href="#cb20-3"></a><span class="fu">geom_errorbar</span>(<span class="fu">aes</span>(<span class="at">ymin =</span> PC_95_LOW, <span class="at">ymax =</span> PC_95_UP), <span class="at">position =</span> <span class="fu">position_dodge</span>(.<span class="dv">7</span>), <span class="at">width =</span> <span class="fl">0.3</span>, <span class="at">size =</span> <span class="fl">0.6</span>)<span class="sc">+</span></span>
<span id="cb20-4"><a href="#cb20-4"></a><span class="fu">geom_hline</span>(<span class="at">yintercept =</span> <span class="dv">0</span>, <span class="at">linetype =</span> <span class="st">"dashed"</span>, <span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="fl">0.5</span>) </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<img data-src="index_files/figure-revealjs/Step%204%20hline-1.png" width="960" class="r-stretch"></section>
<section id="step-5-set-axis" class="slide level2">
<h2>Step 5: <code>Set axis</code></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb21" data-code-line-numbers="5-6"><pre class="sourceCode numberSource r fourlinesish number-lines code-with-copy"><code class="sourceCode r"><span id="cb21-1"><a href="#cb21-1"></a><span class="fu">ggplot</span>(dat, <span class="fu">aes</span>(<span class="at">x =</span> Disease, <span class="at">y =</span> PC, <span class="at">shape =</span> group, <span class="at">fill =</span> group, <span class="at">colour =</span> group, <span class="at">group =</span> group)) <span class="sc">+</span></span>
<span id="cb21-2"><a href="#cb21-2"></a><span class="fu">geom_hline</span>(<span class="at">yintercept =</span> <span class="dv">0</span>, <span class="at">linetype =</span> <span class="st">"dashed"</span>, <span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="fl">0.5</span>) <span class="sc">+</span></span>
<span id="cb21-3"><a href="#cb21-3"></a><span class="fu">geom_point</span>(<span class="at">position =</span> <span class="fu">position_dodge</span>(.<span class="dv">7</span>), <span class="at">size =</span> <span class="dv">2</span>) <span class="sc">+</span></span>
<span id="cb21-4"><a href="#cb21-4"></a><span class="fu">geom_errorbar</span>(<span class="fu">aes</span>(<span class="at">ymin =</span> PC_95_LOW, <span class="at">ymax =</span> PC_95_UP), <span class="at">position =</span> <span class="fu">position_dodge</span>(.<span class="dv">7</span>), <span class="at">width =</span> <span class="fl">0.3</span>, <span class="at">size =</span> <span class="fl">0.6</span>) <span class="sc">+</span></span>
<span id="cb21-5"><a href="#cb21-5"></a><span class="fu">xlab</span>(<span class="st">""</span>)<span class="sc">+</span></span>
<span id="cb21-6"><a href="#cb21-6"></a><span class="fu">scale_y_continuous</span>(<span class="st">"Percentage Change (%) and 95% CI"</span>, <span class="at">labels =</span> scales<span class="sc">::</span><span class="fu">number_format</span>(<span class="at">accuracy =</span> <span class="fl">0.01</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<img data-src="index_files/figure-revealjs/Step%205%20axis%20setting-1.png" width="960" class="r-stretch"></section>
<section id="step-6-set-point-shape-and-color" class="slide level2">
<h2>Step 6: <code>Set point shape and color</code></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb22" data-code-line-numbers="7-9"><pre class="sourceCode numberSource r fourlinesish number-lines code-with-copy"><code class="sourceCode r"><span id="cb22-1"><a href="#cb22-1"></a><span class="fu">ggplot</span>(dat, <span class="fu">aes</span>(<span class="at">x =</span> Disease, <span class="at">y =</span> PC, <span class="at">shape =</span> group, <span class="at">fill =</span> group, <span class="at">colour =</span> group, <span class="at">group =</span> group)) <span class="sc">+</span></span>
<span id="cb22-2"><a href="#cb22-2"></a><span class="fu">geom_hline</span>(<span class="at">yintercept =</span> <span class="dv">0</span>, <span class="at">linetype =</span> <span class="st">"dashed"</span>, <span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="fl">0.5</span>) <span class="sc">+</span></span>
<span id="cb22-3"><a href="#cb22-3"></a><span class="fu">geom_point</span>(<span class="at">position =</span> <span class="fu">position_dodge</span>(.<span class="dv">7</span>), <span class="at">size =</span> <span class="dv">2</span>) <span class="sc">+</span></span>
<span id="cb22-4"><a href="#cb22-4"></a><span class="fu">geom_errorbar</span>(<span class="fu">aes</span>(<span class="at">ymin =</span> PC_95_LOW, <span class="at">ymax =</span> PC_95_UP), <span class="at">position =</span> <span class="fu">position_dodge</span>(.<span class="dv">7</span>), <span class="at">width =</span> <span class="fl">0.3</span>, <span class="at">size =</span> <span class="fl">0.6</span>) <span class="sc">+</span></span>
<span id="cb22-5"><a href="#cb22-5"></a><span class="fu">xlab</span>(<span class="st">""</span>)<span class="sc">+</span></span>
<span id="cb22-6"><a href="#cb22-6"></a><span class="fu">scale_y_continuous</span>(<span class="st">"Percentage Change (%) and 95% CI"</span>, <span class="at">labels =</span> scales<span class="sc">::</span><span class="fu">number_format</span>(<span class="at">accuracy =</span> <span class="fl">0.01</span>))<span class="sc">+</span></span>
<span id="cb22-7"><a href="#cb22-7"></a><span class="fu">scale_shape_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="dv">16</span>, <span class="dv">23</span>, <span class="dv">24</span>, <span class="dv">15</span>), <span class="at">guide =</span> <span class="fu">guide_legend</span>(<span class="at">title =</span> <span class="cn">NULL</span>)) <span class="sc">+</span></span>
<span id="cb22-8"><a href="#cb22-8"></a><span class="fu">scale_fill_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"#ea4a50"</span>, <span class="st">"#325788"</span>, <span class="st">"dodgerblue"</span>, <span class="st">"coral1"</span>), <span class="at">guide =</span> <span class="fu">guide_legend</span>(<span class="at">title =</span> <span class="cn">NULL</span>)) <span class="sc">+</span></span>
<span id="cb22-9"><a href="#cb22-9"></a><span class="fu">scale_colour_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"#ea4a50"</span>, <span class="st">"#325788"</span>, <span class="st">"dodgerblue"</span>, <span class="st">"coral1"</span>), <span class="at">guide =</span> <span class="fu">guide_legend</span>(<span class="at">title =</span> <span class="cn">NULL</span>)) </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<img data-src="index_files/figure-revealjs/Step%206-1.png" width="960" class="r-stretch"></section>
<section id="step-7-set-theme" class="slide level2">
<h2>Step 7: <code>Set theme</code></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb23" data-code-line-numbers="10-18"><pre class="sourceCode numberSource r fourlinesish number-lines code-with-copy"><code class="sourceCode r"><span id="cb23-1"><a href="#cb23-1"></a><span class="fu">ggplot</span>(dat, <span class="fu">aes</span>(<span class="at">x =</span> Disease, <span class="at">y =</span> PC, <span class="at">shape =</span> group, <span class="at">fill =</span> group, <span class="at">colour =</span> group, <span class="at">group =</span> group)) <span class="sc">+</span></span>
<span id="cb23-2"><a href="#cb23-2"></a><span class="fu">geom_hline</span>(<span class="at">yintercept =</span> <span class="dv">0</span>, <span class="at">linetype =</span> <span class="st">"dashed"</span>, <span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="fl">0.5</span>) <span class="sc">+</span></span>
<span id="cb23-3"><a href="#cb23-3"></a><span class="fu">geom_point</span>(<span class="at">position =</span> <span class="fu">position_dodge</span>(.<span class="dv">7</span>), <span class="at">size =</span> <span class="dv">2</span>) <span class="sc">+</span></span>
<span id="cb23-4"><a href="#cb23-4"></a><span class="fu">geom_errorbar</span>(<span class="fu">aes</span>(<span class="at">ymin =</span> PC_95_LOW, <span class="at">ymax =</span> PC_95_UP), <span class="at">position =</span> <span class="fu">position_dodge</span>(.<span class="dv">7</span>), <span class="at">width =</span> <span class="fl">0.3</span>, <span class="at">size =</span> <span class="fl">0.6</span>) <span class="sc">+</span></span>
<span id="cb23-5"><a href="#cb23-5"></a><span class="fu">xlab</span>(<span class="st">""</span>)<span class="sc">+</span></span>
<span id="cb23-6"><a href="#cb23-6"></a><span class="fu">scale_y_continuous</span>(<span class="st">"Percentage Change (%) and 95% CI"</span>, <span class="at">labels =</span> scales<span class="sc">::</span><span class="fu">number_format</span>(<span class="at">accuracy =</span> <span class="fl">0.01</span>))<span class="sc">+</span></span>
<span id="cb23-7"><a href="#cb23-7"></a><span class="fu">scale_shape_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="dv">16</span>, <span class="dv">23</span>, <span class="dv">24</span>, <span class="dv">15</span>), <span class="at">guide =</span> <span class="fu">guide_legend</span>(<span class="at">title =</span> <span class="cn">NULL</span>)) <span class="sc">+</span></span>
<span id="cb23-8"><a href="#cb23-8"></a><span class="fu">scale_fill_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"#ea4a50"</span>, <span class="st">"#325788"</span>, <span class="st">"dodgerblue"</span>, <span class="st">"coral1"</span>), <span class="at">guide =</span> <span class="fu">guide_legend</span>(<span class="at">title =</span> <span class="cn">NULL</span>)) <span class="sc">+</span></span>
<span id="cb23-9"><a href="#cb23-9"></a><span class="fu">scale_colour_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"#ea4a50"</span>, <span class="st">"#325788"</span>, <span class="st">"dodgerblue"</span>, <span class="st">"coral1"</span>), <span class="at">guide =</span> <span class="fu">guide_legend</span>(<span class="at">title =</span> <span class="cn">NULL</span>)) <span class="sc">+</span></span>
<span id="cb23-10"><a href="#cb23-10"></a><span class="fu">theme_bw</span>() <span class="sc">+</span></span>
<span id="cb23-11"><a href="#cb23-11"></a><span class="fu">theme</span>(<span class="at">panel.grid.major =</span> <span class="fu">element_blank</span>(), <span class="at">panel.grid.minor =</span> <span class="fu">element_blank</span>()) <span class="sc">+</span></span>
<span id="cb23-12"><a href="#cb23-12"></a><span class="fu">theme</span>(<span class="at">legend.position =</span> <span class="st">"top"</span>) <span class="sc">+</span> <span class="co"># top</span></span>
<span id="cb23-13"><a href="#cb23-13"></a><span class="fu">theme</span>(<span class="at">legend.key =</span> <span class="fu">element_blank</span>()) <span class="sc">+</span></span>
<span id="cb23-14"><a href="#cb23-14"></a><span class="fu">theme</span>(<span class="at">legend.background =</span> <span class="fu">element_rect</span>(<span class="at">fill =</span> <span class="st">"white"</span>, <span class="at">colour =</span> <span class="st">"black"</span>)) <span class="sc">+</span></span>
<span id="cb23-15"><a href="#cb23-15"></a><span class="fu">theme</span>(<span class="at">legend.text =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">10</span>, <span class="at">color =</span> <span class="st">"black"</span>)) <span class="sc">+</span></span>
<span id="cb23-16"><a href="#cb23-16"></a><span class="fu">theme</span>(<span class="at">legend.key.height =</span> <span class="fu">unit</span>(<span class="fl">0.3</span>, <span class="st">"cm"</span>)) <span class="sc">+</span></span>
<span id="cb23-17"><a href="#cb23-17"></a><span class="fu">theme</span>(<span class="at">axis.text.y =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">12</span>, <span class="at">angle =</span> <span class="dv">0</span>, <span class="at">color =</span> <span class="st">"black"</span>)) <span class="sc">+</span></span>
<span id="cb23-18"><a href="#cb23-18"></a><span class="fu">theme</span>(<span class="at">axis.text.x =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">12</span>, <span class="at">color =</span> <span class="st">"black"</span>)) </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<img data-src="index_files/figure-revealjs/Step%207-1.png" width="960" class="r-stretch"></section>
<section id="more-categorical-variables" class="slide level2">
<h2>More <code>categorical</code> variables?</h2>
<div class="cell">
<div class="cell-output cell-output-stdout">
<pre><code> Disease group PC PC_95_LOW PC_95_UP country
1 Arrhythmia <65 -2.14 -4.02 -0.27 China
2 Arrhythmia >=65 -0.31 -1.80 1.19 China
3 Arrhythmia Male -1.22 -3.10 0.65 China
4 Arrhythmia Female -0.55 -2.23 1.12 China
5 Cerebrovascular <65 -0.11 -0.62 0.40 China
6 Cerebrovascular >=65 -0.05 -0.51 0.41 China
7 Cerebrovascular Male 0.12 -0.36 0.59 China
8 Cerebrovascular Female -0.30 -0.86 0.25 China
9 CHD <65 1.67 0.68 2.67 China
10 CHD >=65 0.84 0.09 1.58 China
11 CHD Male 1.28 0.42 2.15 China
12 CHD Female 1.01 0.18 1.83 China
13 Heart failure <65 1.23 -2.65 5.11 China
14 Heart failure >=65 -0.67 -2.65 1.32 China
15 Heart failure Male 0.54 -1.95 3.03 China
16 Heart failure Female -1.09 -3.60 1.42 China
17 Arrhythmia <65 -2.14 -4.02 -0.27 USA
18 Arrhythmia >=65 -0.31 -1.80 1.19 USA
19 Arrhythmia Male -1.22 -3.10 0.65 USA
20 Arrhythmia Female -0.55 -2.23 1.12 USA
21 Cerebrovascular <65 -0.11 -0.62 0.40 USA
22 Cerebrovascular >=65 -0.05 -0.51 0.41 USA
23 Cerebrovascular Male 0.12 -0.36 0.59 USA
24 Cerebrovascular Female -0.30 -0.86 0.25 USA
25 CHD <65 1.67 0.68 2.67 USA
26 CHD >=65 0.84 0.09 1.58 USA
27 CHD Male 1.28 0.42 2.15 USA
28 CHD Female 1.01 0.18 1.83 USA
29 Heart failure <65 1.23 -2.65 5.11 USA
30 Heart failure >=65 -0.67 -2.65 1.32 USA
31 Heart failure Male 0.54 -1.95 3.03 USA
32 Heart failure Female -1.09 -3.60 1.42 USA</code></pre>
</div>
</div>
</section>
<section id="facet-in-ggplot2" class="slide level2">
<h2><code>Facet</code> in ggplot2</h2>
<div class="cell" data-fig.dim="[10,4]">
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb25" data-code-line-numbers="19"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb25-1"><a href="#cb25-1"></a><span class="fu">ggplot</span>(dat2, <span class="fu">aes</span>(<span class="at">x =</span> Disease, <span class="at">y =</span> PC, <span class="at">shape =</span> group, <span class="at">fill =</span> group, <span class="at">colour =</span> group, <span class="at">group =</span> group)) <span class="sc">+</span></span>
<span id="cb25-2"><a href="#cb25-2"></a><span class="fu">geom_hline</span>(<span class="at">yintercept =</span> <span class="dv">0</span>, <span class="at">linetype =</span> <span class="st">"dashed"</span>, <span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="fl">0.5</span>) <span class="sc">+</span></span>
<span id="cb25-3"><a href="#cb25-3"></a><span class="fu">geom_point</span>(<span class="at">position =</span> <span class="fu">position_dodge</span>(.<span class="dv">7</span>), <span class="at">size =</span> <span class="dv">2</span>) <span class="sc">+</span></span>
<span id="cb25-4"><a href="#cb25-4"></a><span class="fu">geom_errorbar</span>(<span class="fu">aes</span>(<span class="at">ymin =</span> PC_95_LOW, <span class="at">ymax =</span> PC_95_UP), <span class="at">position =</span> <span class="fu">position_dodge</span>(.<span class="dv">7</span>), <span class="at">width =</span> <span class="fl">0.3</span>, <span class="at">size =</span> <span class="fl">0.6</span>) <span class="sc">+</span></span>
<span id="cb25-5"><a href="#cb25-5"></a><span class="fu">scale_y_continuous</span>(<span class="st">"Percentage Change (%) and 95% CI"</span>, <span class="at">labels =</span> scales<span class="sc">::</span><span class="fu">number_format</span>(<span class="at">accuracy =</span> <span class="fl">0.01</span>))<span class="sc">+</span></span>
<span id="cb25-6"><a href="#cb25-6"></a><span class="fu">scale_shape_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="dv">16</span>, <span class="dv">23</span>, <span class="dv">24</span>, <span class="dv">15</span>), <span class="at">guide =</span> <span class="fu">guide_legend</span>(<span class="at">title =</span> <span class="cn">NULL</span>)) <span class="sc">+</span></span>
<span id="cb25-7"><a href="#cb25-7"></a><span class="fu">scale_fill_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"#ea4a50"</span>, <span class="st">"#325788"</span>, <span class="st">"dodgerblue"</span>, <span class="st">"coral1"</span>), <span class="at">guide =</span> <span class="fu">guide_legend</span>(<span class="at">title =</span> <span class="cn">NULL</span>)) <span class="sc">+</span></span>
<span id="cb25-8"><a href="#cb25-8"></a><span class="fu">scale_colour_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"#ea4a50"</span>, <span class="st">"#325788"</span>, <span class="st">"dodgerblue"</span>, <span class="st">"coral1"</span>), <span class="at">guide =</span> <span class="fu">guide_legend</span>(<span class="at">title =</span> <span class="cn">NULL</span>)) <span class="sc">+</span></span>
<span id="cb25-9"><a href="#cb25-9"></a><span class="fu">theme_bw</span>() <span class="sc">+</span></span>
<span id="cb25-10"><a href="#cb25-10"></a> <span class="fu">theme</span>(<span class="at">panel.grid.major =</span> <span class="fu">element_blank</span>(), <span class="at">panel.grid.minor =</span> <span class="fu">element_blank</span>()) <span class="sc">+</span></span>
<span id="cb25-11"><a href="#cb25-11"></a> <span class="fu">theme</span>(<span class="at">legend.position =</span> <span class="st">"top"</span>) <span class="sc">+</span> </span>
<span id="cb25-12"><a href="#cb25-12"></a> <span class="fu">theme</span>(<span class="at">legend.key =</span> <span class="fu">element_blank</span>()) <span class="sc">+</span></span>
<span id="cb25-13"><a href="#cb25-13"></a> <span class="fu">theme</span>(<span class="at">legend.background =</span> <span class="fu">element_rect</span>(<span class="at">fill =</span> <span class="st">"white"</span>, <span class="at">colour =</span> <span class="st">"black"</span>)) <span class="sc">+</span></span>
<span id="cb25-14"><a href="#cb25-14"></a> <span class="fu">theme</span>(<span class="at">legend.text =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">10</span>, <span class="at">color =</span> <span class="st">"black"</span>)) <span class="sc">+</span></span>
<span id="cb25-15"><a href="#cb25-15"></a> <span class="fu">theme</span>(<span class="at">legend.key.height =</span> <span class="fu">unit</span>(<span class="fl">0.3</span>, <span class="st">"cm"</span>)) <span class="sc">+</span></span>
<span id="cb25-16"><a href="#cb25-16"></a> <span class="fu">theme</span>(<span class="at">axis.text.y =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">12</span>, <span class="at">angle =</span> <span class="dv">0</span>, <span class="at">color =</span> <span class="st">"black"</span>)) <span class="sc">+</span></span>
<span id="cb25-17"><a href="#cb25-17"></a> <span class="fu">theme</span>(<span class="at">axis.text.x =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">12</span>, <span class="at">color =</span> <span class="st">"black"</span>)) <span class="sc">+</span></span>
<span id="cb25-18"><a href="#cb25-18"></a> <span class="fu">xlab</span>(<span class="st">""</span>) <span class="sc">+</span></span>
<span id="cb25-19"><a href="#cb25-19"></a> <span class="fu">facet_wrap</span>(<span class="fu">vars</span>(country))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
<img data-src="index_files/figure-revealjs/facet-1.png" width="2000" class="r-stretch"></section>
<section id="a-more-simple-ggplot2-method-ggfp-packages" class="slide level2">
<h2>A more simple ggplot2 method: <code>ggfp</code> packages</h2>
<p><code>The goal of ggfp is to simplify the process of drawing forest plots using ggplot2</code>. We have packaged the main code for drawing forest plots to form the gg_fp() function. gg_fp() has the advantage that only a few parameters need to be provided to draw a nice forest plot. Of course, it also has the obvious disadvantage that some of the more fine-grained graph adjustment parameters are not available in gg_fp().</p>
<hr>
<p><br> You can install the development version of ggfp like so:</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb26"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb26-1"><a href="#cb26-1"></a>devtools<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">'lizhiwei1994/ggfp'</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="creat-forestplot-using-ggfp-package" class="slide level2">
<h2>Creat forestplot using <code>ggfp</code> package</h2>
<div class="cell" data-fig.dim="[10,4]">
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb27"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb27-1"><a href="#cb27-1"></a><span class="fu">ggplot</span>(dat2, <span class="fu">aes</span>(<span class="at">x =</span> Disease, <span class="at">y =</span> PC, <span class="at">shape =</span> group, <span class="at">fill =</span> group, <span class="at">colour =</span> group, <span class="at">group =</span> group)) <span class="sc">+</span></span>
<span id="cb27-2"><a href="#cb27-2"></a><span class="fu">geom_hline</span>(<span class="at">yintercept =</span> <span class="dv">0</span>, <span class="at">linetype =</span> <span class="st">"dashed"</span>, <span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="fl">0.5</span>) <span class="sc">+</span></span>
<span id="cb27-3"><a href="#cb27-3"></a><span class="fu">geom_point</span>(<span class="at">position =</span> <span class="fu">position_dodge</span>(.<span class="dv">7</span>), <span class="at">size =</span> <span class="dv">2</span>) <span class="sc">+</span></span>
<span id="cb27-4"><a href="#cb27-4"></a><span class="fu">geom_errorbar</span>(<span class="fu">aes</span>(<span class="at">ymin =</span> PC_95_LOW, <span class="at">ymax =</span> PC_95_UP), <span class="at">position =</span> <span class="fu">position_dodge</span>(.<span class="dv">7</span>), <span class="at">width =</span> <span class="fl">0.3</span>, <span class="at">size =</span> <span class="fl">0.6</span>) <span class="sc">+</span></span>
<span id="cb27-5"><a href="#cb27-5"></a><span class="fu">scale_y_continuous</span>(<span class="st">"Percentage Change (%) and 95% CI"</span>, <span class="at">labels =</span> scales<span class="sc">::</span><span class="fu">number_format</span>(<span class="at">accuracy =</span> <span class="fl">0.01</span>))<span class="sc">+</span></span>
<span id="cb27-6"><a href="#cb27-6"></a><span class="fu">scale_shape_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="dv">16</span>, <span class="dv">23</span>, <span class="dv">24</span>, <span class="dv">15</span>), <span class="at">guide =</span> <span class="fu">guide_legend</span>(<span class="at">title =</span> <span class="cn">NULL</span>)) <span class="sc">+</span></span>
<span id="cb27-7"><a href="#cb27-7"></a><span class="fu">scale_fill_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"#ea4a50"</span>, <span class="st">"#325788"</span>, <span class="st">"dodgerblue"</span>, <span class="st">"coral1"</span>), <span class="at">guide =</span> <span class="fu">guide_legend</span>(<span class="at">title =</span> <span class="cn">NULL</span>)) <span class="sc">+</span></span>
<span id="cb27-8"><a href="#cb27-8"></a><span class="fu">scale_colour_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"#ea4a50"</span>, <span class="st">"#325788"</span>, <span class="st">"dodgerblue"</span>, <span class="st">"coral1"</span>), <span class="at">guide =</span> <span class="fu">guide_legend</span>(<span class="at">title =</span> <span class="cn">NULL</span>)) <span class="sc">+</span></span>
<span id="cb27-9"><a href="#cb27-9"></a><span class="fu">theme_bw</span>() <span class="sc">+</span></span>
<span id="cb27-10"><a href="#cb27-10"></a> <span class="fu">theme</span>(<span class="at">panel.grid.major =</span> <span class="fu">element_blank</span>(), <span class="at">panel.grid.minor =</span> <span class="fu">element_blank</span>()) <span class="sc">+</span></span>
<span id="cb27-11"><a href="#cb27-11"></a> <span class="fu">theme</span>(<span class="at">legend.position =</span> <span class="st">"top"</span>) <span class="sc">+</span> </span>
<span id="cb27-12"><a href="#cb27-12"></a> <span class="fu">theme</span>(<span class="at">legend.key =</span> <span class="fu">element_blank</span>()) <span class="sc">+</span></span>
<span id="cb27-13"><a href="#cb27-13"></a> <span class="fu">theme</span>(<span class="at">legend.background =</span> <span class="fu">element_rect</span>(<span class="at">fill =</span> <span class="st">"white"</span>, <span class="at">colour =</span> <span class="st">"black"</span>)) <span class="sc">+</span></span>
<span id="cb27-14"><a href="#cb27-14"></a> <span class="fu">theme</span>(<span class="at">legend.text =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">10</span>, <span class="at">color =</span> <span class="st">"black"</span>)) <span class="sc">+</span></span>
<span id="cb27-15"><a href="#cb27-15"></a> <span class="fu">theme</span>(<span class="at">legend.key.height =</span> <span class="fu">unit</span>(<span class="fl">0.3</span>, <span class="st">"cm"</span>)) <span class="sc">+</span></span>
<span id="cb27-16"><a href="#cb27-16"></a> <span class="fu">theme</span>(<span class="at">axis.text.y =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">12</span>, <span class="at">angle =</span> <span class="dv">0</span>, <span class="at">color =</span> <span class="st">"black"</span>)) <span class="sc">+</span></span>
<span id="cb27-17"><a href="#cb27-17"></a> <span class="fu">theme</span>(<span class="at">axis.text.x =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">12</span>, <span class="at">color =</span> <span class="st">"black"</span>)) <span class="sc">+</span></span>
<span id="cb27-18"><a href="#cb27-18"></a> <span class="fu">xlab</span>(<span class="st">""</span>) <span class="sc">+</span></span>
<span id="cb27-19"><a href="#cb27-19"></a> <span class="fu">facet_wrap</span>(<span class="fu">vars</span>(country))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>