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CompareRaw.html
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Participant QC
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Prepare phenotype table
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Pheno skim
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2. Matching + Veg. Effect
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Compare raw phenotype values
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3. Vegetarianism GWAS
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<h1 class="title toc-ignore">Compare raw phenotypes</h1>
<h4 class="author">Mike Francis</h4>
<h4 class="date">2022-10-09 21:02:38</h4>
</div>
<div id="load-packages-functions" class="section level3">
<h3>Load packages + functions</h3>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">suppressMessages</span>(silent <span class="ot"><-</span> <span class="fu">lapply</span>(</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(<span class="st">"bestNormalize"</span>,<span class="st">"plyr"</span>, <span class="st">"dplyr"</span>, <span class="st">"tidyverse"</span>, <span class="st">"ggpubr"</span>, </span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> <span class="st">"RNOmni"</span>, <span class="st">"genpwr"</span>, </span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a> <span class="st">"data.table"</span>, <span class="st">"vroom"</span>,<span class="st">"kableExtra"</span>), </span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a> library, <span class="at">character.only=</span>T))</span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a>calc_stat <span class="ot"><-</span> <span class="cf">function</span>(x) {</span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a> coef <span class="ot"><-</span> <span class="fl">1.5</span></span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a> n <span class="ot"><-</span> <span class="fu">sum</span>(<span class="sc">!</span><span class="fu">is.na</span>(x))</span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a> <span class="co"># calculate quantiles</span></span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a> stats <span class="ot"><-</span> <span class="fu">quantile</span>(x, <span class="at">probs =</span> <span class="fu">c</span>(<span class="fl">0.1</span>, <span class="fl">0.25</span>, <span class="fl">0.5</span>, <span class="fl">0.75</span>, <span class="fl">0.9</span>))</span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">names</span>(stats) <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"ymin"</span>, <span class="st">"lower"</span>, <span class="st">"middle"</span>, <span class="st">"upper"</span>, <span class="st">"ymax"</span>)</span>
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a> <span class="fu">return</span>(stats)</span>
<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a>fun_mean <span class="ot"><-</span> <span class="cf">function</span>(x){</span>
<span id="cb1-17"><a href="#cb1-17" aria-hidden="true" tabindex="-1"></a> <span class="fu">return</span>(<span class="fu">data.frame</span>(<span class="at">y=</span><span class="fu">round</span>(<span class="fu">mean</span>(x),<span class="dv">4</span>),<span class="at">label=</span><span class="fu">round</span>(<span class="fu">mean</span>(x,<span class="at">na.rm=</span>T),<span class="dv">2</span>)))}</span>
<span id="cb1-18"><a href="#cb1-18" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-19"><a href="#cb1-19" aria-hidden="true" tabindex="-1"></a>table <span class="ot">=</span> <span class="cf">function</span> (..., <span class="at">useNA =</span> <span class="st">'always'</span>) base<span class="sc">::</span><span class="fu">table</span>(..., <span class="at">useNA =</span> useNA)</span></code></pre></div>
</div>
<div id="load-phenotype-files" class="section level3">
<h3>Load phenotype files</h3>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>new<span class="ot"><-</span><span class="fu">as_tibble</span>(<span class="fu">vroom</span>(<span class="st">"/Users/mike/Documents/R_files/VegMarkdown/pheno/BioxVeg_pheno_09112022.txt"</span>))</span></code></pre></div>
<pre><code>## Rows: 155375 Columns: 132
## ── Column specification ─────────────────────────────────────────────────────────────────────────
## Delimiter: " "
## dbl (132): FID, IID, Age, Sex, Townsend, Geno_batch, AlcoholFreq, Alanine_am...
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.</code></pre>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a>phenotypes<span class="ot">=</span>new<span class="sc">%>%</span><span class="fu">select</span>(Alanine_aminotransferase<span class="sc">:</span>Vitamin_D, </span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a> bioavailableTest, freeTest, eGFR, Veg5yr1,Sex)<span class="sc">%>%</span></span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">select</span>(<span class="sc">-</span><span class="fu">c</span>(Oestradiol, Rheumatoid_factor, Glucose))</span>
<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a>phenotypes<span class="ot">=</span>phenotypes[<span class="fu">c</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">6</span>, <span class="dv">28</span>, <span class="dv">7</span><span class="sc">:</span><span class="dv">12</span>, <span class="dv">30</span>, <span class="dv">29</span>, <span class="dv">13</span><span class="sc">:</span><span class="dv">27</span>,<span class="dv">31</span>,<span class="dv">32</span>)]</span>
<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a><span class="fu">colnames</span>(phenotypes)<span class="ot">=</span><span class="fu">gsub</span>(<span class="fu">colnames</span>(phenotypes), <span class="at">pattern =</span> <span class="st">"_"</span>, <span class="at">replacement =</span> <span class="st">" "</span>)</span>
<span id="cb4-8"><a href="#cb4-8" aria-hidden="true" tabindex="-1"></a><span class="fu">colnames</span>(phenotypes)[<span class="fu">c</span>(<span class="dv">7</span>,<span class="dv">15</span>)]<span class="ot">=</span><span class="fu">c</span>(<span class="st">"Bioavailable testosterone"</span>, <span class="st">"Free testosterone"</span>)</span>
<span id="cb4-9"><a href="#cb4-9" aria-hidden="true" tabindex="-1"></a><span class="fu">colnames</span>(phenotypes)<span class="sc">%>%</span><span class="fu">kbl</span>()<span class="sc">%>%</span> </span>
<span id="cb4-10"><a href="#cb4-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">scroll_box</span>(<span class="at">width =</span> <span class="st">"200px"</span>, <span class="at">height =</span> <span class="st">"200px"</span>)</span></code></pre></div>
<div
style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:200px; overflow-x: scroll; width:200px; ">
<table>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;">
x
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
Alanine aminotransferase
</td>
</tr>
<tr>
<td style="text-align:left;">
Albumin
</td>
</tr>
<tr>
<td style="text-align:left;">
Alkaline phosphatase
</td>
</tr>
<tr>
<td style="text-align:left;">
Apolipoprotein A
</td>
</tr>
<tr>
<td style="text-align:left;">
Apolipoprotein B
</td>
</tr>
<tr>
<td style="text-align:left;">
Aspartate aminotransferase
</td>
</tr>
<tr>
<td style="text-align:left;">
Bioavailable testosterone
</td>
</tr>
<tr>
<td style="text-align:left;">
C reactive protein
</td>
</tr>
<tr>
<td style="text-align:left;">
Calcium
</td>
</tr>
<tr>
<td style="text-align:left;">
Cholesterol
</td>
</tr>
<tr>
<td style="text-align:left;">
Creatinine
</td>
</tr>
<tr>
<td style="text-align:left;">
Cystatin C
</td>
</tr>
<tr>
<td style="text-align:left;">
Direct bilirubin
</td>
</tr>
<tr>
<td style="text-align:left;">
eGFR
</td>
</tr>
<tr>
<td style="text-align:left;">
Free testosterone
</td>
</tr>
<tr>
<td style="text-align:left;">
Gamma glutamyltransferase
</td>
</tr>
<tr>
<td style="text-align:left;">
HbA1c
</td>
</tr>
<tr>
<td style="text-align:left;">
HDL cholesterol
</td>
</tr>
<tr>
<td style="text-align:left;">
IGF 1
</td>
</tr>
<tr>
<td style="text-align:left;">
LDL direct
</td>
</tr>
<tr>
<td style="text-align:left;">
Lipoprotein A
</td>
</tr>
<tr>
<td style="text-align:left;">
Phosphate
</td>
</tr>
<tr>
<td style="text-align:left;">
SHBG
</td>
</tr>
<tr>
<td style="text-align:left;">
Testosterone
</td>
</tr>
<tr>
<td style="text-align:left;">
Total bilirubin
</td>
</tr>
<tr>
<td style="text-align:left;">
Total protein
</td>
</tr>
<tr>
<td style="text-align:left;">
Triglycerides
</td>
</tr>
<tr>
<td style="text-align:left;">
Urate
</td>
</tr>
<tr>
<td style="text-align:left;">
Urea
</td>
</tr>
<tr>
<td style="text-align:left;">
Vitamin D
</td>
</tr>
<tr>
<td style="text-align:left;">
Veg5yr1
</td>
</tr>
<tr>
<td style="text-align:left;">
Sex
</td>
</tr>
</tbody>
</table>
</div>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="co">#From matching script</span></span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>md1<span class="ot">=</span><span class="fu">as_tibble</span>(<span class="fu">read.csv</span>(<span class="st">"/Users/mike/Documents/R_files/VegMarkdown/MATCHED.pheno.10042022.csv"</span>))</span></code></pre></div>
</div>
<div id="prep-for-plotting" class="section level3">
<h3>Prep for plotting</h3>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a>pheno<span class="ot">=</span>phenotypes<span class="sc">%>%</span><span class="fu">select</span>(<span class="sc">-</span>Sex)</span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a>phe<span class="ot">=</span>md1<span class="sc">%>%</span><span class="fu">select</span>(Alanine_aminotransferase_rint<span class="sc">:</span>Free_testosterone_rint)<span class="sc">%>%</span><span class="fu">colnames</span>()</span>
<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a>phe2<span class="ot">=</span><span class="fu">str_split</span>(phe, <span class="st">"_rint"</span>, <span class="at">simplify=</span><span class="cn">TRUE</span>)[,<span class="dv">1</span>]</span>
<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a>longpheno<span class="ot"><-</span><span class="fu">as_tibble</span>(<span class="fu">melt</span>(<span class="fu">setDT</span>(pheno), <span class="at">id.vars =</span> <span class="fu">c</span>(<span class="st">"Veg5yr1"</span>)))</span>
<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a>longpheno<span class="sc">$</span>Diet<span class="ot"><-</span><span class="st">"Non-vegetarian"</span></span>
<span id="cb6-6"><a href="#cb6-6" aria-hidden="true" tabindex="-1"></a>longpheno<span class="sc">$</span>Diet[longpheno<span class="sc">$</span>Veg5yr1<span class="sc">==</span><span class="dv">1</span>]<span class="ot"><-</span><span class="st">"Vegetarian"</span></span>
<span id="cb6-7"><a href="#cb6-7" aria-hidden="true" tabindex="-1"></a>longpheno<span class="sc">$</span>Diet<span class="ot"><-</span><span class="fu">as.factor</span>(longpheno<span class="sc">$</span>Diet)</span>
<span id="cb6-8"><a href="#cb6-8" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb6-9"><a href="#cb6-9" aria-hidden="true" tabindex="-1"></a>longpheno2<span class="ot"><-</span><span class="fu">as_tibble</span>(<span class="fu">melt</span>(<span class="fu">setDT</span>(md1<span class="sc">%>%</span><span class="fu">select</span>(<span class="fu">all_of</span>(<span class="fu">sort</span>(phe2)), Veg5yr1)), <span class="at">id.vars =</span> <span class="fu">c</span>(<span class="st">"Veg5yr1"</span>)))</span>
<span id="cb6-10"><a href="#cb6-10" aria-hidden="true" tabindex="-1"></a>longpheno2<span class="sc">$</span>variable<span class="ot">=</span><span class="fu">gsub</span>(longpheno2<span class="sc">$</span>variable, <span class="at">pattern =</span> <span class="st">"_"</span>, <span class="at">replacement =</span> <span class="st">" "</span>)</span>
<span id="cb6-11"><a href="#cb6-11" aria-hidden="true" tabindex="-1"></a>longpheno2<span class="sc">$</span>Diet<span class="ot"><-</span><span class="st">"Matched non-vegetarian"</span></span>
<span id="cb6-12"><a href="#cb6-12" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb6-13"><a href="#cb6-13" aria-hidden="true" tabindex="-1"></a>longpheno2<span class="sc">$</span>Diet[longpheno2<span class="sc">$</span>Veg5yr1<span class="sc">==</span><span class="dv">1</span>]<span class="ot"><-</span><span class="st">"Vegetarian"</span></span>
<span id="cb6-14"><a href="#cb6-14" aria-hidden="true" tabindex="-1"></a>longpheno2<span class="ot">=</span>longpheno2<span class="sc">%>%</span><span class="fu">filter</span>(Diet<span class="sc">!=</span><span class="st">"Vegetarian"</span>)</span>
<span id="cb6-15"><a href="#cb6-15" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb6-16"><a href="#cb6-16" aria-hidden="true" tabindex="-1"></a>bind<span class="ot">=</span><span class="fu">rbind</span>(longpheno, longpheno2)</span>
<span id="cb6-17"><a href="#cb6-17" aria-hidden="true" tabindex="-1"></a>bind<span class="sc">$</span>Diet<span class="ot"><-</span><span class="fu">factor</span>(bind<span class="sc">$</span>Diet, <span class="at">levels=</span><span class="fu">c</span>(<span class="st">"Non-vegetarian"</span>, <span class="st">"Matched non-vegetarian"</span>,</span>
<span id="cb6-18"><a href="#cb6-18" aria-hidden="true" tabindex="-1"></a> <span class="st">"Vegetarian"</span>))</span></code></pre></div>
</div>
<div id="full-cohort-boxplot" class="section level3">
<h3>Full cohort boxplot</h3>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="co">#png("boxplot.10042022.png",width = 13, height = 9, units = 'in', res = 600)</span></span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb7-4"><a href="#cb7-4" aria-hidden="true" tabindex="-1"></a>p1<span class="ot">=</span><span class="fu">ggplot</span>(bind, <span class="fu">aes</span>(<span class="at">x=</span>Diet, <span class="at">y=</span>value, <span class="at">color=</span>Diet))<span class="sc">+</span></span>
<span id="cb7-5"><a href="#cb7-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_bw</span>()<span class="sc">+</span></span>
<span id="cb7-6"><a href="#cb7-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_summary</span>(<span class="at">fun.data =</span> calc_stat, <span class="at">geom=</span><span class="st">"boxplot"</span>) <span class="sc">+</span> </span>
<span id="cb7-7"><a href="#cb7-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">facet_wrap</span>(<span class="sc">~</span>variable,<span class="at">scales =</span> <span class="st">"free_y"</span>,<span class="at">nrow =</span> <span class="dv">6</span>)<span class="sc">+</span></span>
<span id="cb7-8"><a href="#cb7-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(<span class="at">axis.text.x =</span> <span class="fu">element_text</span>(<span class="at">angle =</span> <span class="dv">60</span>,</span>
<span id="cb7-9"><a href="#cb7-9" aria-hidden="true" tabindex="-1"></a> <span class="at">vjust =</span> <span class="dv">1</span>, <span class="at">hjust=</span><span class="dv">1</span>),</span>
<span id="cb7-10"><a href="#cb7-10" aria-hidden="true" tabindex="-1"></a> <span class="at">strip.text.x =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">7</span>))<span class="sc">+</span></span>
<span id="cb7-11"><a href="#cb7-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_summary</span>(<span class="at">fun=</span>mean, <span class="at">geom=</span><span class="st">"point"</span>, </span>
<span id="cb7-12"><a href="#cb7-12" aria-hidden="true" tabindex="-1"></a> <span class="at">shape=</span><span class="dv">18</span>, <span class="at">size=</span><span class="dv">1</span>, <span class="at">color=</span><span class="st">"black"</span>, <span class="at">fill=</span><span class="st">"black"</span>)<span class="sc">+</span></span>
<span id="cb7-13"><a href="#cb7-13" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_summary</span>(<span class="at">fun.data =</span> fun_mean, </span>
<span id="cb7-14"><a href="#cb7-14" aria-hidden="true" tabindex="-1"></a> <span class="at">geom=</span><span class="st">"text"</span>, <span class="at">vjust=</span><span class="sc">-</span><span class="fl">0.7</span>, <span class="at">size=</span><span class="fl">2.5</span>)<span class="sc">+</span></span>
<span id="cb7-15"><a href="#cb7-15" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_color_manual</span>(<span class="at">values=</span><span class="fu">c</span>(<span class="st">"#E0951F"</span>, <span class="st">"#2FA3F7"</span>,<span class="st">"#36E072"</span>))<span class="sc">+</span></span>
<span id="cb7-16"><a href="#cb7-16" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_manual</span>(<span class="at">values=</span><span class="fu">c</span>(<span class="st">"white"</span>))</span>
<span id="cb7-17"><a href="#cb7-17" aria-hidden="true" tabindex="-1"></a>p1</span></code></pre></div>
<pre><code>## Warning: Removed 469679 rows containing non-finite values (stat_summary).
## Removed 469679 rows containing non-finite values (stat_summary).
## Removed 469679 rows containing non-finite values (stat_summary).</code></pre>
<p><img src="CompareRaw_files/figure-html/full-boxplot-1.png" width="672" /></p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="co">#dev.off()</span></span></code></pre></div>
</div>
<div id="sex-stratified-boxplot" class="section level3">
<h3>Sex-stratified boxplot</h3>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a>MF<span class="ot"><-</span><span class="fu">as_tibble</span>(<span class="fu">melt</span>(<span class="fu">setDT</span>(phenotypes), <span class="at">id.vars =</span> <span class="fu">c</span>(<span class="st">"Veg5yr1"</span>, <span class="st">"Sex"</span>)))</span>
<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a>MF<span class="sc">$</span>Diet<span class="ot"><-</span><span class="st">"Non-vegetarian"</span></span>
<span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a>MF<span class="sc">$</span>Diet[MF<span class="sc">$</span>Veg5yr1<span class="sc">==</span><span class="dv">1</span>]<span class="ot"><-</span><span class="st">"Vegetarian"</span></span>
<span id="cb10-4"><a href="#cb10-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb10-5"><a href="#cb10-5" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb10-6"><a href="#cb10-6" aria-hidden="true" tabindex="-1"></a>MF2<span class="ot"><-</span><span class="fu">as_tibble</span>(<span class="fu">melt</span>(<span class="fu">setDT</span>(md1<span class="sc">%>%</span><span class="fu">select</span>(<span class="fu">all_of</span>(<span class="fu">sort</span>(phe2)), Veg5yr1, Sex)), <span class="at">id.vars =</span> <span class="fu">c</span>(<span class="st">"Veg5yr1"</span>,<span class="st">"Sex"</span>)))</span>
<span id="cb10-7"><a href="#cb10-7" aria-hidden="true" tabindex="-1"></a>MF2<span class="sc">$</span>variable<span class="ot">=</span><span class="fu">gsub</span>(MF2<span class="sc">$</span>variable, <span class="at">pattern =</span> <span class="st">"_"</span>, <span class="at">replacement =</span> <span class="st">" "</span>)</span>
<span id="cb10-8"><a href="#cb10-8" aria-hidden="true" tabindex="-1"></a>MF2<span class="sc">$</span>Diet<span class="ot"><-</span><span class="st">"Matched non-vegetarian"</span></span>
<span id="cb10-9"><a href="#cb10-9" aria-hidden="true" tabindex="-1"></a>MF2<span class="sc">$</span>Diet[MF2<span class="sc">$</span>Veg5yr1<span class="sc">==</span><span class="dv">1</span>]<span class="ot"><-</span><span class="st">"Vegetarian"</span></span>
<span id="cb10-10"><a href="#cb10-10" aria-hidden="true" tabindex="-1"></a>MF2<span class="ot">=</span>MF2<span class="sc">%>%</span><span class="fu">filter</span>(Diet<span class="sc">!=</span><span class="st">"Vegetarian"</span>)</span>
<span id="cb10-11"><a href="#cb10-11" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb10-12"><a href="#cb10-12" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb10-13"><a href="#cb10-13" aria-hidden="true" tabindex="-1"></a>bindMF<span class="ot">=</span><span class="fu">rbind</span>(MF, MF2)</span>
<span id="cb10-14"><a href="#cb10-14" aria-hidden="true" tabindex="-1"></a>bindMF<span class="sc">$</span>Diet<span class="ot"><-</span><span class="fu">factor</span>(bind<span class="sc">$</span>Diet, <span class="at">levels=</span><span class="fu">c</span>(<span class="st">"Non-vegetarian"</span>, <span class="st">"Matched non-vegetarian"</span>,</span>
<span id="cb10-15"><a href="#cb10-15" aria-hidden="true" tabindex="-1"></a> <span class="st">"Vegetarian"</span>))</span>
<span id="cb10-16"><a href="#cb10-16" aria-hidden="true" tabindex="-1"></a>bindMF<span class="sc">$</span>Sex<span class="ot">=</span><span class="fu">mapvalues</span>(bindMF<span class="sc">$</span>Sex, <span class="at">from=</span><span class="fu">c</span>(<span class="dv">1</span>,<span class="dv">2</span>), <span class="at">to=</span><span class="fu">c</span>(<span class="st">"Male"</span>,<span class="st">"Female"</span>))</span>
<span id="cb10-17"><a href="#cb10-17" aria-hidden="true" tabindex="-1"></a>bindMF<span class="sc">$</span>Sex<span class="ot">=</span><span class="fu">factor</span>(bindMF<span class="sc">$</span>Sex, <span class="at">levels=</span><span class="fu">c</span>(<span class="st">"Male"</span>, <span class="st">"Female"</span>))</span>
<span id="cb10-18"><a href="#cb10-18" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb10-19"><a href="#cb10-19" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb10-20"><a href="#cb10-20" aria-hidden="true" tabindex="-1"></a><span class="co">#png("boxplot.MF.10042022.png",width = 13, height = 9, units = 'in', res = 600)</span></span>
<span id="cb10-21"><a href="#cb10-21" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb10-22"><a href="#cb10-22" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb10-23"><a href="#cb10-23" aria-hidden="true" tabindex="-1"></a>p2<span class="ot">=</span><span class="fu">ggplot</span>(bindMF, <span class="fu">aes</span>(<span class="at">x=</span>Diet, <span class="at">y=</span>value, <span class="at">fill=</span>Sex, <span class="at">color=</span>Diet))<span class="sc">+</span></span>
<span id="cb10-24"><a href="#cb10-24" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_bw</span>()<span class="sc">+</span></span>
<span id="cb10-25"><a href="#cb10-25" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_summary</span>(<span class="at">fun.data =</span> calc_stat, <span class="at">geom=</span><span class="st">"boxplot"</span>, </span>
<span id="cb10-26"><a href="#cb10-26" aria-hidden="true" tabindex="-1"></a> <span class="at">position=</span><span class="fu">position_dodge</span>(<span class="fl">0.7</span>), <span class="at">width=</span><span class="fl">0.5</span>) <span class="sc">+</span> </span>
<span id="cb10-27"><a href="#cb10-27" aria-hidden="true" tabindex="-1"></a> <span class="fu">facet_wrap</span>(<span class="sc">~</span>variable,<span class="at">scales =</span> <span class="st">"free_y"</span>,<span class="at">nrow =</span> <span class="dv">6</span>)<span class="sc">+</span></span>
<span id="cb10-28"><a href="#cb10-28" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(<span class="at">axis.text.x =</span> <span class="fu">element_text</span>(<span class="at">angle =</span> <span class="dv">60</span>,</span>
<span id="cb10-29"><a href="#cb10-29" aria-hidden="true" tabindex="-1"></a> <span class="at">vjust =</span> <span class="dv">1</span>, <span class="at">hjust=</span><span class="dv">1</span>),</span>
<span id="cb10-30"><a href="#cb10-30" aria-hidden="true" tabindex="-1"></a> <span class="at">strip.text.x =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">7</span>))<span class="sc">+</span></span>
<span id="cb10-31"><a href="#cb10-31" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_summary</span>(<span class="at">fun=</span>mean, <span class="at">geom=</span><span class="st">"point"</span>, </span>
<span id="cb10-32"><a href="#cb10-32" aria-hidden="true" tabindex="-1"></a> <span class="at">shape=</span><span class="dv">18</span>, <span class="at">size=</span><span class="dv">1</span>, </span>
<span id="cb10-33"><a href="#cb10-33" aria-hidden="true" tabindex="-1"></a> <span class="at">color=</span><span class="st">"black"</span>, <span class="at">fill=</span><span class="st">"black"</span>,</span>
<span id="cb10-34"><a href="#cb10-34" aria-hidden="true" tabindex="-1"></a> <span class="fu">aes</span>(<span class="at">Diet =</span> <span class="fu">interaction</span>(Diet,Sex)),</span>
<span id="cb10-35"><a href="#cb10-35" aria-hidden="true" tabindex="-1"></a> <span class="at">position=</span><span class="fu">position_dodge</span>(<span class="fl">0.7</span>), <span class="at">width=</span><span class="fl">0.5</span>)<span class="sc">+</span></span>
<span id="cb10-36"><a href="#cb10-36" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_color_manual</span>(<span class="at">values=</span><span class="fu">c</span>(<span class="st">"#E0951F"</span>, <span class="st">"#2FA3F7"</span>,<span class="st">"#36E072"</span>))<span class="sc">+</span></span>
<span id="cb10-37"><a href="#cb10-37" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_manual</span>(<span class="at">values=</span><span class="fu">c</span>(<span class="st">"#E6F4FF"</span>, <span class="st">"#FFF2FE"</span>))</span></code></pre></div>
<pre><code>## Warning: Ignoring unknown parameters: width</code></pre>
<pre><code>## Warning: Ignoring unknown aesthetics: Diet</code></pre>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a>p2</span></code></pre></div>
<pre><code>## Warning: Removed 469679 rows containing non-finite values (stat_summary).</code></pre>
<pre><code>## Warning: Removed 469679 rows containing non-finite values (stat_summary).</code></pre>
<p><img src="CompareRaw_files/figure-html/unnamed-chunk-2-1.png" width="672" /></p>
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a><span class="co">#dev.off()</span></span></code></pre></div>
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