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<h1 class="title toc-ignore">Effects of Correction of Detection Rate</h1>
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<p><strong>Last updated:</strong> 2018-07-17</p>
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<hr />
<div id="pollen" class="section level2">
<h2>Pollen</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">i =<span class="st"> </span><span class="dv">2</span>
<span class="kw">load</span>(<span class="st">'../data/unnecessary_in_building/2_Pollen.RData'</span>)
X =<span class="st"> </span><span class="kw">as.matrix</span>(Pollen<span class="op">$</span>x)
truth =<span class="st"> </span><span class="kw">as.numeric</span>(<span class="kw">as.factor</span>(Pollen<span class="op">$</span>label))
numClust =<span class="st"> </span><span class="kw">length</span>(<span class="kw">unique</span>(truth))
logX =<span class="st"> </span><span class="kw">log</span>(X<span class="op">+</span><span class="dv">1</span>)
det =<span class="st"> </span><span class="kw">colSums</span>(X<span class="op">!=</span><span class="dv">0</span>) <span class="op">/</span><span class="st"> </span><span class="kw">nrow</span>(X)
det2 =<span class="st"> </span><span class="kw">qr</span>(det)
R =<span class="st"> </span><span class="kw">t</span>(<span class="kw">qr.resid</span>(det2, <span class="kw">t</span>(logX)))
pca1 =<span class="st"> </span><span class="kw">irlba</span>(R,<span class="dv">2</span>); pca2 =<span class="st"> </span><span class="kw">irlba</span>(logX,<span class="dv">2</span>)
dat =<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">pc1=</span><span class="kw">c</span>(pca1<span class="op">$</span>v[,<span class="dv">1</span>], pca2<span class="op">$</span>v[,<span class="dv">1</span>]), <span class="dt">detection.rate=</span><span class="kw">rep</span>(det, <span class="dv">2</span>), <span class="dt">label=</span><span class="kw">rep</span>(<span class="kw">c</span>(<span class="st">"After correction"</span>, <span class="st">"Before correction"</span>), <span class="dt">each=</span><span class="kw">nrow</span>(pca1<span class="op">$</span>v)), <span class="dt">true.label=</span><span class="kw">as.factor</span>(<span class="kw">rep</span>(truth,<span class="dv">2</span>)))
<span class="kw">ggplot</span>(dat, <span class="kw">aes</span>(<span class="dt">x=</span>pc1, <span class="dt">y=</span>detection.rate, <span class="dt">col=</span>true.label)) <span class="op">+</span><span class="st"> </span><span class="kw">facet_grid</span>(<span class="op">~</span>label) <span class="op">+</span><span class="st"> </span><span class="kw">geom_point</span>() <span class="op">+</span><span class="st"> </span><span class="kw">ggtitle</span>(<span class="st">"PCA"</span>)</code></pre></div>
<p><img src="figure/detection_rate_correction.Rmd/Pollen-1.png" width="672" style="display: block; margin: auto;" /></p>
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<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">tsne1 =<span class="st"> </span><span class="kw">Rtsne</span>(<span class="kw">t</span>(R))
tsne2 =<span class="st"> </span><span class="kw">Rtsne</span>(<span class="kw">t</span>(logX))
dat =<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">v1 =</span> <span class="kw">c</span>(tsne1<span class="op">$</span>Y[,<span class="dv">1</span>], tsne2<span class="op">$</span>Y[,<span class="dv">1</span>]), <span class="dt">v2 =</span> <span class="kw">c</span>(tsne1<span class="op">$</span>Y[,<span class="dv">2</span>], tsne2<span class="op">$</span>Y[,<span class="dv">2</span>]), <span class="dt">label=</span><span class="kw">rep</span>(<span class="kw">c</span>(<span class="st">"After correction"</span>, <span class="st">"Before correction"</span>), <span class="dt">each=</span><span class="kw">nrow</span>(tsne1<span class="op">$</span>Y)), <span class="dt">true.label =</span> <span class="kw">as.factor</span>(<span class="kw">rep</span>(truth, <span class="dv">2</span>)))
<span class="kw">ggplot</span>(dat, <span class="kw">aes</span>(<span class="dt">x=</span>v1, <span class="dt">y=</span>v2, <span class="dt">col=</span>true.label)) <span class="op">+</span><span class="st"> </span><span class="kw">facet_grid</span>(<span class="op">~</span>label) <span class="op">+</span><span class="st"> </span><span class="kw">geom_point</span>() <span class="op">+</span><span class="st"> </span><span class="kw">ggtitle</span>(<span class="st">"tSNE"</span>)</code></pre></div>
<p><img src="figure/detection_rate_correction.Rmd/Pollen-2.png" width="672" style="display: block; margin: auto;" /></p>
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<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res1 =<span class="st"> </span><span class="kw">SLSL</span>(R, <span class="dt">log=</span>F, <span class="dt">filter=</span>F, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res1<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.7755788</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res2 =<span class="st"> </span><span class="kw">SLSL</span>(X, <span class="dt">log=</span>T, <span class="dt">filter=</span>F, <span class="dt">correct_detection_rate =</span> F, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res2<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.8325414</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res3 =<span class="st"> </span><span class="kw">SLSL</span>(X, <span class="dt">log=</span>T, <span class="dt">filter=</span>F, <span class="dt">correct_detection_rate =</span> T, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res3<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.7665684</code></pre>
</div>
<div id="usoskin" class="section level2">
<h2>Usoskin</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">i =<span class="st"> </span><span class="dv">3</span>
<span class="kw">load</span>(<span class="st">'../data/unnecessary_in_building/3_Usoskin.RData'</span>)
X =<span class="st"> </span><span class="kw">as.matrix</span>(Usoskin<span class="op">$</span>X)
truth =<span class="st"> </span><span class="kw">as.numeric</span>(<span class="kw">as.factor</span>(<span class="kw">as.character</span>(Usoskin<span class="op">$</span>lab1)))
numClust =<span class="st"> </span><span class="dv">4</span>
<span class="kw">rm</span>(Usoskin)
logX =<span class="st"> </span><span class="kw">log</span>(X<span class="op">+</span><span class="dv">1</span>)
det =<span class="st"> </span><span class="kw">colSums</span>(X<span class="op">!=</span><span class="dv">0</span>) <span class="op">/</span><span class="st"> </span><span class="kw">nrow</span>(X)
<span class="kw">plot</span>(<span class="kw">irlba</span>(logX,<span class="dv">1</span>)<span class="op">$</span>v[,<span class="dv">1</span>]<span class="op">~</span><span class="kw">log</span>(det))</code></pre></div>
<p><img src="figure/detection_rate_correction.Rmd/Usoskin-1.png" width="672" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of Usoskin-1.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
<tr>
<th style="text-align:left;">
Version
</th>
<th style="text-align:left;">
Author
</th>
<th style="text-align:left;">
Date
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
<a href="https://github.com/tk382/SCNoisyClustering/blob/b7e4475a778b99f389303acbac3e5a9b5d09d752/docs/figure/detection_rate_correction.Rmd/Usoskin-1.png" target="_blank">b7e4475</a>
</td>
<td style="text-align:left;">
tk382
</td>
<td style="text-align:left;">
2018-07-16
</td>
</tr>
</tbody>
</table>
<p></details></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">det2 =<span class="st"> </span><span class="kw">qr</span>(<span class="kw">cbind</span>(<span class="kw">rep</span>(<span class="dv">1</span>, <span class="kw">length</span>(det)), <span class="kw">log</span>(det)))
R =<span class="st"> </span><span class="kw">t</span>(<span class="kw">qr.resid</span>(det2, <span class="kw">t</span>(logX)))
pca1 =<span class="st"> </span><span class="kw">irlba</span>(R,<span class="dv">2</span>); pca2 =<span class="st"> </span><span class="kw">irlba</span>(logX,<span class="dv">2</span>)
dat =<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">pc1=</span><span class="kw">c</span>(pca1<span class="op">$</span>v[,<span class="dv">1</span>], pca2<span class="op">$</span>v[,<span class="dv">1</span>]), <span class="dt">detection.rate=</span><span class="kw">rep</span>(det, <span class="dv">2</span>), <span class="dt">label=</span><span class="kw">rep</span>(<span class="kw">c</span>(<span class="st">"After correction"</span>, <span class="st">"Before correction"</span>), <span class="dt">each=</span><span class="kw">nrow</span>(pca1<span class="op">$</span>v)), <span class="dt">true.label=</span><span class="kw">as.factor</span>(<span class="kw">rep</span>(truth,<span class="dv">2</span>)))
<span class="kw">ggplot</span>(dat, <span class="kw">aes</span>(<span class="dt">x=</span>pc1, <span class="dt">y=</span>detection.rate, <span class="dt">col=</span>true.label)) <span class="op">+</span><span class="st"> </span><span class="kw">facet_grid</span>(<span class="op">~</span>label) <span class="op">+</span><span class="st"> </span><span class="kw">geom_point</span>() <span class="op">+</span><span class="st"> </span><span class="kw">ggtitle</span>(<span class="st">"PCA"</span>)</code></pre></div>
<p><img src="figure/detection_rate_correction.Rmd/Usoskin-2.png" width="672" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of Usoskin-2.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
<tr>
<th style="text-align:left;">
Version
</th>
<th style="text-align:left;">
Author
</th>
<th style="text-align:left;">
Date
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
<a href="https://github.com/tk382/SCNoisyClustering/blob/b7e4475a778b99f389303acbac3e5a9b5d09d752/docs/figure/detection_rate_correction.Rmd/Usoskin-2.png" target="_blank">b7e4475</a>
</td>
<td style="text-align:left;">
tk382
</td>
<td style="text-align:left;">
2018-07-16
</td>
</tr>
</tbody>
</table>
<p></details></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">tsne1 =<span class="st"> </span><span class="kw">Rtsne</span>(<span class="kw">t</span>(R), <span class="dt">perplexity=</span><span class="dv">20</span>)
tsne2 =<span class="st"> </span><span class="kw">Rtsne</span>(<span class="kw">t</span>(logX))
dat =<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">v1 =</span> <span class="kw">c</span>(tsne1<span class="op">$</span>Y[,<span class="dv">1</span>], tsne2<span class="op">$</span>Y[,<span class="dv">1</span>]), <span class="dt">v2 =</span> <span class="kw">c</span>(tsne1<span class="op">$</span>Y[,<span class="dv">2</span>], tsne2<span class="op">$</span>Y[,<span class="dv">2</span>]), <span class="dt">label=</span><span class="kw">rep</span>(<span class="kw">c</span>(<span class="st">"After correction"</span>, <span class="st">"Before correction"</span>), <span class="dt">each=</span><span class="kw">nrow</span>(tsne1<span class="op">$</span>Y)), <span class="dt">true.label =</span> <span class="kw">as.factor</span>(<span class="kw">rep</span>(truth, <span class="dv">2</span>)))
<span class="kw">ggplot</span>(dat, <span class="kw">aes</span>(<span class="dt">x=</span>v1, <span class="dt">y=</span>v2, <span class="dt">col=</span>true.label)) <span class="op">+</span><span class="st"> </span><span class="kw">facet_grid</span>(<span class="op">~</span>label) <span class="op">+</span><span class="st"> </span><span class="kw">geom_point</span>() <span class="op">+</span><span class="st"> </span><span class="kw">ggtitle</span>(<span class="st">"tSNE"</span>)</code></pre></div>
<p><img src="figure/detection_rate_correction.Rmd/Usoskin-3.png" width="672" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of Usoskin-3.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
<tr>
<th style="text-align:left;">
Version
</th>
<th style="text-align:left;">
Author
</th>
<th style="text-align:left;">
Date
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
<a href="https://github.com/tk382/SCNoisyClustering/blob/b7e4475a778b99f389303acbac3e5a9b5d09d752/docs/figure/detection_rate_correction.Rmd/Usoskin-3.png" target="_blank">b7e4475</a>
</td>
<td style="text-align:left;">
tk382
</td>
<td style="text-align:left;">
2018-07-16
</td>
</tr>
</tbody>
</table>
<p></details></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res1 =<span class="st"> </span><span class="kw">SLSL</span>(R, <span class="dt">log=</span>F, <span class="dt">filter=</span>F, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res1<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.6188269</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res2 =<span class="st"> </span><span class="kw">SLSL</span>(X, <span class="dt">log=</span>T, <span class="dt">filter=</span>F, <span class="dt">correct_detection_rate =</span> F, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res2<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.8746858</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res3 =<span class="st"> </span><span class="kw">SLSL</span>(X, <span class="dt">log=</span>T, <span class="dt">filter=</span>F, <span class="dt">correct_detection_rate =</span> T, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res3<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.6348444</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rm</span>(R,X,logX,res1,res2,res3); <span class="kw">gc</span>()</code></pre></div>
<pre><code> used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
Ncells 2221109 118.7 3972565 212.2 NA 3972565 212.2
Vcells 5410323 41.3 166030754 1266.8 16384 207538345 1583.4</code></pre>
</div>
<div id="buettner" class="section level2">
<h2>Buettner</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">i =<span class="st"> </span><span class="dv">4</span>
<span class="co">#read data</span>
<span class="kw">load</span>(<span class="st">'../data/unnecessary_in_building/4_Buettner.RData'</span>)
X =<span class="st"> </span><span class="kw">as.matrix</span>(Buettner<span class="op">$</span>X)
truth =<span class="st"> </span><span class="kw">as.numeric</span>(<span class="kw">as.factor</span>(Buettner<span class="op">$</span>label))
numClust =<span class="st"> </span><span class="dv">3</span>
<span class="kw">rm</span>(Buettner)
logX =<span class="st"> </span><span class="kw">log</span>(X<span class="op">+</span><span class="dv">1</span>)
det =<span class="st"> </span><span class="kw">colSums</span>(X<span class="op">!=</span><span class="dv">0</span>) <span class="op">/</span><span class="st"> </span><span class="kw">nrow</span>(X)
det2 =<span class="st"> </span><span class="kw">qr</span>(det)
R =<span class="st"> </span><span class="kw">t</span>(<span class="kw">qr.resid</span>(det2, <span class="kw">t</span>(logX)))
pca1 =<span class="st"> </span><span class="kw">irlba</span>(R,<span class="dv">2</span>); pca2 =<span class="st"> </span><span class="kw">irlba</span>(logX,<span class="dv">2</span>)
dat =<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">pc1=</span><span class="kw">c</span>(pca1<span class="op">$</span>v[,<span class="dv">1</span>], pca2<span class="op">$</span>v[,<span class="dv">1</span>]), <span class="dt">detection.rate=</span><span class="kw">rep</span>(det, <span class="dv">2</span>), <span class="dt">label=</span><span class="kw">rep</span>(<span class="kw">c</span>(<span class="st">"After correction"</span>, <span class="st">"Before correction"</span>), <span class="dt">each=</span><span class="kw">nrow</span>(pca1<span class="op">$</span>v)), <span class="dt">true.label=</span><span class="kw">as.factor</span>(<span class="kw">rep</span>(truth,<span class="dv">2</span>)))
<span class="kw">ggplot</span>(dat, <span class="kw">aes</span>(<span class="dt">x=</span>pc1, <span class="dt">y=</span>detection.rate, <span class="dt">col=</span>true.label)) <span class="op">+</span><span class="st"> </span><span class="kw">facet_grid</span>(<span class="op">~</span>label) <span class="op">+</span><span class="st"> </span><span class="kw">geom_point</span>() <span class="op">+</span><span class="st"> </span><span class="kw">ggtitle</span>(<span class="st">"PCA"</span>)</code></pre></div>
<p><img src="figure/detection_rate_correction.Rmd/Buettner-1.png" width="672" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of Buettner-1.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
<tr>
<th style="text-align:left;">
Version
</th>
<th style="text-align:left;">
Author
</th>
<th style="text-align:left;">
Date
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
<a href="https://github.com/tk382/SCNoisyClustering/blob/b7e4475a778b99f389303acbac3e5a9b5d09d752/docs/figure/detection_rate_correction.Rmd/Buettner-1.png" target="_blank">b7e4475</a>
</td>
<td style="text-align:left;">
tk382
</td>
<td style="text-align:left;">
2018-07-16
</td>
</tr>
</tbody>
</table>
<p></details></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">tsne1 =<span class="st"> </span><span class="kw">Rtsne</span>(<span class="kw">t</span>(R), <span class="dt">perplexity=</span><span class="dv">20</span>)
tsne2 =<span class="st"> </span><span class="kw">Rtsne</span>(<span class="kw">t</span>(logX), <span class="dt">perplexity=</span><span class="dv">20</span>)
dat =<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">v1 =</span> <span class="kw">c</span>(tsne1<span class="op">$</span>Y[,<span class="dv">1</span>], tsne2<span class="op">$</span>Y[,<span class="dv">1</span>]), <span class="dt">v2 =</span> <span class="kw">c</span>(tsne1<span class="op">$</span>Y[,<span class="dv">2</span>], tsne2<span class="op">$</span>Y[,<span class="dv">2</span>]), <span class="dt">label=</span><span class="kw">rep</span>(<span class="kw">c</span>(<span class="st">"After correction"</span>, <span class="st">"Before correction"</span>), <span class="dt">each=</span><span class="kw">nrow</span>(tsne1<span class="op">$</span>Y)), <span class="dt">true.label =</span> <span class="kw">as.factor</span>(<span class="kw">rep</span>(truth, <span class="dv">2</span>)))
<span class="kw">ggplot</span>(dat, <span class="kw">aes</span>(<span class="dt">x=</span>v1, <span class="dt">y=</span>v2, <span class="dt">col=</span>true.label)) <span class="op">+</span><span class="st"> </span><span class="kw">facet_grid</span>(<span class="op">~</span>label) <span class="op">+</span><span class="st"> </span><span class="kw">geom_point</span>() <span class="op">+</span><span class="st"> </span><span class="kw">ggtitle</span>(<span class="st">"tSNE"</span>)</code></pre></div>
<p><img src="figure/detection_rate_correction.Rmd/Buettner-2.png" width="672" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of Buettner-2.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
<tr>
<th style="text-align:left;">
Version
</th>
<th style="text-align:left;">
Author
</th>
<th style="text-align:left;">
Date
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
<a href="https://github.com/tk382/SCNoisyClustering/blob/b7e4475a778b99f389303acbac3e5a9b5d09d752/docs/figure/detection_rate_correction.Rmd/Buettner-2.png" target="_blank">b7e4475</a>
</td>
<td style="text-align:left;">
tk382
</td>
<td style="text-align:left;">
2018-07-16
</td>
</tr>
</tbody>
</table>
<p></details></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res1 =<span class="st"> </span><span class="kw">SLSL</span>(R, <span class="dt">log=</span>F, <span class="dt">filter=</span>F, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res1<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.4329975</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res2 =<span class="st"> </span><span class="kw">SLSL</span>(X, <span class="dt">log=</span>T, <span class="dt">filter=</span>F, <span class="dt">correct_detection_rate =</span> F, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res2<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.428236</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res3 =<span class="st"> </span><span class="kw">SLSL</span>(X, <span class="dt">log=</span>T, <span class="dt">filter=</span>F, <span class="dt">correct_detection_rate =</span> T, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res3<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.4145447</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rm</span>(R,X,logX,res1,res2,res3); <span class="kw">gc</span>()</code></pre></div>
<pre><code> used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
Ncells 2203793 117.7 3972484 212.2 NA 3972484 212.2
Vcells 5419519 41.4 138305840 1055.2 16384 172882188 1319.0</code></pre>
</div>
<div id="yan" class="section level2">
<h2>Yan</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">i =<span class="st"> </span><span class="dv">5</span>
<span class="kw">load</span>(<span class="st">'../data/unnecessary_in_building/5_Yan.rda'</span>)
X =<span class="st"> </span><span class="kw">as.matrix</span>(yan)
truth =<span class="st"> </span><span class="kw">as.character</span>(ann<span class="op">$</span>cell_type1)
truth =<span class="st"> </span><span class="kw">as.numeric</span>(<span class="kw">as.factor</span>(truth))
numClust =<span class="st"> </span><span class="dv">6</span>
<span class="kw">rm</span>(ann, yan)
logX =<span class="st"> </span><span class="kw">log</span>(X<span class="op">+</span><span class="dv">1</span>)
det =<span class="st"> </span><span class="kw">colSums</span>(X<span class="op">!=</span><span class="dv">0</span>) <span class="op">/</span><span class="st"> </span><span class="kw">nrow</span>(X)
det2 =<span class="st"> </span><span class="kw">qr</span>(det)
R =<span class="st"> </span><span class="kw">t</span>(<span class="kw">qr.resid</span>(det2, <span class="kw">t</span>(logX)))
pca1 =<span class="st"> </span><span class="kw">irlba</span>(R,<span class="dv">2</span>); pca2 =<span class="st"> </span><span class="kw">irlba</span>(logX,<span class="dv">2</span>)
dat =<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">pc1=</span><span class="kw">c</span>(pca1<span class="op">$</span>v[,<span class="dv">1</span>], pca2<span class="op">$</span>v[,<span class="dv">1</span>]), <span class="dt">detection.rate=</span><span class="kw">rep</span>(det, <span class="dv">2</span>), <span class="dt">label=</span><span class="kw">rep</span>(<span class="kw">c</span>(<span class="st">"After correction"</span>, <span class="st">"Before correction"</span>), <span class="dt">each=</span><span class="kw">nrow</span>(pca1<span class="op">$</span>v)), <span class="dt">true.label=</span><span class="kw">as.factor</span>(<span class="kw">rep</span>(truth,<span class="dv">2</span>)))
<span class="kw">ggplot</span>(dat, <span class="kw">aes</span>(<span class="dt">x=</span>pc1, <span class="dt">y=</span>detection.rate, <span class="dt">col=</span>true.label)) <span class="op">+</span><span class="st"> </span><span class="kw">facet_grid</span>(<span class="op">~</span>label) <span class="op">+</span><span class="st"> </span><span class="kw">geom_point</span>() <span class="op">+</span><span class="st"> </span><span class="kw">ggtitle</span>(<span class="st">"PCA"</span>)</code></pre></div>
<p><img src="figure/detection_rate_correction.Rmd/Yan-1.png" width="672" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of Yan-1.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
<tr>
<th style="text-align:left;">
Version
</th>
<th style="text-align:left;">
Author
</th>
<th style="text-align:left;">
Date
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
<a href="https://github.com/tk382/SCNoisyClustering/blob/b7e4475a778b99f389303acbac3e5a9b5d09d752/docs/figure/detection_rate_correction.Rmd/Yan-1.png" target="_blank">b7e4475</a>
</td>
<td style="text-align:left;">
tk382
</td>
<td style="text-align:left;">
2018-07-16
</td>
</tr>
</tbody>
</table>
<p></details></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">tsne1 =<span class="st"> </span><span class="kw">Rtsne</span>(<span class="kw">t</span>(R), <span class="dt">perplexity=</span><span class="dv">20</span>)
tsne2 =<span class="st"> </span><span class="kw">Rtsne</span>(<span class="kw">t</span>(logX), <span class="dt">perplexity=</span><span class="dv">20</span>)
dat =<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">v1 =</span> <span class="kw">c</span>(tsne1<span class="op">$</span>Y[,<span class="dv">1</span>], tsne2<span class="op">$</span>Y[,<span class="dv">1</span>]), <span class="dt">v2 =</span> <span class="kw">c</span>(tsne1<span class="op">$</span>Y[,<span class="dv">2</span>], tsne2<span class="op">$</span>Y[,<span class="dv">2</span>]), <span class="dt">label=</span><span class="kw">rep</span>(<span class="kw">c</span>(<span class="st">"After correction"</span>, <span class="st">"Before correction"</span>), <span class="dt">each=</span><span class="kw">nrow</span>(tsne1<span class="op">$</span>Y)), <span class="dt">true.label =</span> <span class="kw">as.factor</span>(<span class="kw">rep</span>(truth, <span class="dv">2</span>)))
<span class="kw">ggplot</span>(dat, <span class="kw">aes</span>(<span class="dt">x=</span>v1, <span class="dt">y=</span>v2, <span class="dt">col=</span>true.label)) <span class="op">+</span><span class="st"> </span><span class="kw">facet_grid</span>(<span class="op">~</span>label) <span class="op">+</span><span class="st"> </span><span class="kw">geom_point</span>() <span class="op">+</span><span class="st"> </span><span class="kw">ggtitle</span>(<span class="st">"tSNE"</span>)</code></pre></div>
<p><img src="figure/detection_rate_correction.Rmd/Yan-2.png" width="672" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of Yan-2.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
<tr>
<th style="text-align:left;">
Version
</th>
<th style="text-align:left;">
Author
</th>
<th style="text-align:left;">
Date
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
<a href="https://github.com/tk382/SCNoisyClustering/blob/36ebfc22180cfa5fe94d018f30be3872b66a15d2/docs/figure/detection_rate_correction.Rmd/Yan-2.png" target="_blank">36ebfc2</a>
</td>
<td style="text-align:left;">
tk382
</td>
<td style="text-align:left;">
2018-07-16
</td>
</tr>
<tr>
<td style="text-align:left;">
<a href="https://github.com/tk382/SCNoisyClustering/blob/b7e4475a778b99f389303acbac3e5a9b5d09d752/docs/figure/detection_rate_correction.Rmd/Yan-2.png" target="_blank">b7e4475</a>
</td>
<td style="text-align:left;">
tk382
</td>
<td style="text-align:left;">
2018-07-16
</td>
</tr>
</tbody>
</table>
<p></details></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res1 =<span class="st"> </span><span class="kw">SLSL</span>(R, <span class="dt">log=</span>F, <span class="dt">filter=</span>F, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res1<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.8954618</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res2 =<span class="st"> </span><span class="kw">SLSL</span>(X, <span class="dt">log=</span>T, <span class="dt">filter=</span>F, <span class="dt">correct_detection_rate =</span> F, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res2<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.8954618</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res3 =<span class="st"> </span><span class="kw">SLSL</span>(X, <span class="dt">log=</span>T, <span class="dt">filter=</span>F, <span class="dt">correct_detection_rate =</span> T, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res3<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.675345</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rm</span>(R,X,logX,res1,res2,res3); <span class="kw">gc</span>()</code></pre></div>
<pre><code> used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
Ncells 2236314 119.5 3972484 212.2 NA 3972484 212.2
Vcells 5358557 40.9 110644672 844.2 16384 172882188 1319.0</code></pre>
</div>
<div id="treutlein" class="section level2">
<h2>Treutlein</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">i =<span class="st"> </span><span class="dv">6</span>
<span class="kw">load</span>(<span class="st">'../data/unnecessary_in_building/6_Treutlein.rda'</span>)
X =<span class="st"> </span><span class="kw">as.matrix</span>(treutlein)
truth =<span class="st"> </span><span class="kw">as.numeric</span>(<span class="kw">colnames</span>(treutlein))
ind =<span class="st"> </span><span class="kw">sort</span>(truth, <span class="dt">index.return=</span><span class="ot">TRUE</span>)<span class="op">$</span>ix
X =<span class="st"> </span>X[,ind]
truth =<span class="st"> </span>truth[ind]
numClust =<span class="st"> </span><span class="kw">length</span>(<span class="kw">unique</span>(truth))
<span class="kw">rm</span>(treutlein)
logX =<span class="st"> </span><span class="kw">log</span>(X<span class="op">+</span><span class="dv">1</span>)
det =<span class="st"> </span><span class="kw">colSums</span>(X<span class="op">!=</span><span class="dv">0</span>) <span class="op">/</span><span class="st"> </span><span class="kw">nrow</span>(X)
det2 =<span class="st"> </span><span class="kw">qr</span>(<span class="kw">cbind</span>(<span class="kw">log</span>(det), <span class="kw">rep</span>(<span class="dv">1</span>, <span class="kw">length</span>(det))))
R =<span class="st"> </span><span class="kw">t</span>(<span class="kw">qr.resid</span>(det2, <span class="kw">t</span>(logX)))
pca1 =<span class="st"> </span><span class="kw">irlba</span>(R,<span class="dv">2</span>); pca2 =<span class="st"> </span><span class="kw">irlba</span>(logX,<span class="dv">2</span>)
dat =<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">pc1=</span><span class="kw">c</span>(pca1<span class="op">$</span>v[,<span class="dv">1</span>], pca2<span class="op">$</span>v[,<span class="dv">1</span>]), <span class="dt">detection.rate=</span><span class="kw">rep</span>(det, <span class="dv">2</span>), <span class="dt">label=</span><span class="kw">rep</span>(<span class="kw">c</span>(<span class="st">"After correction"</span>, <span class="st">"Before correction"</span>), <span class="dt">each=</span><span class="kw">nrow</span>(pca1<span class="op">$</span>v)), <span class="dt">true.label=</span><span class="kw">as.factor</span>(<span class="kw">rep</span>(truth,<span class="dv">2</span>)))
<span class="kw">ggplot</span>(dat, <span class="kw">aes</span>(<span class="dt">x=</span>pc1, <span class="dt">y=</span>detection.rate, <span class="dt">col=</span>true.label)) <span class="op">+</span><span class="st"> </span><span class="kw">facet_grid</span>(<span class="op">~</span>label) <span class="op">+</span><span class="st"> </span><span class="kw">geom_point</span>() <span class="op">+</span><span class="st"> </span><span class="kw">ggtitle</span>(<span class="st">"PCA"</span>)</code></pre></div>
<p><img src="figure/detection_rate_correction.Rmd/Treutlein-1.png" width="672" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of Treutlein-1.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
<tr>
<th style="text-align:left;">
Version
</th>
<th style="text-align:left;">
Author
</th>
<th style="text-align:left;">
Date
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
<a href="https://github.com/tk382/SCNoisyClustering/blob/36ebfc22180cfa5fe94d018f30be3872b66a15d2/docs/figure/detection_rate_correction.Rmd/Treutlein-1.png" target="_blank">36ebfc2</a>
</td>
<td style="text-align:left;">
tk382
</td>
<td style="text-align:left;">
2018-07-16
</td>
</tr>
<tr>
<td style="text-align:left;">
<a href="https://github.com/tk382/SCNoisyClustering/blob/b7e4475a778b99f389303acbac3e5a9b5d09d752/docs/figure/detection_rate_correction.Rmd/Treutlein-1.png" target="_blank">b7e4475</a>
</td>
<td style="text-align:left;">
tk382
</td>
<td style="text-align:left;">
2018-07-16
</td>
</tr>
</tbody>
</table>
<p></details></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">tsne1 =<span class="st"> </span><span class="kw">Rtsne</span>(<span class="kw">t</span>(R), <span class="dt">perplexity=</span><span class="dv">10</span>)
tsne2 =<span class="st"> </span><span class="kw">Rtsne</span>(<span class="kw">t</span>(logX), <span class="dt">perplexity=</span><span class="dv">10</span>)
dat =<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">v1 =</span> <span class="kw">c</span>(tsne1<span class="op">$</span>Y[,<span class="dv">1</span>], tsne2<span class="op">$</span>Y[,<span class="dv">1</span>]), <span class="dt">v2 =</span> <span class="kw">c</span>(tsne1<span class="op">$</span>Y[,<span class="dv">2</span>], tsne2<span class="op">$</span>Y[,<span class="dv">2</span>]), <span class="dt">label=</span><span class="kw">rep</span>(<span class="kw">c</span>(<span class="st">"After correction"</span>, <span class="st">"Before correction"</span>), <span class="dt">each=</span><span class="kw">nrow</span>(tsne1<span class="op">$</span>Y)), <span class="dt">true.label =</span> <span class="kw">as.factor</span>(<span class="kw">rep</span>(truth, <span class="dv">2</span>)))
<span class="kw">ggplot</span>(dat, <span class="kw">aes</span>(<span class="dt">x=</span>v1, <span class="dt">y=</span>v2, <span class="dt">col=</span>true.label)) <span class="op">+</span><span class="st"> </span><span class="kw">facet_grid</span>(<span class="op">~</span>label) <span class="op">+</span><span class="st"> </span><span class="kw">geom_point</span>() <span class="op">+</span><span class="st"> </span><span class="kw">ggtitle</span>(<span class="st">"tSNE"</span>)</code></pre></div>
<p><img src="figure/detection_rate_correction.Rmd/Treutlein-2.png" width="672" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of Treutlein-2.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
<tr>
<th style="text-align:left;">
Version
</th>
<th style="text-align:left;">
Author
</th>
<th style="text-align:left;">
Date
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
<a href="https://github.com/tk382/SCNoisyClustering/blob/36ebfc22180cfa5fe94d018f30be3872b66a15d2/docs/figure/detection_rate_correction.Rmd/Treutlein-2.png" target="_blank">36ebfc2</a>
</td>
<td style="text-align:left;">
tk382
</td>
<td style="text-align:left;">
2018-07-16
</td>
</tr>
<tr>
<td style="text-align:left;">
<a href="https://github.com/tk382/SCNoisyClustering/blob/b7e4475a778b99f389303acbac3e5a9b5d09d752/docs/figure/detection_rate_correction.Rmd/Treutlein-2.png" target="_blank">b7e4475</a>
</td>
<td style="text-align:left;">
tk382
</td>
<td style="text-align:left;">
2018-07-16
</td>
</tr>
</tbody>
</table>
<p></details></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res1 =<span class="st"> </span><span class="kw">SLSL</span>(R, <span class="dt">log=</span>F, <span class="dt">filter=</span>F, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res1<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.3672819</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res2 =<span class="st"> </span><span class="kw">SLSL</span>(X, <span class="dt">log=</span>T, <span class="dt">filter=</span>F, <span class="dt">correct_detection_rate =</span> F, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res2<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.4136064</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res3 =<span class="st"> </span><span class="kw">SLSL</span>(X, <span class="dt">log=</span>T, <span class="dt">filter=</span>F, <span class="dt">correct_detection_rate =</span> T, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res3<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.3488583</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rm</span>(R,X,logX,res1,res2,res3); <span class="kw">gc</span>()</code></pre></div>
<pre><code> used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
Ncells 2225549 118.9 3972484 212.2 NA 3972484 212.2
Vcells 5350667 40.9 88515737 675.4 16384 172882188 1319.0</code></pre>
</div>
<div id="chu-cell-type" class="section level2">
<h2>Chu (cell type)</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">i =<span class="st"> </span><span class="dv">7</span>
<span class="kw">load</span>(<span class="st">'../data/unnecessary_in_building/7_Chu_celltype.Rdata'</span>)
X =<span class="st"> </span><span class="kw">as.matrix</span>(Chu_celltype<span class="op">$</span>X)
truth =<span class="st"> </span><span class="kw">as.numeric</span>(<span class="kw">as.factor</span>(Chu_celltype<span class="op">$</span>label))
numClust =<span class="st"> </span><span class="dv">7</span>
<span class="kw">rm</span>(Chu_celltype)
logX =<span class="st"> </span><span class="kw">log</span>(X<span class="op">+</span><span class="dv">1</span>)
det =<span class="st"> </span><span class="kw">colSums</span>(X<span class="op">!=</span><span class="dv">0</span>) <span class="op">/</span><span class="st"> </span><span class="kw">nrow</span>(X)
det2 =<span class="st"> </span><span class="kw">qr</span>(det)
R =<span class="st"> </span><span class="kw">t</span>(<span class="kw">qr.resid</span>(det2, <span class="kw">t</span>(logX)))
pca1 =<span class="st"> </span><span class="kw">irlba</span>(R,<span class="dv">2</span>); pca2 =<span class="st"> </span><span class="kw">irlba</span>(logX,<span class="dv">2</span>)
dat =<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">pc1=</span><span class="kw">c</span>(pca1<span class="op">$</span>v[,<span class="dv">1</span>], pca2<span class="op">$</span>v[,<span class="dv">1</span>]), <span class="dt">detection.rate=</span><span class="kw">rep</span>(det, <span class="dv">2</span>), <span class="dt">label=</span><span class="kw">rep</span>(<span class="kw">c</span>(<span class="st">"After correction"</span>, <span class="st">"Before correction"</span>), <span class="dt">each=</span><span class="kw">nrow</span>(pca1<span class="op">$</span>v)), <span class="dt">true.label=</span><span class="kw">as.factor</span>(<span class="kw">rep</span>(truth,<span class="dv">2</span>)))
<span class="kw">ggplot</span>(dat, <span class="kw">aes</span>(<span class="dt">x=</span>pc1, <span class="dt">y=</span>detection.rate, <span class="dt">col=</span>true.label)) <span class="op">+</span><span class="st"> </span><span class="kw">facet_grid</span>(<span class="op">~</span>label) <span class="op">+</span><span class="st"> </span><span class="kw">geom_point</span>() <span class="op">+</span><span class="st"> </span><span class="kw">ggtitle</span>(<span class="st">"PCA"</span>)</code></pre></div>
<p><img src="figure/detection_rate_correction.Rmd/Chu_celltype-1.png" width="672" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of Chu_celltype-1.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
<tr>
<th style="text-align:left;">
Version
</th>
<th style="text-align:left;">
Author
</th>
<th style="text-align:left;">
Date
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
<a href="https://github.com/tk382/SCNoisyClustering/blob/b7e4475a778b99f389303acbac3e5a9b5d09d752/docs/figure/detection_rate_correction.Rmd/Chu_celltype-1.png" target="_blank">b7e4475</a>
</td>
<td style="text-align:left;">
tk382
</td>
<td style="text-align:left;">
2018-07-16
</td>
</tr>
</tbody>
</table>
<p></details></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">tsne1 =<span class="st"> </span><span class="kw">Rtsne</span>(<span class="kw">t</span>(R))
tsne2 =<span class="st"> </span><span class="kw">Rtsne</span>(<span class="kw">t</span>(logX))
dat =<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">v1 =</span> <span class="kw">c</span>(tsne1<span class="op">$</span>Y[,<span class="dv">1</span>], tsne2<span class="op">$</span>Y[,<span class="dv">1</span>]), <span class="dt">v2 =</span> <span class="kw">c</span>(tsne1<span class="op">$</span>Y[,<span class="dv">2</span>], tsne2<span class="op">$</span>Y[,<span class="dv">2</span>]), <span class="dt">label=</span><span class="kw">rep</span>(<span class="kw">c</span>(<span class="st">"After correction"</span>, <span class="st">"Before correction"</span>), <span class="dt">each=</span><span class="kw">nrow</span>(tsne1<span class="op">$</span>Y)), <span class="dt">true.label =</span> <span class="kw">as.factor</span>(<span class="kw">rep</span>(truth, <span class="dv">2</span>)))
<span class="kw">ggplot</span>(dat, <span class="kw">aes</span>(<span class="dt">x=</span>v1, <span class="dt">y=</span>v2, <span class="dt">col=</span>true.label)) <span class="op">+</span><span class="st"> </span><span class="kw">facet_grid</span>(<span class="op">~</span>label) <span class="op">+</span><span class="st"> </span><span class="kw">geom_point</span>() <span class="op">+</span><span class="st"> </span><span class="kw">ggtitle</span>(<span class="st">"tSNE"</span>)</code></pre></div>
<p><img src="figure/detection_rate_correction.Rmd/Chu_celltype-2.png" width="672" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of Chu_celltype-2.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
<tr>
<th style="text-align:left;">
Version
</th>
<th style="text-align:left;">
Author
</th>
<th style="text-align:left;">
Date
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
<a href="https://github.com/tk382/SCNoisyClustering/blob/b7e4475a778b99f389303acbac3e5a9b5d09d752/docs/figure/detection_rate_correction.Rmd/Chu_celltype-2.png" target="_blank">b7e4475</a>
</td>
<td style="text-align:left;">
tk382
</td>
<td style="text-align:left;">
2018-07-16
</td>
</tr>
</tbody>
</table>
<p></details></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res1 =<span class="st"> </span><span class="kw">SLSL</span>(R, <span class="dt">log=</span>F, <span class="dt">filter=</span>F, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res1<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.9900038</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res2 =<span class="st"> </span><span class="kw">SLSL</span>(X, <span class="dt">log=</span>T, <span class="dt">filter=</span>F, <span class="dt">correct_detection_rate =</span> F, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res2<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.9956408</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res3 =<span class="st"> </span><span class="kw">SLSL</span>(X, <span class="dt">log=</span>T, <span class="dt">filter=</span>F, <span class="dt">correct_detection_rate =</span> T, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res3<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.7612027</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rm</span>(R,X,logX,res1,res2,res3); <span class="kw">gc</span>()</code></pre></div>
<pre><code> used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
Ncells 2259138 120.7 3972565 212.2 NA 3972565 212.2
Vcells 5473999 41.8 207597943 1583.9 16384 259497187 1979.9</code></pre>
</div>
<div id="chu-timecourse" class="section level2">
<h2>Chu (timecourse)</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">i =<span class="st"> </span><span class="dv">8</span>
<span class="kw">load</span>(<span class="st">'../data/unnecessary_in_building/8_Chu_timecourse.Rdata'</span>)
X =<span class="st"> </span><span class="kw">as.matrix</span>(Chu_timecourse<span class="op">$</span>X)
truth =<span class="st"> </span><span class="kw">as.numeric</span>(<span class="kw">as.factor</span>(Chu_timecourse<span class="op">$</span>label))
numClust =<span class="st"> </span><span class="kw">length</span>(<span class="kw">unique</span>(truth))
logX =<span class="st"> </span><span class="kw">log</span>(X<span class="op">+</span><span class="dv">1</span>)
det =<span class="st"> </span><span class="kw">colSums</span>(X<span class="op">!=</span><span class="dv">0</span>) <span class="op">/</span><span class="st"> </span><span class="kw">nrow</span>(X)
det2 =<span class="st"> </span><span class="kw">qr</span>(det)
R =<span class="st"> </span><span class="kw">t</span>(<span class="kw">qr.resid</span>(det2, <span class="kw">t</span>(logX)))
pca1 =<span class="st"> </span><span class="kw">irlba</span>(R,<span class="dv">2</span>); pca2 =<span class="st"> </span><span class="kw">irlba</span>(logX,<span class="dv">2</span>)
dat =<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">pc1=</span><span class="kw">c</span>(pca1<span class="op">$</span>v[,<span class="dv">1</span>], pca2<span class="op">$</span>v[,<span class="dv">1</span>]), <span class="dt">detection.rate=</span><span class="kw">rep</span>(det, <span class="dv">2</span>), <span class="dt">label=</span><span class="kw">rep</span>(<span class="kw">c</span>(<span class="st">"After correction"</span>, <span class="st">"Before correction"</span>), <span class="dt">each=</span><span class="kw">nrow</span>(pca1<span class="op">$</span>v)), <span class="dt">true.label=</span><span class="kw">as.factor</span>(<span class="kw">rep</span>(truth,<span class="dv">2</span>)))
<span class="kw">ggplot</span>(dat, <span class="kw">aes</span>(<span class="dt">x=</span>pc1, <span class="dt">y=</span>detection.rate, <span class="dt">col=</span>true.label)) <span class="op">+</span><span class="st"> </span><span class="kw">facet_grid</span>(<span class="op">~</span>label) <span class="op">+</span><span class="st"> </span><span class="kw">geom_point</span>() <span class="op">+</span><span class="st"> </span><span class="kw">ggtitle</span>(<span class="st">"PCA"</span>)</code></pre></div>
<p><img src="figure/detection_rate_correction.Rmd/Chu_timecourse-1.png" width="672" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of Chu_timecourse-1.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
<tr>
<th style="text-align:left;">
Version
</th>
<th style="text-align:left;">
Author
</th>
<th style="text-align:left;">
Date
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
<a href="https://github.com/tk382/SCNoisyClustering/blob/b7e4475a778b99f389303acbac3e5a9b5d09d752/docs/figure/detection_rate_correction.Rmd/Chu_timecourse-1.png" target="_blank">b7e4475</a>
</td>
<td style="text-align:left;">
tk382
</td>
<td style="text-align:left;">
2018-07-16
</td>
</tr>
</tbody>
</table>
<p></details></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">tsne1 =<span class="st"> </span><span class="kw">Rtsne</span>(<span class="kw">t</span>(R))
tsne2 =<span class="st"> </span><span class="kw">Rtsne</span>(<span class="kw">t</span>(logX))
dat =<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">v1 =</span> <span class="kw">c</span>(tsne1<span class="op">$</span>Y[,<span class="dv">1</span>], tsne2<span class="op">$</span>Y[,<span class="dv">1</span>]), <span class="dt">v2 =</span> <span class="kw">c</span>(tsne1<span class="op">$</span>Y[,<span class="dv">2</span>], tsne2<span class="op">$</span>Y[,<span class="dv">2</span>]), <span class="dt">label=</span><span class="kw">rep</span>(<span class="kw">c</span>(<span class="st">"After correction"</span>, <span class="st">"Before correction"</span>), <span class="dt">each=</span><span class="kw">nrow</span>(tsne1<span class="op">$</span>Y)), <span class="dt">true.label =</span> <span class="kw">as.factor</span>(<span class="kw">rep</span>(truth, <span class="dv">2</span>)))
<span class="kw">ggplot</span>(dat, <span class="kw">aes</span>(<span class="dt">x=</span>v1, <span class="dt">y=</span>v2, <span class="dt">col=</span>true.label)) <span class="op">+</span><span class="st"> </span><span class="kw">facet_grid</span>(<span class="op">~</span>label) <span class="op">+</span><span class="st"> </span><span class="kw">geom_point</span>() <span class="op">+</span><span class="st"> </span><span class="kw">ggtitle</span>(<span class="st">"tSNE"</span>)</code></pre></div>
<p><img src="figure/detection_rate_correction.Rmd/Chu_timecourse-2.png" width="672" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of Chu_timecourse-2.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
<tr>
<th style="text-align:left;">
Version
</th>
<th style="text-align:left;">
Author
</th>
<th style="text-align:left;">
Date
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
<a href="https://github.com/tk382/SCNoisyClustering/blob/b7e4475a778b99f389303acbac3e5a9b5d09d752/docs/figure/detection_rate_correction.Rmd/Chu_timecourse-2.png" target="_blank">b7e4475</a>
</td>
<td style="text-align:left;">
tk382
</td>
<td style="text-align:left;">
2018-07-16
</td>
</tr>
</tbody>
</table>
<p></details></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res1 =<span class="st"> </span><span class="kw">SLSL</span>(R, <span class="dt">log=</span>F, <span class="dt">filter=</span>F, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res1<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.7321747</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res2 =<span class="st"> </span><span class="kw">SLSL</span>(X, <span class="dt">log=</span>T, <span class="dt">filter=</span>F, <span class="dt">correct_detection_rate =</span> F, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res2<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.7276994</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">set.seed</span>(<span class="dv">1</span>); res3 =<span class="st"> </span><span class="kw">SLSL</span>(X, <span class="dt">log=</span>T, <span class="dt">filter=</span>F, <span class="dt">correct_detection_rate =</span> T, <span class="dt">numClust =</span> numClust)
<span class="kw">adj.rand.index</span>(res3<span class="op">$</span>result, truth)</code></pre></div>
<pre><code>[1] 0.7145637</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rm</span>(R,X,logX,res1,res2,res3); <span class="kw">gc</span>()</code></pre></div>
<pre><code> used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
Ncells 2260642 120.8 3972565 212.2 NA 3972565 212.2
Vcells 20014295 152.7 199358024 1521.0 16384 259497187 1979.9</code></pre>
</div>
<div id="session-information" class="section level2">
<h2>Session information</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">sessionInfo</span>()</code></pre></div>
<pre><code>R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] stargazer_5.2.2 abind_1.4-5
[3] broom_0.4.5 diceR_0.5.1
[5] Rtsne_0.13 fossil_0.3.7
[7] shapefiles_0.7 foreign_0.8-70
[9] maps_3.3.0 sp_1.2-7
[11] reshape_0.8.7 dplyr_0.7.6
[13] ggplot2_3.0.0 irlba_2.3.2
[15] Matrix_1.2-14 quadprog_1.5-5
[17] inline_0.3.15 matrixStats_0.53.1
[19] SCNoisyClustering_0.1.0
loaded via a namespace (and not attached):
[1] tidyselect_0.2.4 reshape2_1.4.3 purrr_0.2.4
[4] lattice_0.20-35 colorspace_1.3-2 htmltools_0.3.6
[7] yaml_2.1.19 rlang_0.2.0 R.oo_1.22.0
[10] pillar_1.2.2 glue_1.2.0 withr_2.1.2
[13] R.utils_2.6.0 bindrcpp_0.2.2 plyr_1.8.4
[16] bindr_0.1.1 stringr_1.3.0 munsell_0.4.3
[19] gtable_0.2.0 workflowr_1.1.1 R.methodsS3_1.7.1
[22] psych_1.8.3.3 evaluate_0.10.1 labeling_0.3
[25] knitr_1.20 parallel_3.5.1 Rcpp_0.12.16
[28] scales_0.5.0 backports_1.1.2 mnormt_1.5-5
[31] digest_0.6.15 stringi_1.1.7 grid_3.5.1
[34] rprojroot_1.3-2 tools_3.5.1 magrittr_1.5
[37] lazyeval_0.2.1 tibble_1.4.2 tidyr_0.8.0
[40] whisker_0.3-2 pkgconfig_2.0.1 assertthat_0.2.0
[43] rmarkdown_1.9 R6_2.2.2 mclust_5.4
[46] nlme_3.1-137 git2r_0.21.0 compiler_3.5.1 </code></pre>
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