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tutorial.html
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<!doctype html>
<html>
<head>
<meta charset='UTF-8'><meta name='viewport' content='width=device-width initial-scale=1'>
<title>CellPhoneDB Tutorial</title><link href='https://fonts.loli.net/css?family=Open+Sans:400italic,700italic,700,400&subset=latin,latin-ext' rel='stylesheet' type='text/css' /><style type='text/css'>html {overflow-x: initial !important;}:root { --bg-color:#ffffff; --text-color:#333333; --select-text-bg-color:#B5D6FC; --select-text-font-color:auto; --monospace:"Lucida Console",Consolas,"Courier",monospace; }
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<body class='typora-export'>
<div id='write' class=''><h2><a name="cellphonedb-cookbook" class="md-header-anchor"></a><span>CellPhoneDB CookBook</span></h2><p><em><span>by James Nagai</span></em></p><h3><a name="0--installation" class="md-header-anchor"></a><span>0- Installation</span></h3><p> </p><p><code>pip3 install cellphonedb</code></p><p> </p><h3><a name="1---step-extract-data-from-seurat-object" class="md-header-anchor"></a><span>1 - Step Extract data from Seurat Object</span></h3><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="R" style="break-inside: unset;"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="r"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">require</span>(<span class="cm-variable">EWCE</span>)</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">require</span>(<span class="cm-variable">tibble</span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">require</span>(<span class="cm-variable">biomaRt</span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">require</span>(<span class="cm-variable">tidyr</span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">require</span>(<span class="cm-variable">dplyr</span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># Basic function to convert mouse to human gene names</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">data_</span> <span class="cm-operator cm-arrow"><-</span> <span class="cm-variable">readRDS</span>(<span class="cm-string">'path_to_data'</span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">alldata</span> <span class="cm-operator cm-arrow"><-</span> <span class="cm-variable">NormalizeData</span>(<span class="cm-variable">alldata</span>, <span class="cm-variable">normalization.method</span> <span class="cm-operator">=</span> <span class="cm-string">"LogNormalize"</span>, <span class="cm-variable">scale.factor</span> <span class="cm-operator">=</span> <span class="cm-number">10000</span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">allgenes</span> <span class="cm-operator cm-arrow"><-</span> <span class="cm-variable">rownames</span>(<span class="cm-variable">alldata</span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">matrix1</span> <span class="cm-operator cm-arrow"><-</span> <span class="cm-variable">as.data.frame</span>(<span class="cm-variable">alldata</span>@<span class="cm-variable">assays</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">RNA</span>@<span class="cm-variable">data</span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">matrix1</span> <span class="cm-operator cm-arrow"><-</span> <span class="cm-variable">matrix1</span>[<span class="cm-variable">rowSums</span>(<span class="cm-variable">matrix1</span>[,<span class="cm-number">2</span><span class="cm-operator">:</span><span class="cm-variable">dim</span>(<span class="cm-variable">matrix1</span>)[<span class="cm-number">2</span>]])<span class="cm-operator">!=</span><span class="cm-number">0</span>,]</span></pre><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment">### If you are using a mouse data, then its needed to convert the gene names to human orthologs</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">human</span> <span class="cm-operator">=</span> <span class="cm-variable">useEnsembl</span>(<span class="cm-string">"ensembl"</span>, <span class="cm-variable">dataset</span> <span class="cm-operator">=</span> <span class="cm-string">"hsapiens_gene_ensembl"</span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">mouse</span> <span class="cm-operator">=</span> <span class="cm-variable">useEnsembl</span>(<span class="cm-string">"ensembl"</span>, <span class="cm-variable">dataset</span> <span class="cm-operator">=</span> <span class="cm-string">"mmusculus_gene_ensembl"</span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">genesV2</span> <span class="cm-operator">=</span> <span class="cm-variable">getLDS</span>(<span class="cm-variable">attributes</span> <span class="cm-operator">=</span> <span class="cm-variable">c</span>(<span class="cm-string">"mgi_symbol"</span>), <span class="cm-variable">filters</span> <span class="cm-operator">=</span> <span class="cm-string">"mgi_symbol"</span>, <span class="cm-variable">values</span> <span class="cm-operator">=</span> <span class="cm-variable">rownames</span>(<span class="cm-variable">alldata</span>@<span class="cm-variable">assays</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">RNA</span>@<span class="cm-variable">data</span>) , <span class="cm-variable">mart</span> <span class="cm-operator">=</span> <span class="cm-variable">mouse</span>, <span class="cm-variable">attributesL</span> <span class="cm-operator">=</span> <span class="cm-variable">c</span>(<span class="cm-string">"hgnc_symbol"</span>,<span class="cm-string">"hgnc_id"</span>,<span class="cm-string">'ensembl_gene_id'</span>), <span class="cm-variable">martL</span> <span class="cm-operator">=</span> <span class="cm-variable">human</span>, <span class="cm-variable">uniqueRows</span><span class="cm-operator">=</span><span class="cm-variable">T</span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">print</span>(<span class="cm-variable">head</span>(<span class="cm-variable">genesV2</span>))</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">matrix1</span> <span class="cm-operator cm-arrow"><-</span> <span class="cm-variable">matrix1</span>[<span class="cm-variable">match</span>(<span class="cm-variable">genesV2</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">MGI.symbol</span>,<span class="cm-variable">rownames</span>(<span class="cm-variable">alldata</span>),<span class="cm-variable">nomatch</span><span class="cm-operator">=</span><span class="cm-variable">F</span>),]</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">matrix1</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">gene</span> <span class="cm-operator cm-arrow"><-</span> <span class="cm-variable">genesV2</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">Gene.stable.ID</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment">#rownames(matrix1) <- genesV2$Gene.stable.ID</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment">### Subseting the matrix</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">s1</span> <span class="cm-operator cm-arrow"><-</span> <span class="cm-variable">grepl</span>(<span class="cm-string">'state1'</span>,<span class="cm-variable">alldata</span>@<span class="cm-variable">meta.data</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">cond</span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">s2</span> <span class="cm-operator cm-arrow"><-</span> <span class="cm-variable">grepl</span>(<span class="cm-string">'state2'</span>,<span class="cm-variable">alldata</span>@<span class="cm-variable">meta.data</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">cond</span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">s1</span>[<span class="cm-variable">match</span>(<span class="cm-string">'gene'</span>,<span class="cm-variable">colnames</span>(<span class="cm-variable">matrix1</span>))] <span class="cm-operator cm-arrow"><-</span> <span class="cm-variable">TRUE</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">s2</span>[<span class="cm-variable">match</span>(<span class="cm-string">'gene'</span>,<span class="cm-variable">colnames</span>(<span class="cm-variable">matrix1</span>))] <span class="cm-operator cm-arrow"><-</span> <span class="cm-variable">TRUE</span></span></pre><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment">## Checking the dimensions</span></span></pre><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">print</span>(<span class="cm-variable">dim</span>(<span class="cm-variable">matrix1</span>[,<span class="cm-variable">s1</span>]))</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">print</span>(<span class="cm-variable">dim</span>(<span class="cm-variable">matrix1</span>[,<span class="cm-variable">s2</span>]))</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment">## If the cluster names are categorical, you will need to convert it to numerical</span></span></pre><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">alldata</span>@<span class="cm-variable">meta.data</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">sub_cell_type</span> <span class="cm-operator cm-arrow"><-</span> <span class="cm-variable">as.factor</span>(<span class="cm-variable">alldata</span>@<span class="cm-variable">meta.data</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">sub_cell_type</span>)</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">print</span>(<span class="cm-variable">levels</span>(<span class="cm-variable">alldata</span>@<span class="cm-variable">meta.data</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">sub_cell_type</span>))</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">levels</span>(<span class="cm-variable">alldata</span>@<span class="cm-variable">meta.data</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">sub_cell_type</span>) <span class="cm-operator cm-arrow"><-</span> <span class="cm-number">1</span><span class="cm-operator">:</span><span class="cm-variable">length</span>(<span class="cm-variable">levels</span>(<span class="cm-variable">alldata</span>@<span class="cm-variable">meta.data</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">sub_cell_type</span>))</span></pre><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">print</span>(<span class="cm-number">1</span><span class="cm-operator">:</span><span class="cm-variable">length</span>(<span class="cm-variable">levels</span>(<span class="cm-variable">alldata</span>@<span class="cm-variable">meta.data</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">sub_cell_type</span>)))</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">alldata</span>@<span class="cm-variable">meta.data</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">sub_cell_type</span> <span class="cm-operator cm-arrow"><-</span> <span class="cm-variable">as.numeric</span>(<span class="cm-variable">alldata</span>@<span class="cm-variable">meta.data</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">sub_cell_type</span>)</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">write.table</span>(<span class="cm-variable">matrix1</span>[,<span class="cm-variable">s1</span>], <span class="cm-string">'s1_filtered_hcount.csv'</span>,<span class="cm-variable">row.names</span><span class="cm-operator">=</span><span class="cm-variable">T</span>,<span class="cm-variable">sep</span><span class="cm-operator">=</span><span class="cm-string">','</span>)</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">write.table</span>(<span class="cm-variable">matrix1</span>[,<span class="cm-variable">s2</span>], <span class="cm-string">'s2_filtered_hcount.csv'</span>,<span class="cm-variable">row.names</span><span class="cm-operator">=</span><span class="cm-variable">T</span>,<span class="cm-variable">sep</span><span class="cm-operator">=</span><span class="cm-string">','</span>)</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">metadata</span> <span class="cm-operator cm-arrow"><-</span> <span class="cm-variable">data.frame</span>(<span class="cm-variable">cells</span><span class="cm-operator">=</span><span class="cm-variable">rownames</span>(<span class="cm-variable">alldata</span>@<span class="cm-variable">meta.data</span>[<span class="cm-variable">grepl</span>(<span class="cm-string">'state1'</span>,<span class="cm-variable">alldata</span>@<span class="cm-variable">meta.data</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">stim</span>),]),<span class="cm-variable">cluster</span><span class="cm-operator">=</span><span class="cm-variable">alldata</span>@<span class="cm-variable">meta.data</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">sub_cell_type</span>[<span class="cm-variable">grepl</span>(<span class="cm-string">'state1'</span>,<span class="cm-variable">alldata</span>@<span class="cm-variable">meta.data</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">stim</span>)])</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">metadata_s2</span> <span class="cm-operator cm-arrow"><-</span> <span class="cm-variable">data.frame</span>(<span class="cm-variable">cells</span><span class="cm-operator">=</span><span class="cm-variable">rownames</span>(<span class="cm-variable">alldata</span>@<span class="cm-variable">meta.data</span>[<span class="cm-operator">!</span><span class="cm-variable">grepl</span>(<span class="cm-string">'state1'</span>,<span class="cm-variable">alldata</span>@<span class="cm-variable">meta.data</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">stim</span>),]),<span class="cm-variable">cluster</span><span class="cm-operator">=</span><span class="cm-variable">alldata</span>@<span class="cm-variable">meta.data</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">sub_cell_type</span>[<span class="cm-operator">!</span><span class="cm-variable">grepl</span>(<span class="cm-string">'state1'</span>,<span class="cm-variable">alldata</span>@<span class="cm-variable">meta.data</span><span class="cm-operator cm-dollar">$</span><span class="cm-variable">stim</span>)]) <span class="cm-comment">## Just negate grepl('state1',[email protected]$stim),]</span></span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">print</span>(<span class="cm-string">'Writing Metadata'</span>)</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">write.csv</span>(<span class="cm-variable">metadata</span>, <span class="cm-string">'s1_filtered_meta.csv'</span>, <span class="cm-variable">row.names</span><span class="cm-operator">=</span><span class="cm-variable">FALSE</span>)</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">write.csv</span>(<span class="cm-variable">metadata_tac</span>, <span class="cm-string">'s2_filtered_meta.csv'</span>, <span class="cm-variable">row.names</span><span class="cm-operator">=</span><span class="cm-variable">FALSE</span>)<span class="cm-variable-3">```</span></span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 1196px;"></div><div class="CodeMirror-gutters" style="display: none; height: 1196px; left: 0px;"></div></div></div></pre><p><strong><span>Note that the gene ID needs to be unique, you will need to use an approach to combine multiple mapped orthologs (sum, max or bitwiseor )</span></strong></p><h3><a name="run-cellphonedb" class="md-header-anchor"></a><span>Run CellPhoneDB</span></h3><p><span>** The parameters list is available at </span><a href='https://github.com/Teichlab/cellphonedb' target='_blank' class='url'>https://github.com/Teichlab/cellphonedb</a></p><h4><a name="ensembl-based-id" class="md-header-anchor"></a><span>Ensembl based ID</span></h4><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">#! /bin/bash</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">mkdir s1 s2 # creating the output folders</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">cellphonedb method statistical_analysis s1_filtered_meta.csv s1_filtered_hcount.csv --threads 30 --output-path s1/</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">cellphonedb method statistical_analysis s2_filtered_meta.csv s2_filtered_hcount.csv --threads 30 --output-path s2/</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 161px;"></div><div class="CodeMirror-gutters" style="display: none; height: 161px;"></div></div></div></pre><h4><a name="hugo-based-id" class="md-header-anchor"></a><span>HUGO based ID</span></h4><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">#! /bin/bash</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">mkdir s1 s2 # creating the output folders</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">cellphonedb method statistical_analysis s1_filtered_meta.csv --counts-data hgnc_symbol s1_filtered_hcount.csv --threads 30 --output-path s1/ </span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">cellphonedb method statistical_analysis s2_filtered_meta.csv --counts-data hgnc_symbol s2_filtered_hcount.csv --threads 30 --output-path s2/ </span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 207px;"></div><div class="CodeMirror-gutters" style="display: none; height: 207px;"></div></div></div></pre><h3><a name="extracting-lr" class="md-header-anchor"></a><span>Extracting LR</span></h3><pre lang="python" class="md-fences md-end-block ty-contain-cm modeLoaded" spellcheck="false" style="break-inside: unset;"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="python"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-keyword">def</span> <span class="cm-def">correct_lr</span>(<span class="cm-variable">data</span>):</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-string">'''</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-string"> Invert the RL to LR and R1R2 to r2>r1</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-string"> '''</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-keyword">import</span> <span class="cm-variable">pandas</span> <span class="cm-keyword">as</span> <span class="cm-variable">pd</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-keyword">def</span> <span class="cm-def">swap</span>(<span class="cm-variable">a</span>,<span class="cm-variable">b</span>): <span class="cm-keyword">return</span> <span class="cm-variable">b</span>,<span class="cm-variable">a</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">data</span> = <span class="cm-variable">data</span>.<span class="cm-property">to_dict</span>(<span class="cm-string">'index'</span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-keyword">for</span> <span class="cm-variable">k</span>,<span class="cm-variable">v</span> <span class="cm-keyword">in</span> <span class="cm-variable">data</span>.<span class="cm-property">items</span>():</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-keyword">if</span> <span class="cm-variable">v</span>[<span class="cm-string">'isReceptor_fst'</span>] <span class="cm-keyword">and</span> <span class="cm-variable">v</span>[<span class="cm-string">'isReceptor_scn'</span>]:</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">v</span>[<span class="cm-string">'isReceptor_fst'</span>],<span class="cm-variable">v</span>[<span class="cm-string">'isReceptor_scn'</span>] = <span class="cm-variable">swap</span>(<span class="cm-variable">v</span>[<span class="cm-string">'isReceptor_fst'</span>],<span class="cm-variable">v</span>[<span class="cm-string">'isReceptor_scn'</span>])</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">v</span>[<span class="cm-string">'Ligand'</span>],<span class="cm-variable">v</span>[<span class="cm-string">'Receptor'</span>] = <span class="cm-variable">swap</span>(<span class="cm-variable">v</span>[<span class="cm-string">'Ligand'</span>],<span class="cm-variable">v</span>[<span class="cm-string">'Receptor'</span>])</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">v</span>[<span class="cm-string">'Ligand.Cluster'</span>],<span class="cm-variable">v</span>[<span class="cm-string">'Receptor.Cluster'</span>] = <span class="cm-variable">swap</span>(<span class="cm-variable">v</span>[<span class="cm-string">'Ligand.Cluster'</span>],<span class="cm-variable">v</span>[<span class="cm-string">'Receptor.Cluster'</span>])</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-keyword">elif</span> <span class="cm-variable">v</span>[<span class="cm-string">'isReceptor_fst'</span>] <span class="cm-keyword">and</span> <span class="cm-keyword">not</span> <span class="cm-variable">v</span>[<span class="cm-string">'isReceptor_scn'</span>]:</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">v</span>[<span class="cm-string">'isReceptor_fst'</span>],<span class="cm-variable">v</span>[<span class="cm-string">'isReceptor_scn'</span>] = <span class="cm-variable">swap</span>(<span class="cm-variable">v</span>[<span class="cm-string">'isReceptor_fst'</span>],<span class="cm-variable">v</span>[<span class="cm-string">'isReceptor_scn'</span>])</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">v</span>[<span class="cm-string">'Ligand'</span>],<span class="cm-variable">v</span>[<span class="cm-string">'Receptor'</span>] = <span class="cm-variable">swap</span>(<span class="cm-variable">v</span>[<span class="cm-string">'Ligand'</span>],<span class="cm-variable">v</span>[<span class="cm-string">'Receptor'</span>])</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">v</span>[<span class="cm-string">'Ligand.Cluster'</span>],<span class="cm-variable">v</span>[<span class="cm-string">'Receptor.Cluster'</span>] = <span class="cm-variable">swap</span>(<span class="cm-variable">v</span>[<span class="cm-string">'Ligand.Cluster'</span>],<span class="cm-variable">v</span>[<span class="cm-string">'Receptor.Cluster'</span>])</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">res_df</span> = <span class="cm-variable">pd</span>.<span class="cm-property">DataFrame</span>.<span class="cm-property">from_dict</span>(<span class="cm-variable">data</span>,<span class="cm-variable">orient</span>=<span class="cm-string">'index'</span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-keyword">return</span> (<span class="cm-variable">res_df</span>)</span></pre><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-keyword">def</span> <span class="cm-def">cpdb2df</span>(<span class="cm-variable">data</span>,<span class="cm-variable">clsmapping</span>):</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">data</span> = <span class="cm-variable">data</span>.<span class="cm-property">fillna</span>(<span class="cm-number">0</span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">df_data</span> = {}</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">df_data</span>[<span class="cm-string">'Ligand'</span>] = []</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">df_data</span>[<span class="cm-string">'Receptor'</span>] = []</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">df_data</span>[<span class="cm-string">'Ligand.Cluster'</span>] = []</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">df_data</span>[<span class="cm-string">'Receptor.Cluster'</span>] = []</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">df_data</span>[<span class="cm-string">'isReceptor_fst'</span>] = []</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">df_data</span>[<span class="cm-string">'isReceptor_scn'</span>] = []</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">df_data</span>[<span class="cm-string">'MeanLR'</span>] = []</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-keyword">for</span> <span class="cm-variable">i</span> <span class="cm-keyword">in</span> <span class="cm-builtin">range</span>(<span class="cm-variable">data</span>.<span class="cm-property">shape</span>[<span class="cm-number">0</span>]):</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">pair</span> = <span class="cm-builtin">list</span>(<span class="cm-variable">data</span>[<span class="cm-string">'interacting_pair'</span>])[<span class="cm-variable">i</span>].<span class="cm-property">split</span>(<span class="cm-string">'_'</span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-keyword">for</span> <span class="cm-variable">j</span> <span class="cm-keyword">in</span> <span class="cm-builtin">range</span>(<span class="cm-variable">data</span>.<span class="cm-property">iloc</span>[:,<span class="cm-number">12</span>:].<span class="cm-property">shape</span>[<span class="cm-number">1</span>]):</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">c_pair</span> = <span class="cm-builtin">list</span>(<span class="cm-variable">data</span>.<span class="cm-property">columns</span>)[<span class="cm-variable">j</span><span class="cm-operator">+</span><span class="cm-number">12</span>].<span class="cm-property">split</span>(<span class="cm-string">'|'</span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-keyword">if</span> <span class="cm-builtin">int</span>(<span class="cm-variable">data</span>.<span class="cm-property">iloc</span>[<span class="cm-variable">i</span>,<span class="cm-variable">j</span><span class="cm-operator">+</span><span class="cm-number">12</span>]) <span class="cm-operator">!</span>=<span class="cm-number">0.0</span>:</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">df_data</span>[<span class="cm-string">'Ligand'</span>].<span class="cm-property">append</span>(<span class="cm-variable">pair</span>[<span class="cm-number">0</span>])</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">df_data</span>[<span class="cm-string">'Receptor'</span>].<span class="cm-property">append</span>(<span class="cm-variable">pair</span>[<span class="cm-number">1</span>])</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">df_data</span>[<span class="cm-string">'Ligand.Cluster'</span>].<span class="cm-property">append</span>(<span class="cm-variable">clsmapping</span>[<span class="cm-variable">c_pair</span>[<span class="cm-number">0</span>]])</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">df_data</span>[<span class="cm-string">'Receptor.Cluster'</span>].<span class="cm-property">append</span>(<span class="cm-variable">clsmapping</span>[<span class="cm-variable">c_pair</span>[<span class="cm-number">1</span>]])</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">df_data</span>[<span class="cm-string">'isReceptor_fst'</span>].<span class="cm-property">append</span>(<span class="cm-builtin">list</span>(<span class="cm-variable">data</span>[<span class="cm-string">'receptor_a'</span>])[<span class="cm-variable">i</span>])</span></pre><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">df_data</span>[<span class="cm-string">'isReceptor_scn'</span>].<span class="cm-property">append</span>(<span class="cm-builtin">list</span>(<span class="cm-variable">data</span>[<span class="cm-string">'receptor_b'</span>])[<span class="cm-variable">i</span>])</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">df_data</span>[<span class="cm-string">'MeanLR'</span>].<span class="cm-property">append</span>(<span class="cm-variable">data</span>.<span class="cm-property">iloc</span>[<span class="cm-variable">i</span>,<span class="cm-variable">j</span><span class="cm-operator">+</span><span class="cm-number">12</span>])</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-variable">data_final</span> = <span class="cm-variable">pd</span>.<span class="cm-property">DataFrame</span>.<span class="cm-property">from_dict</span>(<span class="cm-variable">df_data</span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-keyword">return</span>(<span class="cm-variable">data_final</span>)</span></pre><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">s1</span> = <span class="cm-variable">pd</span>.<span class="cm-property">read_csv</span>(<span class="cm-string">'./s1/significant_means.txt'</span>,<span class="cm-variable">sep</span>=<span class="cm-string">'\t'</span>)</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">s2</span> = <span class="cm-variable">pd</span>.<span class="cm-property">read_csv</span>(<span class="cm-string">'./s2/ significant_means.txt'</span>,<span class="cm-variable">sep</span>=<span class="cm-string">'\t'</span>)</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment">#dict with the mapping</span></span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">num_to_clust</span> = {<span class="cm-string">'1'</span>:<span class="cm-string">'Cluters 1'</span>,</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-string">'2'</span>:<span class="cm-string">'Cluters 2'</span>,</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-string">'3'</span>:<span class="cm-string">'Cluters 3'</span>,</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-string">'4'</span>:<span class="cm-string">'Cluters 4'</span>,</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-string">'5'</span>:<span class="cm-string">'Cluters 5'</span>}</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">s1_filtered</span> = <span class="cm-variable">cpdb2df</span>(<span class="cm-variable">s1</span>,<span class="cm-variable">num_to_clust</span>)</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">s2_filtered</span> = <span class="cm-variable">cpdb2df</span>(<span class="cm-variable">s2</span>,<span class="cm-variable">num_to_clust</span>)</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">s1_filtered</span> = <span class="cm-variable">correct_lr</span>(<span class="cm-variable">s1_filtered</span>)</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">s2_filtered</span> = <span class="cm-variable">correct_lr</span>(<span class="cm-variable">s2_filtered</span>)</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">s1_filtered</span>.<span class="cm-property">to_csv</span>(<span class="cm-string">'s1_filtered_corrected.csv'</span>)</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">s2_filtered</span>.<span class="cm-property">to_csv</span>(<span class="cm-string">'s2_filtered_corrected.csv'</span>)</span></pre></div><div class="" style="position: relative;"><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 1357px;"></div><div class="CodeMirror-gutters" style="display: none; height: 1357px;"></div></div></div></pre><h3><a name="crosstalk" class="md-header-anchor"></a><span>CrossTalk </span></h3><pre lang="R" class="md-fences md-end-block ty-contain-cm modeLoaded" spellcheck="false" style="break-inside: unset;"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="r"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">library</span>(<span class="cm-string">'LRAnalytics'</span>)</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># the method always consider the first path as control: the multiple control case will be handle soon</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">paths</span> <span class="cm-operator cm-arrow"><-</span> <span class="cm-variable">c</span>(<span class="cm-string">'CTR'</span> <span class="cm-operator">=</span> <span class="cm-string">'s1_filtered_corrected.csv'</span>, </span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-string">'EXP'</span> <span class="cm-operator">=</span> <span class="cm-string">'s1_filtered_corrected.csv'</span>,</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-string">'EXP1'</span> <span class="cm-operator">=</span> <span class="cm-string">'s1_filtered_corrected.csv'</span>,)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># Selected gene list </span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">genes</span> <span class="cm-operator cm-arrow"><-</span> <span class="cm-variable">c</span>(<span class="cm-string">'TGFB1'</span>, <span class="cm-string">'PF4'</span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># Generating the report and the object</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">data</span> <span class="cm-operator cm-arrow"><-</span> <span class="cm-variable">generate_report</span>(<span class="cm-variable">paths</span><span class="cm-operator">=</span><span class="cm-variable">paths</span>, <span class="cm-comment"># paths list</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-variable">selected_genes</span><span class="cm-operator">=</span><span class="cm-variable">genes</span>, <span class="cm-comment"># Selected list</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-variable">output</span><span class="cm-operator">=</span><span class="cm-string">'/home/nagai/Documents/'</span>, <span class="cm-comment"># output path</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-variable">threshold</span> <span class="cm-operator">=</span> <span class="cm-number">0</span>, <span class="cm-comment"># threshold of prune edges 0=keep all</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-variable">out_file</span><span class="cm-operator">=</span><span class="cm-string">'All_Nils.html'</span> <span class="cm-variable">report</span> <span class="cm-variable">name</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span><span class="cm-tab" role="presentation" cm-text=" "> </span>)</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 414px;"></div><div class="CodeMirror-gutters" style="display: none; height: 414px;"></div></div></div></pre><p> </p><p> </p></div>
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