limour
/
b.limour.top


			
							123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680681682683684685686687688689690691692693694695696697698699700701
							

<!DOCTYPE html>
<html lang="en" data-default-color-scheme=auto>


<head><!-- hexo injector head_begin start -->
  <script async src="https://analytics.umami.is/script.js" data-website-id="e59ec28a-c9a7-4104-9e62-a9f7eb3fac0b"></script>
<!-- hexo injector head_begin end -->
  <meta charset="UTF-8">
  <link rel="apple-touch-icon" sizes="76x76" href="https://img.limour.top/2023/08/29/64ee07361815a.webp">
  <link rel="icon" href="https://img.limour.top/2023/08/29/64ee07361815a.webp">
  <meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=5.0, shrink-to-fit=no">
  <meta http-equiv="x-ua-compatible" content="ie=edge">
  
  <meta name="theme-color" content="#2f4154">
  <meta name="author" content="Limour">
  <meta name="keywords" content="">
  
    <meta name="description" content="12345678910111213141516171819202122232425262728293031323334353637383940414243444546474849505152535455565758596061626364656667686970717273747576777879808182838485868788899091929394959697989910010110210">
<meta property="og:type" content="article">
<meta property="og:title" content="Seurat (五) 简单总结">
<meta property="og:url" content="https://b.limour.top/886.html">
<meta property="og:site_name" content="Limour&#39;s Blog">
<meta property="og:description" content="12345678910111213141516171819202122232425262728293031323334353637383940414243444546474849505152535455565758596061626364656667686970717273747576777879808182838485868788899091929394959697989910010110210">
<meta property="og:locale" content="en_US">
<meta property="article:published_time" content="2021-10-04T12:43:00.000Z">
<meta property="article:modified_time" content="2023-09-01T13:32:00.589Z">
<meta property="article:author" content="Limour">
<meta name="twitter:card" content="summary_large_image">
  
  
  <title>Seurat (五) 简单总结 - Limour&#39;s Blog</title>

  <link  rel="stylesheet" href="https://jscdn.limour.top/npm/bootstrap@4.6.1/dist/css/bootstrap.min.css" />


  <link  rel="stylesheet" href="https://jscdn.limour.top/npm/github-markdown-css@4.0.0/github-markdown.min.css" />

  <link  rel="stylesheet" href="https://jscdn.limour.top/npm/hint.css@2.7.0/hint.min.css" />

  <link  rel="stylesheet" href="https://lib.baomitu.com/fancybox/3.5.7/jquery.fancybox.min.css" />


<!-- 主题依赖的图标库，不要自行修改 -->
<!-- Do not modify the link that theme dependent icons -->

<link rel="stylesheet" href="//at.alicdn.com/t/font_1749284_hj8rtnfg7um.css">


<link rel="stylesheet" href="//at.alicdn.com/t/font_1736178_lbnruvf0jn.css">


<link  rel="stylesheet" href="/css/main.css" />


  <link id="highlight-css" rel="stylesheet" href="/css/highlight.css" />
  
    <link id="highlight-css-dark" rel="stylesheet" href="/css/highlight-dark.css" />
  

<link rel="stylesheet" href="/theme-inject/custom.css">


  <script id="fluid-configs">
    var Fluid = window.Fluid || {};
    Fluid.ctx = Object.assign({}, Fluid.ctx)
    var CONFIG = {"hostname":"b.limour.top","root":"/","version":"1.9.5-a","typing":{"enable":true,"typeSpeed":70,"cursorChar":"_","loop":false,"scope":[]},"anchorjs":{"enable":true,"element":"h1,h2,h3,h4,h5,h6","placement":"left","visible":"hover","icon":"§"},"progressbar":{"enable":true,"height_px":3,"color":"#29d","options":{"showSpinner":false,"trickleSpeed":100}},"code_language":{"enable":true,"default":"TEXT"},"copy_btn":true,"image_caption":{"enable":true},"image_zoom":{"enable":true,"img_url_replace":["",""]},"toc":{"enable":true,"placement":"right","headingSelector":"h1,h2,h3,h4,h5,h6","collapseDepth":0},"lazyload":{"enable":true,"loading_img":"https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg","onlypost":false,"offset_factor":2},"web_analytics":{"enable":false,"follow_dnt":true,"baidu":null,"google":{"measurement_id":null},"tencent":{"sid":null,"cid":null},"woyaola":null,"cnzz":null,"leancloud":{"app_id":null,"app_key":null,"server_url":null,"path":"window.location.pathname","ignore_local":false}},"search_path":"/local-search.xml","include_content_in_search":true};

    if (CONFIG.web_analytics.follow_dnt) {
      var dntVal = navigator.doNotTrack || window.doNotTrack || navigator.msDoNotTrack;
      Fluid.ctx.dnt = dntVal && (dntVal.startsWith('1') || dntVal.startsWith('yes') || dntVal.startsWith('on'));
    }
  </script>
  <script  src="/js/utils.js" ></script>
  <script  src="/js/color-schema.js" ></script>
  

<meta name="generator" content="Hexo 6.3.0"></head>


<body>
  

  <header>
    

<div class="header-inner" style="height: 70vh;">
  <nav id="navbar" class="navbar fixed-top  navbar-expand-lg navbar-dark scrolling-navbar">
  <div class="container">
    <a class="navbar-brand" href="/">
      <strong>Limour&#39;s Blog</strong>
    </a>

    <button id="navbar-toggler-btn" class="navbar-toggler" type="button" data-toggle="collapse"
            data-target="#navbarSupportedContent"
            aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
      <div class="animated-icon"><span></span><span></span><span></span></div>
    </button>

    <!-- Collapsible content -->
    <div class="collapse navbar-collapse" id="navbarSupportedContent">
      <ul class="navbar-nav ml-auto text-center">
        
          
            <li class="nav-item">
              <a class="nav-link" href="/">
                <i class="iconfont icon-home-fill"></i>
                <span>Home</span>
              </a>
            </li>
          
        
            <li class="nav-item">
              <a class="nav-link" href="/archives/">
                <i class="iconfont icon-archive-fill"></i>
                <span>Archives</span>
              </a>
            </li>
          
        
          <li class="nav-item" id="search-btn">
            <a class="nav-link" target="_self" href="javascript:;" data-toggle="modal" data-target="#modalSearch" aria-label="Search">
              <i class="iconfont icon-search"></i>
            </a>
          </li>
          
        
          <li class="nav-item" id="color-toggle-btn">
            <a class="nav-link" target="_self" href="javascript:;" aria-label="Color Toggle">
              <i class="iconfont icon-dark" id="color-toggle-icon"></i>
            </a>
          </li>
        
      </ul>
    </div>
  </div>
</nav>

  
<div id="banner" class="banner" parallax=true
     style="background: url('https://img.limour.top/2023/08/29/64ee08e108638.webp') no-repeat center center; background-size: cover;">
  <div class="full-bg-img">
    <div class="mask flex-center" style="background-color: rgba(0, 0, 0, 0.3)">
      <div class="banner-text text-center fade-in-up">
        <div class="h2">
          
            <span id="subtitle" data-typed-text="Seurat (五) 简单总结"></span>
          
        </div>

        
  <div class="mt-3">
    
    
      <span class="post-meta">
        <i class="iconfont icon-date-fill" aria-hidden="true"></i>
        <time datetime="2021-10-04 20:43" pubdate>
          October 4, 2021 pm
        </time>
      </span>
    
  </div>

  <div class="mt-1">
    
      <span class="post-meta mr-2">
        <i class="iconfont icon-chart"></i>
        
          20k words
        
      </span>
    

      <span class="post-meta mr-2">
        <i class="iconfont icon-clock-fill"></i>
        
        
          170 mins
        
      </span>
    

  </div>


      </div>

      
    </div>
  </div>
</div>

</div>

  </header>

  <main>
    
      
<div class="container-fluid nopadding-x">
  <div class="row nomargin-x">
    <div class="side-col d-none d-lg-block col-lg-2">
      

    </div>

    <div class="col-lg-8 nopadding-x-md">
      <div class="container nopadding-x-md" id="board-ctn">
        <div id="board">
          <article class="post-content mx-auto">
            <h1 id="seo-header">Seurat (五) 简单总结</h1>
            
            
              <div class="markdown-body">
                
                <figure class="highlight reasonml"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br><span class="line">37</span><br><span class="line">38</span><br><span class="line">39</span><br><span class="line">40</span><br><span class="line">41</span><br><span class="line">42</span><br><span class="line">43</span><br><span class="line">44</span><br><span class="line">45</span><br><span class="line">46</span><br><span class="line">47</span><br><span class="line">48</span><br><span class="line">49</span><br><span class="line">50</span><br><span class="line">51</span><br><span class="line">52</span><br><span class="line">53</span><br><span class="line">54</span><br><span class="line">55</span><br><span class="line">56</span><br><span class="line">57</span><br><span class="line">58</span><br><span class="line">59</span><br><span class="line">60</span><br><span class="line">61</span><br><span class="line">62</span><br><span class="line">63</span><br><span class="line">64</span><br><span class="line">65</span><br><span class="line">66</span><br><span class="line">67</span><br><span class="line">68</span><br><span class="line">69</span><br><span class="line">70</span><br><span class="line">71</span><br><span class="line">72</span><br><span class="line">73</span><br><span class="line">74</span><br><span class="line">75</span><br><span class="line">76</span><br><span class="line">77</span><br><span class="line">78</span><br><span class="line">79</span><br><span class="line">80</span><br><span class="line">81</span><br><span class="line">82</span><br><span class="line">83</span><br><span class="line">84</span><br><span class="line">85</span><br><span class="line">86</span><br><span class="line">87</span><br><span class="line">88</span><br><span class="line">89</span><br><span class="line">90</span><br><span class="line">91</span><br><span class="line">92</span><br><span class="line">93</span><br><span class="line">94</span><br><span class="line">95</span><br><span class="line">96</span><br><span class="line">97</span><br><span class="line">98</span><br><span class="line">99</span><br><span class="line">100</span><br><span class="line">101</span><br><span class="line">102</span><br><span class="line">103</span><br><span class="line">104</span><br><span class="line">105</span><br><span class="line">106</span><br><span class="line">107</span><br><span class="line">108</span><br><span class="line">109</span><br><span class="line">110</span><br><span class="line">111</span><br><span class="line">112</span><br><span class="line">113</span><br><span class="line">114</span><br><span class="line">115</span><br><span class="line">116</span><br><span class="line">117</span><br><span class="line">118</span><br><span class="line">119</span><br><span class="line">120</span><br><span class="line">121</span><br><span class="line">122</span><br><span class="line">123</span><br><span class="line">124</span><br><span class="line">125</span><br><span class="line">126</span><br><span class="line">127</span><br><span class="line">128</span><br><span class="line">129</span><br><span class="line">130</span><br><span class="line">131</span><br><span class="line">132</span><br><span class="line">133</span><br><span class="line">134</span><br><span class="line">135</span><br><span class="line">136</span><br><span class="line">137</span><br><span class="line">138</span><br><span class="line">139</span><br><span class="line">140</span><br><span class="line">141</span><br><span class="line">142</span><br><span class="line">143</span><br><span class="line">144</span><br><span class="line">145</span><br><span class="line">146</span><br><span class="line">147</span><br><span class="line">148</span><br><span class="line">149</span><br><span class="line">150</span><br><span class="line">151</span><br><span class="line">152</span><br><span class="line">153</span><br><span class="line">154</span><br><span class="line">155</span><br><span class="line">156</span><br><span class="line">157</span><br><span class="line">158</span><br><span class="line">159</span><br><span class="line">160</span><br><span class="line">161</span><br><span class="line">162</span><br><span class="line">163</span><br><span class="line">164</span><br><span class="line">165</span><br><span class="line">166</span><br><span class="line">167</span><br><span class="line">168</span><br><span class="line">169</span><br><span class="line">170</span><br><span class="line">171</span><br><span class="line">172</span><br><span class="line">173</span><br><span class="line">174</span><br><span class="line">175</span><br><span class="line">176</span><br><span class="line">177</span><br><span class="line">178</span><br><span class="line">179</span><br><span class="line">180</span><br><span class="line">181</span><br><span class="line">182</span><br><span class="line">183</span><br><span class="line">184</span><br><span class="line">185</span><br><span class="line">186</span><br><span class="line">187</span><br><span class="line">188</span><br><span class="line">189</span><br><span class="line">190</span><br><span class="line">191</span><br><span class="line">192</span><br><span class="line">193</span><br><span class="line">194</span><br><span class="line">195</span><br><span class="line">196</span><br><span class="line">197</span><br><span class="line">198</span><br><span class="line">199</span><br><span class="line">200</span><br><span class="line">201</span><br><span class="line">202</span><br><span class="line">203</span><br><span class="line">204</span><br><span class="line">205</span><br><span class="line">206</span><br><span class="line">207</span><br><span class="line">208</span><br><span class="line">209</span><br><span class="line">210</span><br><span class="line">211</span><br><span class="line">212</span><br><span class="line">213</span><br><span class="line">214</span><br><span class="line">215</span><br><span class="line">216</span><br><span class="line">217</span><br><span class="line">218</span><br><span class="line">219</span><br><span class="line">220</span><br><span class="line">221</span><br><span class="line">222</span><br><span class="line">223</span><br><span class="line">224</span><br><span class="line">225</span><br><span class="line">226</span><br><span class="line">227</span><br><span class="line">228</span><br><span class="line">229</span><br><span class="line">230</span><br><span class="line">231</span><br><span class="line">232</span><br><span class="line">233</span><br><span class="line">234</span><br><span class="line">235</span><br><span class="line">236</span><br><span class="line">237</span><br><span class="line">238</span><br><span class="line">239</span><br><span class="line">240</span><br><span class="line">241</span><br><span class="line">242</span><br><span class="line">243</span><br><span class="line">244</span><br><span class="line">245</span><br><span class="line">246</span><br><span class="line">247</span><br><span class="line">248</span><br><span class="line">249</span><br><span class="line">250</span><br><span class="line">251</span><br><span class="line">252</span><br><span class="line">253</span><br><span class="line">254</span><br><span class="line">255</span><br><span class="line">256</span><br><span class="line">257</span><br><span class="line">258</span><br><span class="line">259</span><br><span class="line">260</span><br><span class="line">261</span><br><span class="line">262</span><br><span class="line">263</span><br><span class="line">264</span><br><span class="line">265</span><br><span class="line">266</span><br><span class="line">267</span><br><span class="line">268</span><br><span class="line">269</span><br><span class="line">270</span><br><span class="line">271</span><br><span class="line">272</span><br><span class="line">273</span><br><span class="line">274</span><br><span class="line">275</span><br><span class="line">276</span><br><span class="line">277</span><br><span class="line">278</span><br><span class="line">279</span><br><span class="line">280</span><br><span class="line">281</span><br><span class="line">282</span><br><span class="line">283</span><br><span class="line">284</span><br><span class="line">285</span><br><span class="line">286</span><br><span class="line">287</span><br><span class="line">288</span><br><span class="line">289</span><br><span class="line">290</span><br><span class="line">291</span><br><span class="line">292</span><br><span class="line">293</span><br><span class="line">294</span><br><span class="line">295</span><br><span class="line">296</span><br><span class="line">297</span><br><span class="line">298</span><br><span class="line">299</span><br><span class="line">300</span><br><span class="line">301</span><br><span class="line">302</span><br><span class="line">303</span><br><span class="line">304</span><br><span class="line">305</span><br><span class="line">306</span><br><span class="line">307</span><br></pre></td><td class="code"><pre><code class="hljs reasonml">library(Matrix)<br>library(Seurat)<br>library(plyr)<br>library(dplyr)<br>library(patchwork)<br>library(purrr)<br><br>library(RColorBrewer)<br>library(ggplot2)<br>library(ggrepel)<br>blank_theme &lt;- theme<span class="hljs-constructor">_minimal()</span>+<br>    theme(<br>        axis.title.x = element<span class="hljs-constructor">_blank()</span>,<br>        axis.text.x=element<span class="hljs-constructor">_blank()</span>,<br>        axis.title.y = element<span class="hljs-constructor">_blank()</span>,<br>        axis.text.y=element<span class="hljs-constructor">_blank()</span>,<br>        panel.border = element<span class="hljs-constructor">_blank()</span>,<br>        panel.grid=element<span class="hljs-constructor">_blank()</span>,<br>        axis.ticks = element<span class="hljs-constructor">_blank()</span>,<br>        plot.title=element<span class="hljs-constructor">_text(<span class="hljs-params">size</span>=14, <span class="hljs-params">face</span>=<span class="hljs-string">&quot;bold&quot;</span>,<span class="hljs-params">hjust</span> = 0.5)</span><br>    )<br>col_Paired &lt;- color<span class="hljs-constructor">RampPalette(<span class="hljs-params">brewer</span>.<span class="hljs-params">pal</span>(12, <span class="hljs-string">&quot;Paired&quot;</span>)</span>)<br>f_pie &lt;- <span class="hljs-keyword">function</span>(lc_x, lc_main, lc_x_p = <span class="hljs-number">1.3</span>, lc_r = T)&#123;<br>    lc_cols &lt;- col<span class="hljs-constructor">_Paired(<span class="hljs-params">length</span>(<span class="hljs-params">lc_x</span>)</span>)<br>    lc_v &lt;- <span class="hljs-keyword">as</span>.vector(<span class="hljs-number">100</span>*lc_x)<br>    lc_df &lt;- data.frame(<span class="hljs-keyword">type</span> = names(lc_x), nums = lc_v)<br>    lc_df &lt;- lc_df<span class="hljs-literal">[<span class="hljs-identifier">order</span>(<span class="hljs-identifier">lc_df$type</span>),]</span><br>    lc_percent = sprintf(&#x27;%<span class="hljs-number">0.2</span>f%%&#x27;,lc_df$nums)<br>    <span class="hljs-keyword">if</span>(lc_r)&#123;<br>        lc_df$pos &lt;- <span class="hljs-keyword">with</span>(lc_df, <span class="hljs-number">100</span>-cumsum(nums)+nums/<span class="hljs-number">2</span>)<br>    &#125;<span class="hljs-keyword">else</span>&#123;<br>        lc_df$pos &lt;- <span class="hljs-keyword">with</span>(lc_df, cumsum(nums)-nums/<span class="hljs-number">2</span>)<br>    &#125; <br>    lc_pie &lt;- ggplot(data = lc_df, mapping = aes(x = <span class="hljs-number">1</span>, y = nums, fill = <span class="hljs-keyword">type</span>)) + geom<span class="hljs-constructor">_bar(<span class="hljs-params">stat</span> = &#x27;<span class="hljs-params">identity</span>&#x27;)</span><br>#     print(lc_df)<br>#     print(lc_pie)<br>    lc_pie &lt;- lc_pie + coord<span class="hljs-constructor">_polar(<span class="hljs-string">&quot;y&quot;</span>, <span class="hljs-params">start</span>=0, <span class="hljs-params">direction</span> = 1)</span> + scale<span class="hljs-constructor">_fill_manual(<span class="hljs-params">values</span>=<span class="hljs-params">lc_cols</span>)</span> + blank_theme <br>    lc_pie &lt;- lc_pie + geom<span class="hljs-constructor">_text_repel(<span class="hljs-params">aes</span>(<span class="hljs-params">x</span> = <span class="hljs-params">lc_x_p</span>, <span class="hljs-params">y</span>=<span class="hljs-params">pos</span>)</span>,label= lc_percent, force = T, <br>                        arrow = arrow(length=<span class="hljs-built_in">unit</span>(<span class="hljs-number">0.01</span>, <span class="hljs-string">&quot;npc&quot;</span>)), segment.color = <span class="hljs-string">&quot;#cccccc&quot;</span>, segment.size = <span class="hljs-number">0.5</span>)<br>    lc_pie &lt;- lc_pie + labs(title = lc_main)<br>    lc_pie<br>&#125;<br><br>f_pie_metaN &lt;- <span class="hljs-keyword">function</span>(sObject, lc_group.by)&#123;<br>    tp_data &lt;- prop.table(table(sObject<span class="hljs-literal">[[<span class="hljs-identifier">lc_group</span>.<span class="hljs-identifier">by</span>]</span>]))<br>    f<span class="hljs-constructor">_pie(<span class="hljs-params">tp_data</span>, <span class="hljs-params">sprintf</span>(&#x27;Proportion <span class="hljs-params">of</span> %<span class="hljs-params">s</span>&#x27;, <span class="hljs-params">lc_group</span>.<span class="hljs-params">by</span>)</span>)<br>&#125;<br><br>f_UMAP_more &lt;- <span class="hljs-keyword">function</span>(sObject, lc_group.by, lc_reduction=<span class="hljs-string">&quot;umap&quot;</span>)&#123;<br>    res &lt;- (<span class="hljs-constructor">DimPlot(<span class="hljs-params">sObject</span>, <span class="hljs-params">reduction</span> = <span class="hljs-params">lc_reduction</span>, <span class="hljs-params">group</span>.<span class="hljs-params">by</span> = <span class="hljs-params">lc_group</span>.<span class="hljs-params">by</span>[1], <span class="hljs-params">label</span> = T, <span class="hljs-params">repel</span> = T, <span class="hljs-params">label</span>.<span class="hljs-params">size</span> = 6)</span> + <br>    labs(title = lc_group.by<span class="hljs-literal">[<span class="hljs-number">1</span>]</span>))<br>    <span class="hljs-keyword">for</span>(lc_i <span class="hljs-keyword">in</span> <span class="hljs-number">2</span>:length(lc_group.by))&#123;<br>        res &lt;- res/<br>        (<span class="hljs-constructor">DimPlot(<span class="hljs-params">sObject</span>, <span class="hljs-params">reduction</span> = <span class="hljs-params">lc_reduction</span>, <span class="hljs-params">group</span>.<span class="hljs-params">by</span> = <span class="hljs-params">lc_group</span>.<span class="hljs-params">by</span>[<span class="hljs-params">lc_i</span>], <span class="hljs-params">label</span> = T, <span class="hljs-params">repel</span> = T, <span class="hljs-params">label</span>.<span class="hljs-params">size</span> = 6)</span> + <br>        labs(title = lc_group.by<span class="hljs-literal">[<span class="hljs-identifier">lc_i</span>]</span>))<br>    &#125;<br>    res<br>&#125;<br><br>f_br_cluster_f &lt;- <span class="hljs-keyword">function</span>(sObject, lc_groupN)&#123;<br>    lc_filter &lt;- unlist(unique(sObject<span class="hljs-literal">[[<span class="hljs-identifier">lc_groupN</span>]</span>]))<br>    lc_filter &lt;- lc_filter<span class="hljs-literal">[!<span class="hljs-identifier">is</span>.<span class="hljs-identifier">na</span>(<span class="hljs-identifier">lc_filter</span>)]</span><br>    lc_filter<br>&#125;<br><br>f_br_cluster &lt;- <span class="hljs-keyword">function</span>(sObject, lc_groupN, lc_labelN, lc_prop = F)&#123;<br>    lc_all &lt;- unique(sObject<span class="hljs-literal">[[<span class="hljs-identifier">lc_labelN</span>]</span>])<br>    rownames(lc_all) &lt;- lc_all<span class="hljs-literal">[[<span class="hljs-number">1</span>]</span>]<br>    colnames(lc_all) &lt;- <span class="hljs-string">&quot;CB&quot;</span><br>    lc_tp  &lt;- <span class="hljs-constructor">SplitObject(<span class="hljs-params">subset</span>(<span class="hljs-params">x</span> = <span class="hljs-params">sObject</span>, !!<span class="hljs-params">sym</span>(<span class="hljs-params">lc_groupN</span>)</span>%<span class="hljs-keyword">in</span>%f<span class="hljs-constructor">_br_cluster_f(<span class="hljs-params">sObject</span>, <span class="hljs-params">lc_groupN</span>)</span>), split.by = lc_groupN)<br>    <span class="hljs-keyword">for</span>(lc_i <span class="hljs-keyword">in</span> <span class="hljs-number">1</span>:length(lc_tp))&#123;<br>        <span class="hljs-keyword">if</span>(lc_prop)&#123;<br>            lc_tp<span class="hljs-literal">[[<span class="hljs-identifier">lc_i</span>]</span>] &lt;- prop.table(table(lc_tp<span class="hljs-literal">[[<span class="hljs-identifier">lc_i</span>]</span>]<span class="hljs-literal">[[<span class="hljs-identifier">lc_labelN</span>]</span>]))<br>        &#125;<span class="hljs-keyword">else</span>&#123;<br>            lc_tp<span class="hljs-literal">[[<span class="hljs-identifier">lc_i</span>]</span>] &lt;- table(lc_tp<span class="hljs-literal">[[<span class="hljs-identifier">lc_i</span>]</span>]<span class="hljs-literal">[[<span class="hljs-identifier">lc_labelN</span>]</span>])<br>        &#125;<br>    &#125;<br>    <span class="hljs-keyword">for</span>(lc_name <span class="hljs-keyword">in</span> names(lc_tp))&#123;<br>        lc_all<span class="hljs-literal">[[<span class="hljs-identifier">lc_name</span>]</span>] = <span class="hljs-number">0</span><br>        lc_all<span class="hljs-literal">[<span class="hljs-identifier">names</span>(<span class="hljs-identifier">lc_tp</span>[[<span class="hljs-identifier">lc_name</span>]</span>]), lc_name] = lc_tp<span class="hljs-literal">[[<span class="hljs-identifier">lc_name</span>]</span>]<br>    &#125;<br>    lc_all<span class="hljs-literal">[,-<span class="hljs-number">1</span>]</span><br>&#125;<br> <br>f_q2l &lt;- <span class="hljs-keyword">function</span>(lc_q)&#123;<br>    res  &lt;- NULL<br>    <span class="hljs-keyword">for</span>(lc_c <span class="hljs-keyword">in</span> colnames(lc_q))&#123;<br>        <span class="hljs-keyword">for</span>(lc_r <span class="hljs-keyword">in</span> rownames(lc_q))&#123;<br>            res  &lt;- rbind(res, c(group=lc_c, label=lc_r, value=lc_q<span class="hljs-literal">[<span class="hljs-identifier">lc_r</span>,<span class="hljs-identifier">lc_c</span>]</span>))<br>        &#125;<br>    &#125;<br>    res &lt;- data.frame(res)<br>    res$value = <span class="hljs-keyword">as</span>.numeric(res$value)<br>    res<br>&#125;<br> <br>library(RColorBrewer)<br>library(ggplot2)<br>col_Paired &lt;- color<span class="hljs-constructor">RampPalette(<span class="hljs-params">brewer</span>.<span class="hljs-params">pal</span>(12, <span class="hljs-string">&quot;Paired&quot;</span>)</span>)<br>f_q_frequnency &lt;- <span class="hljs-keyword">function</span>(lc_q)&#123;<br>    ggplot(f<span class="hljs-constructor">_q2l(<span class="hljs-params">lc_q</span>)</span>,mapping = aes(group,value,fill=label))+<br>    geom<span class="hljs-constructor">_bar(<span class="hljs-params">stat</span>=&#x27;<span class="hljs-params">identity</span>&#x27;,<span class="hljs-params">position</span>=&#x27;<span class="hljs-params">fill</span>&#x27;)</span> + scale<span class="hljs-constructor">_fill_manual(<span class="hljs-params">values</span>= <span class="hljs-params">col_Paired</span>(<span class="hljs-params">nrow</span>(<span class="hljs-params">lc_q</span>)</span>))+<br>    labs(x = &#x27;group&#x27;,y = &#x27;frequnency&#x27;) +<br>    theme(axis.title =element<span class="hljs-constructor">_text(<span class="hljs-params">size</span> = 16)</span>,axis.text =element<span class="hljs-constructor">_text(<span class="hljs-params">size</span> = 14, <span class="hljs-params">color</span> = &#x27;<span class="hljs-params">black</span>&#x27;)</span>)+<br>    theme(axis.text.x = element<span class="hljs-constructor">_text(<span class="hljs-params">angle</span> = 45, <span class="hljs-params">hjust</span> = 1)</span>)+coord<span class="hljs-constructor">_flip()</span> <br>&#125;<br><br>f_DEG_Volcano &lt;- <span class="hljs-keyword">function</span>(lc_logFC, lc_p, lc_gene, Threshold_logFC = <span class="hljs-number">1</span>, Threshold_p = <span class="hljs-number">0.05</span>, lc_rep=<span class="hljs-number">1</span>:<span class="hljs-number">10</span>)&#123;<br>    col_vector = rep(rgb(<span class="hljs-number">108</span>, <span class="hljs-number">200</span>, <span class="hljs-number">228</span>, maxColorValue = <span class="hljs-number">255</span>), length(lc_logFC))<br>    col_vector<span class="hljs-literal">[<span class="hljs-identifier">lc_p</span> &lt; T<span class="hljs-identifier">hreshold_p</span> &amp; <span class="hljs-identifier">lc_logFC</span> &gt; T<span class="hljs-identifier">hreshold_logFC</span>]</span> = rgb(<span class="hljs-number">226</span>, <span class="hljs-number">61</span>, <span class="hljs-number">75</span>, maxColorValue = <span class="hljs-number">255</span>)<br>    col_vector<span class="hljs-literal">[<span class="hljs-identifier">lc_p</span> &lt; T<span class="hljs-identifier">hreshold_p</span> &amp; <span class="hljs-identifier">lc_logFC</span> &lt; -T<span class="hljs-identifier">hreshold_logFC</span>]</span> = rgb(<span class="hljs-number">232</span>, <span class="hljs-number">168</span>, <span class="hljs-number">71</span>, maxColorValue = <span class="hljs-number">255</span>)<br>    lc_p<span class="hljs-literal">[<span class="hljs-identifier">lc_p</span> &lt; <span class="hljs-number">1e-10</span>]</span> = <span class="hljs-number">1e-10</span><br>    lc_p<span class="hljs-literal">[<span class="hljs-identifier">lc_p</span> &gt; <span class="hljs-number">1</span>  <span class="hljs-identifier">is</span>.<span class="hljs-identifier">na</span>(<span class="hljs-identifier">lc_p</span>)]</span> = <span class="hljs-number">1</span><br>    df = data.frame(logFC &lt;- lc_logFC, `-log10(P)` &lt;- -log10(lc_p), col &lt;- col_vector, gene &lt;- lc_gene)<br>    colnames(df) &lt;- c(&#x27;logFC&#x27;, &#x27;-log10(P)&#x27;, <span class="hljs-string">&quot;col&quot;</span>, <span class="hljs-string">&quot;gene&quot;</span>)<br>    lc_tp_logFC &lt;- df$logFC<br>    lc_tp_logFC<span class="hljs-literal">[<span class="hljs-identifier">lc_p</span>&gt;=T<span class="hljs-identifier">hreshold_p</span>]</span> = <span class="hljs-number">0</span><br>    lc_idx &lt;- order(lc_tp_logFC)<span class="hljs-literal">[<span class="hljs-identifier">c</span>(<span class="hljs-identifier">lc_rep</span>, <span class="hljs-identifier">length</span>(<span class="hljs-identifier">lc_gene</span>)+<span class="hljs-number">1</span>-<span class="hljs-identifier">lc_rep</span>)]</span><br>    df$logFC<span class="hljs-literal">[<span class="hljs-identifier">df$logFC</span> &gt; <span class="hljs-number">10</span>]</span> = <span class="hljs-number">10</span><br>    df$logFC<span class="hljs-literal">[<span class="hljs-identifier">df$logFC</span> &lt; -<span class="hljs-number">10</span>]</span> = -<span class="hljs-number">10</span><br>    res &lt;- ggplot<span class="hljs-literal">()</span> + geom<span class="hljs-constructor">_point(<span class="hljs-params">aes</span>(<span class="hljs-params">logFC</span>, `-<span class="hljs-params">log10</span>(P)</span>`, col=<span class="hljs-constructor">I(<span class="hljs-params">col</span>)</span>), data = df) <br>    res &lt;- res + theme<span class="hljs-constructor">_bw()</span> + theme(panel.grid=element<span class="hljs-constructor">_line(<span class="hljs-params">colour</span>=NA)</span>)<br>    res &lt;- res + geom<span class="hljs-constructor">_hline(<span class="hljs-params">yintercept</span>=-<span class="hljs-params">log10</span>(Threshold_p)</span>, linetype=<span class="hljs-string">&quot;longdash&quot;</span>)<br>    res &lt;- res + geom<span class="hljs-constructor">_vline(<span class="hljs-params">xintercept</span>=<span class="hljs-params">c</span>(Threshold_logFC, -Threshold_logFC)</span>, linetype=<span class="hljs-string">&quot;longdash&quot;</span>)<br>    res &lt;- res + geom<span class="hljs-constructor">_text_repel(<span class="hljs-params">data</span>=<span class="hljs-params">df</span>[<span class="hljs-params">lc_idx</span>,],<span class="hljs-params">aes</span>(<span class="hljs-params">logFC</span>,`-<span class="hljs-params">log10</span>(P)</span>`,label=gene), force=T, max.overlaps=Inf)<br>    res<br>&#125;<br><br>f_cluster_averages &lt;- <span class="hljs-keyword">function</span>(lc_scRNA, lc_metaN=&#x27;ident&#x27;)&#123;<br>    # 切分出Clusters<br>    lc_clusters &lt;- <span class="hljs-constructor">SplitObject(<span class="hljs-params">lc_scRNA</span>, <span class="hljs-params">split</span>.<span class="hljs-params">by</span> = <span class="hljs-params">lc_metaN</span>)</span><br>    <span class="hljs-keyword">for</span> (lc_i <span class="hljs-keyword">in</span> <span class="hljs-number">1</span>:length(lc_clusters))&#123;<br>        lc_clusters<span class="hljs-literal">[[<span class="hljs-identifier">lc_i</span>]</span>]  &lt;- lc_clusters<span class="hljs-literal">[[<span class="hljs-identifier">lc_i</span>]</span>]<span class="hljs-literal">[[<span class="hljs-identifier">lc_clusters</span>[[<span class="hljs-identifier">lc_i</span>]</span>]@active.assay]]@scale.data<br>    &#125;<br>    <span class="hljs-keyword">for</span> (lc_i <span class="hljs-keyword">in</span> <span class="hljs-number">1</span>:length(lc_clusters))&#123;<br>        lc_clusters<span class="hljs-literal">[[<span class="hljs-identifier">lc_i</span>]</span>]  &lt;- apply(lc_clusters<span class="hljs-literal">[[<span class="hljs-identifier">lc_i</span>]</span>],<span class="hljs-number">1</span>,mean)<br>    &#125;<br>    lc_clusters &lt;- data.frame(lc_clusters)<br>    scale(lc_clusters)<br>&#125;<br> <br>library(clusterProfiler)<br>library(pheatmap)<br>library(ggdendro)<br>f_DEG_hclust &lt;- <span class="hljs-keyword">function</span>(lc_counts)&#123;<br>    ggdendrogram(hclust(dist(t(lc_counts))), rotate = T, size = <span class="hljs-number">3</span>)+theme(axis.text = element<span class="hljs-constructor">_text(<span class="hljs-params">size</span>=14,<span class="hljs-params">face</span> = <span class="hljs-string">&quot;bold&quot;</span>)</span>)<br>&#125;<br><br>f_DEG_pheatmap_choose_matrix &lt;- <span class="hljs-keyword">function</span>(lc_tp_d, lc_significant_markers, lc_n = <span class="hljs-number">120</span>, Threshold_logFC = <span class="hljs-number">1</span>)&#123;<br>    res &lt;- subset(lc_significant_markers, abs(avg_log2FC) &gt; Threshold_logFC)<br>    res &lt;- res<span class="hljs-literal">[<span class="hljs-identifier">order</span>(<span class="hljs-identifier">abs</span>(<span class="hljs-identifier">res$avg_log2FC</span>), <span class="hljs-identifier">decreasing</span> = T),]</span><br>    res &lt;- head(unique(res$gene), n = lc_n)<br>    res &lt;- lc_tp_d<span class="hljs-literal">[<span class="hljs-identifier">res</span>,]</span><br>    res<br>&#125;<br><br>require(ggplotify)<br>f_DEG_pheatmap &lt;- <span class="hljs-keyword">function</span>(choose_matrix)&#123;<br>    choose_matrix = t(scale(t(choose_matrix)))<br>    <span class="hljs-keyword">as</span>.ggplot(pheatmap(choose_matrix))<br>&#125;<br><br>f_prepare4CSOmap &lt;- <span class="hljs-keyword">function</span>(lc_scRNA, lc_csomap_data_dir, lc_className)&#123;<br>    lc_csomap_data_dir &lt;- system(paste(<span class="hljs-string">&quot;echo&quot;</span>, lc_csomap_data_dir), intern = T)<br>    <span class="hljs-keyword">if</span>(!file.exists(lc_csomap_data_dir))&#123;dir.create(lc_csomap_data_dir)&#125;<br>    # 导出label.txt<br>    labels &lt;- lc_scRNA<span class="hljs-literal">[[<span class="hljs-identifier">lc_className</span>]</span>]<br>    labels$cells &lt;- gsub(<span class="hljs-string">&quot;-&quot;</span>, <span class="hljs-string">&quot;.&quot;</span> ,rownames(labels)) # TPM的colnames 不知为何导出时被替换了，这里也替换一下<br>    labels$labels &lt;- <span class="hljs-keyword">as</span>.character(labels<span class="hljs-literal">[[<span class="hljs-identifier">lc_className</span>]</span>])<br>    rownames(labels) &lt;- NULL<br>    labels = labels<span class="hljs-literal">[,<span class="hljs-identifier">c</span>(&quot;<span class="hljs-identifier">cells</span>&quot;, &quot;<span class="hljs-identifier">labels</span>&quot;)]</span><br>    write.table(labels, file.path(lc_csomap_data_dir, <span class="hljs-string">&quot;label.txt&quot;</span>), row.names = F, sep = <span class="hljs-string">&quot;\t&quot;</span>, quote = F) # 不要引号<br> <br>    # copy <span class="hljs-module-access"><span class="hljs-module"><span class="hljs-identifier">LR_pairs</span>.</span></span>txt<br>    file.copy(from = file.path(lc_csomap_data_dir,<span class="hljs-string">&quot;..&quot;</span>,<span class="hljs-string">&quot;demo&quot;</span>,<span class="hljs-string">&quot;LR_pairs.txt&quot;</span>), <span class="hljs-keyword">to</span> = file.path(lc_csomap_data_dir, <span class="hljs-string">&quot;LR_pairs.txt&quot;</span>))<br>    <br>    # 导出<span class="hljs-module-access"><span class="hljs-module"><span class="hljs-identifier">TPM</span>.</span></span>txt<br>    tpm &lt;- exp(lc_scRNA<span class="hljs-literal">[[&#x27;RNA&#x27;]</span>]@data)<br>    tpm &lt;- tpm - <span class="hljs-number">1</span><br>    tpm &lt;- tpm*<span class="hljs-number">100</span> # <span class="hljs-number">1E4</span> <span class="hljs-keyword">to</span> <span class="hljs-number">1E6</span><br>    colnames(tpm)<span class="hljs-literal">[<span class="hljs-number">1</span>]</span> = paste0(<span class="hljs-character">&#x27;T&#x27;</span>, colnames(tpm)<span class="hljs-literal">[<span class="hljs-number">1</span>]</span>) # 预留\t位置<br>    write.table(tpm, file.path(lc_csomap_data_dir, <span class="hljs-string">&quot;TPM.txt&quot;</span>), sep = <span class="hljs-string">&quot;\t&quot;</span>, quote = F) # 不要引号<br>    <br>    lc_fix &lt;- tempfile<span class="hljs-literal">()</span><br>    lc_py &lt;- sprintf(&#x27;<br>import mmap, os<br> <br>def mapfile(filename, *args, size=None, **kwargs):<br>    file = <span class="hljs-keyword">open</span>(filename, *args, **kwargs)<br>    <span class="hljs-keyword">if</span> size is None: size = os.path.getsize(filename)<br>    return mmap.mmap(file.fileno<span class="hljs-literal">()</span>, size)<br> <br>path = <span class="hljs-string">&quot;%s&quot;</span><br>print(path, <span class="hljs-string">&quot;%s&quot;</span>)<br>f = mapfile(path,<span class="hljs-string">&quot;r+&quot;</span>, size=<span class="hljs-number">10</span>)<br>f<span class="hljs-literal">[<span class="hljs-number">0</span>:<span class="hljs-number">1</span>]</span> = b<span class="hljs-string">&quot;\t&quot;</span><br>print(f<span class="hljs-literal">[:]</span>)<br>f.close<span class="hljs-literal">()</span><br>print(<span class="hljs-string">&quot;Done&quot;</span>)<br>&#x27;, file.path(lc_csomap_data_dir, <span class="hljs-string">&quot;TPM.txt&quot;</span>), lc_fix)<br>    print(lc_py)<br>    cat(file=lc_fix, lc_py)<br>    print(system(paste(<span class="hljs-string">&quot;python3&quot;</span>, lc_fix), intern = T))<br>&#125;<br><br>f_prepare4cellphoneDB &lt;- <span class="hljs-keyword">function</span>(lc_scRNA, lc_dir, lc_className)&#123;<br>    <span class="hljs-keyword">if</span> (!file.exists(lc_dir))&#123;dir.create(lc_dir)&#125;<br>    # 生成 count.txt <br>    write.table(<span class="hljs-keyword">as</span>.matrix(lc_scRNA@assays$RNA@data), file.path(lc_dir,&#x27;cellphonedb_count.txt&#x27;), sep=<span class="hljs-character">&#x27;\t&#x27;</span>, quote=F)<br>    # 生成 meta.txt<br>    lc_meta_data &lt;- cbind(rownames(lc_scRNA@meta.data), lc_scRNA@meta.data<span class="hljs-literal">[, <span class="hljs-identifier">lc_className</span>, <span class="hljs-identifier">drop</span>=F]</span>)<br>    lc_meta_data &lt;- <span class="hljs-keyword">as</span>.matrix(lc_meta_data)<br>    lc_meta_data<span class="hljs-literal">[<span class="hljs-identifier">is</span>.<span class="hljs-identifier">na</span>(<span class="hljs-identifier">lc_meta_data</span>)]</span> = <span class="hljs-string">&quot;Unkown&quot;</span> #  细胞类型中不能有NA<br>    write.table(lc_meta_data, file.path(lc_dir,&#x27;cellphonedb_meta.txt&#x27;), sep=<span class="hljs-character">&#x27;\t&#x27;</span>, quote=F, row.names=F)<br>&#125;<br><br>f_image_output &lt;- <span class="hljs-keyword">function</span>(fileName, image, width=<span class="hljs-number">1920</span>, height=<span class="hljs-number">1080</span>, lc_pdf=T, lc_resolution=<span class="hljs-number">72</span>)&#123;<br>    <span class="hljs-keyword">if</span>(lc_pdf)&#123;<br>        width = width<span class="hljs-operator"> / </span>lc_resolution<br>        height = height<span class="hljs-operator"> / </span>lc_resolution<br>        pdf(paste(fileName, <span class="hljs-string">&quot;.pdf&quot;</span>, sep=<span class="hljs-string">&quot;&quot;</span>), width = width, height = height)<br>    &#125;<span class="hljs-keyword">else</span>&#123;<br>        png(paste(fileName, <span class="hljs-string">&quot;.png&quot;</span>, sep=<span class="hljs-string">&quot;&quot;</span>), width = width, height = height)<br>    &#125;<br>    print(image)<br>    dev.off<span class="hljs-literal">()</span><br>&#125;<br> <br># Rearrange data column sequence<br>library(dplyr)<br>f_cDB_order_sequence &lt;- <span class="hljs-keyword">function</span>(lc_df)&#123;<br>    da &lt;- data.frame<span class="hljs-literal">()</span><br>    df &lt;- subset(lc_df, receptor_a<span class="hljs-operator"> == </span>&#x27;True&#x27; &amp; receptor_b<span class="hljs-operator"> == </span>&#x27;False&#x27;  receptor_a<span class="hljs-operator"> == </span>&#x27;False&#x27; &amp; receptor_b<span class="hljs-operator"> == </span>&#x27;True&#x27;)<br>    <span class="hljs-keyword">for</span>(i <span class="hljs-keyword">in</span> <span class="hljs-number">1</span>:length(df$gene_a))&#123;<br>    sub_data &lt;- df<span class="hljs-literal">[<span class="hljs-identifier">i</span>, ]</span><br>    <span class="hljs-keyword">if</span>(sub_data$receptor_b==&#x27;False&#x27;)&#123;<br>        <span class="hljs-keyword">if</span>(sub_data$receptor_a==&#x27;True&#x27;)&#123;<br>            old_names &lt;- colnames(sub_data)<br>            my_list &lt;- strsplit(old_names<span class="hljs-literal">[-<span class="hljs-identifier">c</span>(<span class="hljs-number">1</span>:<span class="hljs-number">11</span>)]</span>, split=<span class="hljs-string">&quot;\\&quot;</span>)<br>            my_character &lt;- paste(sapply(my_list, &#x27;<span class="hljs-literal">[[&#x27;, <span class="hljs-number">2L</span>), <span class="hljs-identifier">sapply</span>(<span class="hljs-identifier">my_list</span>, &#x27;[[&#x27;, <span class="hljs-number">1L</span>), <span class="hljs-identifier">sep</span>=&#x27;&#x27;)</span><br><span class="hljs-literal">            <span class="hljs-identifier">new_names</span> &lt;- <span class="hljs-identifier">c</span>(<span class="hljs-identifier">names</span>(<span class="hljs-identifier">sub_data</span>)[<span class="hljs-number">1</span>:<span class="hljs-number">4</span>]</span>, &#x27;gene_b&#x27;, &#x27;gene_a&#x27;, &#x27;secreted&#x27;, &#x27;receptor_b&#x27;, &#x27;receptor_a&#x27;, <span class="hljs-string">&quot;annotation_strategy&quot;</span>, <span class="hljs-string">&quot;is_integrin&quot;</span>, my_character)<br>            sub_data = dplyr::select(sub_data, new_names)<br>            # print(&#x27;Change sequence!!!&#x27;)<br>            names(sub_data) &lt;- old_names<br>            da = rbind(da, sub_data) <br>        &#125;<br>    &#125;<span class="hljs-keyword">else</span>&#123;<br>            da = rbind(da, sub_data)<br>    &#125;<br>    &#125;<br>    return(da)<br>&#125;<br> <br>f_cDB_mergePandM &lt;- <span class="hljs-keyword">function</span>(means_order, pvals_order)&#123;<br>    means_sub &lt;- means_order<span class="hljs-literal">[, <span class="hljs-identifier">c</span>(&#x27;<span class="hljs-identifier">interacting_pair</span>&#x27;, <span class="hljs-identifier">colnames</span>(<span class="hljs-identifier">means_order</span>)[-<span class="hljs-identifier">c</span>(<span class="hljs-number">1</span>:<span class="hljs-number">11</span>)]</span>)]<br>    pvals_sub &lt;- pvals_order<span class="hljs-literal">[, <span class="hljs-identifier">c</span>(&#x27;<span class="hljs-identifier">interacting_pair</span>&#x27;, <span class="hljs-identifier">colnames</span>(<span class="hljs-identifier">means_order</span>)[-<span class="hljs-identifier">c</span>(<span class="hljs-number">1</span>:<span class="hljs-number">11</span>)]</span>)]<br>    means_gather &lt;- tidyr::gather(means_sub, celltype, mean_expression, names(means_sub)<span class="hljs-literal">[-<span class="hljs-number">1</span>]</span>)<br>    pvals_gather &lt;- tidyr::gather(pvals_sub, celltype, pval, names(pvals_sub)<span class="hljs-literal">[-<span class="hljs-number">1</span>]</span>)<br>    mean_pval &lt;- dplyr::left<span class="hljs-constructor">_join(<span class="hljs-params">means_gather</span>, <span class="hljs-params">pvals_gather</span>, <span class="hljs-params">by</span> = <span class="hljs-params">c</span>(&#x27;<span class="hljs-params">interacting_pair</span>&#x27;, &#x27;<span class="hljs-params">celltype</span>&#x27;)</span>)<br>    mean_pval<br>&#125;<br> <br>f_readcellphoneDB &lt;- <span class="hljs-keyword">function</span>(lc_dir)&#123;<br>    res = <span class="hljs-built_in">list</span><span class="hljs-literal">()</span><br>    res$pvals &lt;- f<span class="hljs-constructor">_cDB_order_sequence(<span class="hljs-params">read</span>.<span class="hljs-params">delim</span>(<span class="hljs-params">file</span>.<span class="hljs-params">path</span>(<span class="hljs-params">lc_dir</span>, <span class="hljs-string">&quot;out&quot;</span>,<span class="hljs-string">&quot;pvalues.txt&quot;</span>)</span>, check.names = FALSE))<br>    res$means &lt;- f<span class="hljs-constructor">_cDB_order_sequence(<span class="hljs-params">read</span>.<span class="hljs-params">delim</span>(<span class="hljs-params">file</span>.<span class="hljs-params">path</span>(<span class="hljs-params">lc_dir</span>, <span class="hljs-string">&quot;out&quot;</span>, <span class="hljs-string">&quot;means.txt&quot;</span>)</span>, check.names = FALSE))<br>    res$s_means &lt;- read.delim(file.path(lc_dir, <span class="hljs-string">&quot;out&quot;</span>, <span class="hljs-string">&quot;significant_means.txt&quot;</span>), check.names = FALSE)<br>    res$m_p &lt;- f<span class="hljs-constructor">_cDB_mergePandM(<span class="hljs-params">res$means</span>, <span class="hljs-params">res$pvals</span>)</span><br>    lc_tp &lt;- res$m_p %&gt;% dplyr::select(interacting_pair, celltype, pval) %&gt;% tidyr::spread(key=celltype, value=pval)<br>    lc_sig_pairs &lt;- lc_tp<span class="hljs-literal">[<span class="hljs-identifier">which</span>(<span class="hljs-identifier">rowSums</span>(<span class="hljs-identifier">lc_tp</span>&lt;=<span class="hljs-number">0.05</span>)!=<span class="hljs-number">0</span>), ]</span><br>    res$s_m_p &lt;- subset(res$m_p, interacting_pair %<span class="hljs-keyword">in</span>% lc_sig_pairs$interacting_pair)<br>    res<br>&#125;<br> <br>f_cDB_dotplot &lt;- <span class="hljs-keyword">function</span>(lc_m_p)&#123;<br>    lc_m_p %&gt;% ggplot(aes(x=interacting_pair, y=celltype)) +<br>    # geom<span class="hljs-constructor">_point(<span class="hljs-params">aes</span>(<span class="hljs-params">color</span>=<span class="hljs-params">log2</span>(<span class="hljs-params">mean_expression</span>)</span>, size=pval)) +<br>    # scale<span class="hljs-constructor">_size(<span class="hljs-params">trans</span> = &#x27;<span class="hljs-params">reverse</span>&#x27;)</span> +<br>    geom<span class="hljs-constructor">_point(<span class="hljs-params">aes</span>(<span class="hljs-params">color</span>=<span class="hljs-params">log2</span>(<span class="hljs-params">mean_expression</span>)</span>, size=-log10(pval+<span class="hljs-number">1</span>*<span class="hljs-number">10</span>^-<span class="hljs-number">3</span>)) ) +<br>    guides(colour = guide<span class="hljs-constructor">_colourbar(<span class="hljs-params">order</span> = 1)</span>,size = guide<span class="hljs-constructor">_legend(<span class="hljs-params">order</span> = 2)</span>) +<br>    labs(x=&#x27;&#x27;, y=&#x27;&#x27;) +<br>    scale<span class="hljs-constructor">_color_gradientn(<span class="hljs-params">name</span>=&#x27;Expression <span class="hljs-params">level</span> \<span class="hljs-params">n</span>(<span class="hljs-params">log2</span> <span class="hljs-params">mean</span> <span class="hljs-params">expression</span> \<span class="hljs-params">nmolecule1</span>, <span class="hljs-params">molecule2</span>)</span>&#x27;, colours = terrain.colors(<span class="hljs-number">100</span>)) +<br>    # scale<span class="hljs-constructor">_color_gradient2(&#x27;Expression <span class="hljs-params">level</span> \<span class="hljs-params">n</span>(<span class="hljs-params">log2</span> <span class="hljs-params">mean</span> <span class="hljs-params">expression</span> \<span class="hljs-params">nmolecule1</span>, <span class="hljs-params">molecule2</span>)</span>&#x27;, low = &#x27;blue&#x27;, mid = &#x27;yellow&#x27;, high = &#x27;red&#x27;) +<br>    theme(axis.text.x= element<span class="hljs-constructor">_text(<span class="hljs-params">angle</span>=45, <span class="hljs-params">hjust</span>=1)</span>) +<br>    # coord<span class="hljs-constructor">_flip()</span> +<br>    theme(<br>    panel.border = element<span class="hljs-constructor">_rect(<span class="hljs-params">color</span> = &#x27;<span class="hljs-params">black</span>&#x27;, <span class="hljs-params">fill</span> = NA)</span>,<br>    panel.grid.major.x = element<span class="hljs-constructor">_blank()</span>,<br>    panel.grid.major.y = element<span class="hljs-constructor">_blank()</span>,<br>    panel.grid.minor.x = element<span class="hljs-constructor">_blank()</span>,<br>    panel.grid.minor.y = element<span class="hljs-constructor">_blank()</span>,<br>    panel.background   = element<span class="hljs-constructor">_blank()</span>,<br>    axis.title.x       = element<span class="hljs-constructor">_blank()</span>,<br>    axis.title.y       = element<span class="hljs-constructor">_blank()</span>,<br>    axis.ticks         = element<span class="hljs-constructor">_blank()</span><br>    # plot.title         = element<span class="hljs-constructor">_text(<span class="hljs-params">hjust</span> = 0.5)</span>,<br>    # legend.position = &#x27;bottom&#x27; # guides(fill = guide<span class="hljs-constructor">_legend(<span class="hljs-params">label</span>.<span class="hljs-params">position</span> = <span class="hljs-string">&quot;bottom&quot;</span>)</span>)<br>    # legend.position    = <span class="hljs-string">&quot;bottom&quot;</span><br>    # axis.text.y.right  = element<span class="hljs-constructor">_text(<span class="hljs-params">angle</span>=270, <span class="hljs-params">hjust</span>=0.5)</span><br>    ) +<br>    theme(legend.key.size = <span class="hljs-built_in">unit</span>(<span class="hljs-number">0.4</span>, &#x27;cm&#x27;), #change legend key size<br>    # legend.key.height = <span class="hljs-built_in">unit</span>(<span class="hljs-number">1</span>, &#x27;cm&#x27;), #change legend key height<br>    # legend.key.width = <span class="hljs-built_in">unit</span>(<span class="hljs-number">1</span>, &#x27;cm&#x27;), #change legend key width<br>    legend.title = element<span class="hljs-constructor">_text(<span class="hljs-params">size</span>=9)</span>, #change legend title font size<br>    legend.text = element<span class="hljs-constructor">_text(<span class="hljs-params">size</span>=8)</span>) #change legend text font size<br>&#125;<br><br></code></pre></td></tr></table></figure>

<figure class="highlight cmake"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br></pre></td><td class="code"><pre><code class="hljs cmake"><span class="hljs-comment"># 配置数据和mark基因表的路径</span><br>root_path = <span class="hljs-string">&quot;~/zlliu/R_data/hBLA&quot;</span><br> <br><span class="hljs-comment"># 配置结果保存路径</span><br>output_path = <span class="hljs-string">&quot;~/zlliu/R_data/21.10.04.split&quot;</span><br><span class="hljs-keyword">if</span> (!<span class="hljs-keyword">file</span>.<span class="hljs-keyword">exists</span>(output_path))&#123;dir.create(output_path)&#125;<br> <br><span class="hljs-comment"># 设置工作目录，输出文件将保存在此目录下</span><br>setwd(output_path)<br>getwd()<br></code></pre></td></tr></table></figure>

<figure class="highlight mipsasm"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br></pre></td><td class="code"><pre><code class="hljs mipsasm"><span class="hljs-comment"># 1、读取数据</span><br><span class="hljs-keyword">scRNA </span>= readRDS(<span class="hljs-string">&quot;~/zlliu/R_output/21.09.21.SingleR/scRNA.rds&quot;</span>)<br><span class="hljs-keyword">scRNA </span>&lt;- <span class="hljs-keyword">subset(x </span>= <span class="hljs-keyword">scRNA, </span>!!sym(<span class="hljs-string">&quot;Region&quot;</span>)%in%f_br_cluster_f(<span class="hljs-keyword">scRNA, </span><span class="hljs-string">&quot;Region&quot;</span>))<br><span class="hljs-keyword">scRNA@meta.data</span><br></code></pre></td></tr></table></figure>

<figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br></pre></td><td class="code"><pre><code class="hljs stylus"><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(repr.plot.width=<span class="hljs-number">12</span>, repr.plot.height=<span class="hljs-number">6</span>)</span></span><br><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(ggrepel.max.overlaps = Inf)</span></span><br><span class="hljs-function"><span class="hljs-title">f_pie_metaN</span><span class="hljs-params">(scRNA, <span class="hljs-string">&quot;Region&quot;</span>)</span></span> + <span class="hljs-built_in">f_pie_metaN</span>(scRNA, <span class="hljs-string">&quot;hM1_hmca_class&quot;</span>)<br></code></pre></td></tr></table></figure>

<figure class="highlight lua"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br></pre></td><td class="code"><pre><code class="hljs lua">n_ExN &lt;- c(<span class="hljs-string">&#x27;L4 IT&#x27;</span>,<span class="hljs-string">&#x27;L5 IT&#x27;</span>,<span class="hljs-string">&#x27;L5 ET&#x27;</span>,<span class="hljs-string">&#x27;IT&#x27;</span>,<span class="hljs-string">&#x27;L6b&#x27;</span>,<span class="hljs-string">&#x27;L5/6 IT Car3&#x27;</span>,<span class="hljs-string">&#x27;L6 IT&#x27;</span>,<span class="hljs-string">&#x27;L2/3 IT&#x27;</span>,<span class="hljs-string">&#x27;L5/6 NP&#x27;</span>,<span class="hljs-string">&#x27;L6 IT Car3&#x27;</span>,<span class="hljs-string">&#x27;L6 CT&#x27;</span>)<br> <br>n_InN &lt;- c(<span class="hljs-string">&#x27;Lamp5&#x27;</span>,<span class="hljs-string">&#x27;Pvalb&#x27;</span>,<span class="hljs-string">&#x27;Sst&#x27;</span>,<span class="hljs-string">&#x27;Vip&#x27;</span>,<span class="hljs-string">&#x27;Sncg&#x27;</span>)<br> <br>n_NoN &lt;- c(<span class="hljs-string">&#x27;Astro&#x27;</span>,<span class="hljs-string">&#x27;PAX6&#x27;</span>,<span class="hljs-string">&#x27;Endo&#x27;</span>,<span class="hljs-string">&#x27;Micro-PVM&#x27;</span>,<span class="hljs-string">&#x27;OPC&#x27;</span>,<span class="hljs-string">&#x27;Oligo&#x27;</span>,<span class="hljs-string">&#x27;Pericyte&#x27;</span>,<span class="hljs-string">&#x27;VLMC&#x27;</span>)<br> <br>n_groups &lt;- list(NoN=n_NoN, ExN=n_ExN, InN=n_InN)<br> <br>f_listUpdateRe &lt;- <span class="hljs-function"><span class="hljs-keyword">function</span><span class="hljs-params">(lc_obj, lc_bool, lc_item)</span></span>&#123;<br>    lc_obj[lc_bool] &lt;- <span class="hljs-built_in">rep</span>(lc_item,times=sum(lc_bool))<br>    lc_obj<br>&#125;<br> <br>f_grouplabel &lt;- <span class="hljs-function"><span class="hljs-keyword">function</span><span class="hljs-params">(lc_meta.data, lc_groups)</span></span>&#123;<br>    res &lt;- lc_meta.data<span class="hljs-string">[[1]]</span><br>    <span class="hljs-keyword">for</span>(lc_g <span class="hljs-keyword">in</span> names(lc_groups))&#123;<br>        lc_bool = (res %<span class="hljs-keyword">in</span>% lc_groups<span class="hljs-string">[[lc_g]]</span>)<br>        <span class="hljs-keyword">for</span>(c_n <span class="hljs-keyword">in</span> colnames(lc_meta.data))&#123;<br>            lc_bool = lc_bool  (lc_meta.data<span class="hljs-string">[[c_n]]</span> %<span class="hljs-keyword">in</span>% lc_groups<span class="hljs-string">[[lc_g]]</span>)<br>        &#125;<br>        res &lt;- f_listUpdateRe(res, lc_bool, lc_g)<br>    &#125;<br>    names(res) &lt;- rownames(lc_meta.data)<br>    res<br>&#125;<br></code></pre></td></tr></table></figure>

<figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br></pre></td><td class="code"><pre><code class="hljs stylus"><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(repr.plot.width=<span class="hljs-number">9</span>, repr.plot.height=<span class="hljs-number">5</span>)</span></span><br>tp_test &lt;- <span class="hljs-built_in">f_br_cluster</span>(scRNA, <span class="hljs-string">&#x27;Region&#x27;</span>, <span class="hljs-string">&#x27;hM1_hmca_class&#x27;</span>)<br><span class="hljs-function"><span class="hljs-title">f_q_frequnency</span><span class="hljs-params">(tp_test)</span></span><br>friedman<span class="hljs-selector-class">.test</span>(as<span class="hljs-selector-class">.matrix</span>(tp_test))<br>chisq<span class="hljs-selector-class">.test</span>(as<span class="hljs-selector-class">.matrix</span>(tp_test), simulate<span class="hljs-selector-class">.p</span><span class="hljs-selector-class">.value</span> = TRUE)<br>fisher<span class="hljs-selector-class">.test</span>(as<span class="hljs-selector-class">.matrix</span>(tp_test), simulate<span class="hljs-selector-class">.p</span><span class="hljs-selector-class">.value</span> = TRUE)<br>tp_test<br><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(repr.plot.width=<span class="hljs-number">9</span>, repr.plot.height=<span class="hljs-number">9</span>)</span></span><br><span class="hljs-function"><span class="hljs-title">f_UMAP_more</span><span class="hljs-params">(scRNA, c(<span class="hljs-string">&#x27;hM1_class&#x27;</span>, <span class="hljs-string">&#x27;hmca_class&#x27;</span>)</span></span>)<br><span class="hljs-function"><span class="hljs-title">f_UMAP_more</span><span class="hljs-params">(scRNA, c(<span class="hljs-string">&#x27;hM1_hmca_class&#x27;</span>, <span class="hljs-string">&#x27;Region&#x27;</span>)</span></span>)<br></code></pre></td></tr></table></figure>

<figure class="highlight lua"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br></pre></td><td class="code"><pre><code class="hljs lua">scRNA<span class="hljs-string">[[&#x27;n_groups&#x27;]]</span> &lt;- f_grouplabel(scRNA<span class="hljs-string">[[c(&quot;hM1_hmca_class&quot;)]]</span>, n_groups)<br>sc_Neuron &lt;- subset(x = scRNA, n_groups %<span class="hljs-keyword">in</span>% c(<span class="hljs-string">&quot;InN&quot;</span>, <span class="hljs-string">&quot;ExN&quot;</span>))<br>sc_Neuron &lt;- subset(x = sc_Neuron, !!sym(<span class="hljs-string">&quot;Region&quot;</span>)%<span class="hljs-keyword">in</span>%f_br_cluster_f(sc_Neuron, <span class="hljs-string">&quot;Region&quot;</span>))<br></code></pre></td></tr></table></figure>

<figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br></pre></td><td class="code"><pre><code class="hljs stylus"><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(repr.plot.width=<span class="hljs-number">12</span>, repr.plot.height=<span class="hljs-number">6</span>)</span></span><br><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(ggrepel.max.overlaps = Inf)</span></span><br><span class="hljs-function"><span class="hljs-title">f_pie_metaN</span><span class="hljs-params">(sc_Neuron, <span class="hljs-string">&quot;Region&quot;</span>)</span></span> + <span class="hljs-built_in">f_pie_metaN</span>(sc_Neuron, <span class="hljs-string">&quot;hM1_hmca_class&quot;</span>)<br><br><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(repr.plot.width=<span class="hljs-number">9</span>, repr.plot.height=<span class="hljs-number">5</span>)</span></span><br>tp_test &lt;- <span class="hljs-built_in">f_br_cluster</span>(sc_Neuron, <span class="hljs-string">&#x27;Region&#x27;</span>, <span class="hljs-string">&#x27;hM1_hmca_class&#x27;</span>)<br><span class="hljs-function"><span class="hljs-title">f_q_frequnency</span><span class="hljs-params">(tp_test)</span></span><br>friedman<span class="hljs-selector-class">.test</span>(as<span class="hljs-selector-class">.matrix</span>(tp_test))<br>chisq<span class="hljs-selector-class">.test</span>(as<span class="hljs-selector-class">.matrix</span>(tp_test), simulate<span class="hljs-selector-class">.p</span><span class="hljs-selector-class">.value</span> = TRUE)<br>fisher<span class="hljs-selector-class">.test</span>(as<span class="hljs-selector-class">.matrix</span>(tp_test), simulate<span class="hljs-selector-class">.p</span><span class="hljs-selector-class">.value</span> = TRUE)<br>tp_test<br><br></code></pre></td></tr></table></figure>

<figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br></pre></td><td class="code"><pre><code class="hljs stylus">sc_Neuron_ExN &lt;- <span class="hljs-built_in">subset</span>(x = sc_Neuron, n_groups == <span class="hljs-string">&quot;ExN&quot;</span>)<br><br><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(repr.plot.width=<span class="hljs-number">12</span>, repr.plot.height=<span class="hljs-number">6</span>)</span></span><br><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(ggrepel.max.overlaps = Inf)</span></span><br><span class="hljs-function"><span class="hljs-title">f_pie_metaN</span><span class="hljs-params">(sc_Neuron_ExN, <span class="hljs-string">&quot;Region&quot;</span>)</span></span> + <span class="hljs-built_in">f_pie_metaN</span>(sc_Neuron_ExN, <span class="hljs-string">&quot;hM1_hmca_class&quot;</span>)<br><br><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(repr.plot.width=<span class="hljs-number">9</span>, repr.plot.height=<span class="hljs-number">5</span>)</span></span><br>tp_test &lt;- <span class="hljs-built_in">f_br_cluster</span>(sc_Neuron_ExN, <span class="hljs-string">&#x27;Region&#x27;</span>, <span class="hljs-string">&#x27;hM1_hmca_class&#x27;</span>)<br><span class="hljs-function"><span class="hljs-title">f_q_frequnency</span><span class="hljs-params">(tp_test)</span></span><br>friedman<span class="hljs-selector-class">.test</span>(as<span class="hljs-selector-class">.matrix</span>(tp_test))<br>chisq<span class="hljs-selector-class">.test</span>(as<span class="hljs-selector-class">.matrix</span>(tp_test), simulate<span class="hljs-selector-class">.p</span><span class="hljs-selector-class">.value</span> = TRUE)<br>fisher<span class="hljs-selector-class">.test</span>(as<span class="hljs-selector-class">.matrix</span>(tp_test), simulate<span class="hljs-selector-class">.p</span><span class="hljs-selector-class">.value</span> = TRUE)<br>tp_test<br><br><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(repr.plot.width=<span class="hljs-number">9</span>, repr.plot.height=<span class="hljs-number">9</span>)</span></span><br><span class="hljs-function"><span class="hljs-title">f_UMAP_more</span><span class="hljs-params">(sc_Neuron_ExN, c(<span class="hljs-string">&#x27;hM1_class&#x27;</span>, <span class="hljs-string">&#x27;hmca_class&#x27;</span>)</span></span>)<br><span class="hljs-function"><span class="hljs-title">f_UMAP_more</span><span class="hljs-params">(sc_Neuron_ExN, c(<span class="hljs-string">&#x27;hM1_hmca_class&#x27;</span>, <span class="hljs-string">&#x27;Region&#x27;</span>)</span></span>)<br><br></code></pre></td></tr></table></figure>

<figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br></pre></td><td class="code"><pre><code class="hljs stylus">sc_Neuron_InN &lt;- <span class="hljs-built_in">subset</span>(x = sc_Neuron, n_groups == <span class="hljs-string">&quot;InN&quot;</span>)<br><br><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(repr.plot.width=<span class="hljs-number">12</span>, repr.plot.height=<span class="hljs-number">6</span>)</span></span><br><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(ggrepel.max.overlaps = Inf)</span></span><br><span class="hljs-function"><span class="hljs-title">f_pie_metaN</span><span class="hljs-params">(sc_Neuron_InN, <span class="hljs-string">&quot;Region&quot;</span>)</span></span> + <span class="hljs-built_in">f_pie_metaN</span>(sc_Neuron_InN, <span class="hljs-string">&quot;hM1_hmca_class&quot;</span>)<br><br><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(repr.plot.width=<span class="hljs-number">9</span>, repr.plot.height=<span class="hljs-number">5</span>)</span></span><br>tp_test &lt;- <span class="hljs-built_in">f_br_cluster</span>(sc_Neuron_InN, <span class="hljs-string">&#x27;Region&#x27;</span>, <span class="hljs-string">&#x27;hM1_hmca_class&#x27;</span>)<br><span class="hljs-function"><span class="hljs-title">f_q_frequnency</span><span class="hljs-params">(tp_test)</span></span><br>friedman<span class="hljs-selector-class">.test</span>(as<span class="hljs-selector-class">.matrix</span>(tp_test))<br>chisq<span class="hljs-selector-class">.test</span>(as<span class="hljs-selector-class">.matrix</span>(tp_test), simulate<span class="hljs-selector-class">.p</span><span class="hljs-selector-class">.value</span> = TRUE)<br>fisher<span class="hljs-selector-class">.test</span>(as<span class="hljs-selector-class">.matrix</span>(tp_test), simulate<span class="hljs-selector-class">.p</span><span class="hljs-selector-class">.value</span> = TRUE)<br>tp_test<br><br><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(repr.plot.width=<span class="hljs-number">9</span>, repr.plot.height=<span class="hljs-number">9</span>)</span></span><br><span class="hljs-function"><span class="hljs-title">f_UMAP_more</span><span class="hljs-params">(sc_Neuron_InN, c(<span class="hljs-string">&#x27;hM1_class&#x27;</span>, <span class="hljs-string">&#x27;hmca_class&#x27;</span>)</span></span>)<br><span class="hljs-function"><span class="hljs-title">f_UMAP_more</span><span class="hljs-params">(sc_Neuron_InN, c(<span class="hljs-string">&#x27;hM1_hmca_class&#x27;</span>, <span class="hljs-string">&#x27;Region&#x27;</span>)</span></span>)<br><br></code></pre></td></tr></table></figure>

<figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br></pre></td><td class="code"><pre><code class="hljs stylus"><span class="hljs-function"><span class="hljs-title">Idents</span><span class="hljs-params">(sc_Neuron)</span></span> &lt;- sc_Neuron<span class="hljs-selector-attr">[[<span class="hljs-string">&#x27;hM1_hmca_class&#x27;</span>]</span>]<br>all_markers &lt;- <span class="hljs-built_in">FindAllMarkers</span>(sc_Neuron, min<span class="hljs-selector-class">.pct</span> = <span class="hljs-number">0.25</span>, logfc<span class="hljs-selector-class">.threshold</span> = <span class="hljs-number">0.25</span>)<br>significant_markers &lt;- <span class="hljs-built_in">subset</span>(all_markers, subset = p_val_adj&lt;<span class="hljs-number">0.05</span>)<br><br></code></pre></td></tr></table></figure>

<figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br></pre></td><td class="code"><pre><code class="hljs stylus"><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(repr.plot.width=<span class="hljs-number">12</span>, repr.plot.height=<span class="hljs-number">6</span>)</span></span><br>tp_d &lt;- <span class="hljs-built_in">f_cluster_averages</span>(sc_Neuron, <span class="hljs-string">&quot;hM1_hmca_class&quot;</span>)<br>tp_d_br &lt;- <span class="hljs-built_in">f_cluster_averages</span>(sc_Neuron, <span class="hljs-string">&quot;Region&quot;</span>)<br><span class="hljs-function"><span class="hljs-title">f_DEG_hclust</span><span class="hljs-params">(tp_d)</span></span> + <span class="hljs-built_in">f_DEG_hclust</span>(tp_d_br)<br></code></pre></td></tr></table></figure>

<figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br></pre></td><td class="code"><pre><code class="hljs stylus"><span class="hljs-function"><span class="hljs-title">Idents</span><span class="hljs-params">(sc_Neuron)</span></span> &lt;- sc_Neuron<span class="hljs-selector-attr">[[<span class="hljs-string">&#x27;hM1_hmca_class&#x27;</span>]</span>]<br>all_markers &lt;- <span class="hljs-built_in">FindAllMarkers</span>(sc_Neuron, min<span class="hljs-selector-class">.pct</span> = <span class="hljs-number">0.25</span>, logfc<span class="hljs-selector-class">.threshold</span> = <span class="hljs-number">0.25</span>)<br>significant_markers &lt;- <span class="hljs-built_in">subset</span>(all_markers, subset = p_val_adj&lt;<span class="hljs-number">0.05</span>)<br><br></code></pre></td></tr></table></figure>

<figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br></pre></td><td class="code"><pre><code class="hljs stylus"><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(repr.plot.width=<span class="hljs-number">9</span>, repr.plot.height=<span class="hljs-number">30</span>)</span></span><br>p1 &lt;- <span class="hljs-built_in">f_DEG_pheatmap</span>(<span class="hljs-built_in">f_DEG_pheatmap_choose_matrix</span>(tp_d, significant_markers))<br><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(repr.plot.width=<span class="hljs-number">9</span>, repr.plot.height=<span class="hljs-number">30</span>)</span></span><br>p2 &lt;- <span class="hljs-built_in">f_DEG_pheatmap</span>(<span class="hljs-built_in">f_DEG_pheatmap_choose_matrix</span>(tp_d_br, significant_markers_br, Threshold_logFC = <span class="hljs-number">0.1</span>))<br><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(repr.plot.width=<span class="hljs-number">18</span>, repr.plot.height=<span class="hljs-number">30</span>)</span></span><br>p1 + p2<br></code></pre></td></tr></table></figure>

<figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br></pre></td><td class="code"><pre><code class="hljs stylus"><span class="hljs-function"><span class="hljs-title">f_prepare4cellphoneDB</span><span class="hljs-params">(sc_Neuron,<span class="hljs-string">&quot;Neuron&quot;</span>, <span class="hljs-string">&quot;hM1_hmca_class&quot;</span>)</span></span><br><span class="hljs-function"><span class="hljs-title">f_prepare4cellphoneDB</span><span class="hljs-params">(sc_Neuron,<span class="hljs-string">&quot;Neuron_br&quot;</span>, <span class="hljs-string">&quot;Region&quot;</span>)</span></span><br><span class="hljs-function"><span class="hljs-title">f_prepare4CSOmap</span><span class="hljs-params">(sc_Neuron, <span class="hljs-string">&quot;~/CSOmap/data/zlliu_s_Neuron&quot;</span>, <span class="hljs-string">&quot;hM1_hmca_class&quot;</span>)</span></span><br><span class="hljs-function"><span class="hljs-title">f_prepare4CSOmap</span><span class="hljs-params">(sc_Neuron, <span class="hljs-string">&quot;~/CSOmap/data/zlliu_s_Neuron_br&quot;</span>, <span class="hljs-string">&quot;Region&quot;</span>)</span></span><br></code></pre></td></tr></table></figure>

<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br></pre></td><td class="code"><pre><code class="hljs bash"><span class="hljs-meta">#!/bin/bash</span><br><span class="hljs-comment">#PBS -q batch</span><br><span class="hljs-comment">#PBS -V</span><br><span class="hljs-comment">#PBS -o /home/rqzhang/cellphonedb.out</span><br><span class="hljs-comment">#PBS -e /home/rqzhang/cellphonedb.err</span><br><span class="hljs-comment">#PBS -l nodes=1:ppn=32</span><br><span class="hljs-comment">#PBS -r y</span><br> <br><span class="hljs-built_in">cd</span> /home/rqzhang/zlliu/R_data/21.10.04.<span class="hljs-built_in">split</span>/Neuron<br>cellphonedb method statistical_analysis  cellphonedb_meta.txt  cellphonedb_count.txt --counts-data=gene_name  --threads=32<br>cellphonedb plot dot_plot<br>cellphonedb plot heatmap_plot cellphonedb_meta.txt<br><br><span class="hljs-built_in">cd</span> /home/rqzhang/zlliu/R_data/21.10.04.<span class="hljs-built_in">split</span>/Neuron_br<br>cellphonedb method statistical_analysis  cellphonedb_meta.txt  cellphonedb_count.txt --counts-data=gene_name  --threads=32<br>cellphonedb plot dot_plot<br>cellphonedb plot heatmap_plot cellphonedb_meta.txt<br><br></code></pre></td></tr></table></figure>

<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br></pre></td><td class="code"><pre><code class="hljs bash"><span class="hljs-meta">#!/bin/bash</span><br><span class="hljs-comment">#PBS -q batch</span><br><span class="hljs-comment">#PBS -V</span><br><span class="hljs-comment">#PBS -o /home/rqzhang/zlliu/PBS/CSOmap/CSOmap.out</span><br><span class="hljs-comment">#PBS -e /home/rqzhang/zlliu/PBS/CSOmap/CSOmap.err</span><br><span class="hljs-comment">#PBS -l nodes=1:ppn=1</span><br><span class="hljs-comment">#PBS -r y</span><br><span class="hljs-built_in">cd</span> /home/rqzhang/CSOmap/code<br>matlab -nodisplay -r <span class="hljs-string">&quot;runme(&#x27;zlliu_s_Neuron&#x27;);exit&quot;</span><br>matlab -nodisplay -r <span class="hljs-string">&quot;runme(&#x27;zlliu_s_Neuron_br&#x27;);exit&quot;</span><br><span class="hljs-built_in">echo</span> <span class="hljs-variable">$HOME</span><br></code></pre></td></tr></table></figure>

<figure class="highlight reasonml"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br></pre></td><td class="code"><pre><code class="hljs reasonml">n_d &lt;- f<span class="hljs-constructor">_readcellphoneDB(&#x27;Neuron&#x27;)</span><br>tp_img &lt;- f<span class="hljs-constructor">_cDB_dotplot(<span class="hljs-params">subset</span>(<span class="hljs-params">n_d$s_m_p</span>, <span class="hljs-params">pval</span>&lt;0.05)</span>)<br>f<span class="hljs-constructor">_image_output(&#x27;Neuron&#x27;,<span class="hljs-params">tp_img</span>, <span class="hljs-params">width</span> = 1080,<span class="hljs-params">height</span> = 1080)</span><br><br></code></pre></td></tr></table></figure>

<h2 id="更新"><a href="#更新" class="headerlink" title="更新"></a>更新</h2><figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br></pre></td><td class="code"><pre><code class="hljs stylus">f_prepare4cellphoneDB_sp &lt;- <span class="hljs-built_in">function</span>(lc_scRNA, lc_dir, lc_className, lc_groupN)&#123;<br>    <span class="hljs-keyword">if</span> (!file<span class="hljs-selector-class">.exists</span>(lc_dir))&#123;dir<span class="hljs-selector-class">.create</span>(lc_dir)&#125;<br>    lc_clusters &lt;- <span class="hljs-built_in">SplitObject</span>(lc_scRNA, split<span class="hljs-selector-class">.by</span> = lc_groupN)<br>    <span class="hljs-built_in">for</span>(lc_g <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span>(lc_clusters))&#123;<br>        c_dir = file<span class="hljs-selector-class">.path</span>(lc_dir,lc_g)<br>        <span class="hljs-keyword">if</span> (!file<span class="hljs-selector-class">.exists</span>(c_dir))&#123;dir<span class="hljs-selector-class">.create</span>(c_dir)&#125;<br>        <span class="hljs-built_in">f_prepare4cellphoneDB</span>(lc_clusters<span class="hljs-selector-attr">[[lc_g]</span>], c_dir, lc_className)<br>    &#125;<br>&#125;<br><br></code></pre></td></tr></table></figure>

<figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br></pre></td><td class="code"><pre><code class="hljs stylus"><span class="hljs-function"><span class="hljs-title">f_prepare4cellphoneDB_sp</span><span class="hljs-params">(sc_Neuron,<span class="hljs-string">&quot;Neuron_br_sp&quot;</span>, <span class="hljs-string">&quot;hM1_hmca_class&quot;</span>, <span class="hljs-string">&quot;Region&quot;</span>)</span></span><br></code></pre></td></tr></table></figure>
                
              </div>
            
            <hr/>
            <div>
              <div class="post-metas my-3">
  
    <div class="post-meta mr-3 d-flex align-items-center">
      <i class="iconfont icon-category"></i>
      

<span class="category-chains">
  
  
      <span class="category-chain">
        
  <a href="/categories/%E7%94%9F%E7%89%A9%E4%BF%A1%E6%81%AF%E5%AD%A6/" class="category-chain-item">生物信息学</a>
  
  
      </span>
    
  
      <span class="category-chain">
        
  <a href="/categories/Seurat%E6%95%99%E7%A8%8B/" class="category-chain-item">Seurat教程</a>
  
  
      </span>
    
  
</span>

    </div>
  
  
</div>


  <div class="license-box my-3">
    <div class="license-title">
      <div>Seurat (五) 简单总结</div>
      <div>https://b.limour.top/886.html</div>
    </div>
    <div class="license-meta">
      
        <div class="license-meta-item">
          <div>Author</div>
          <div>Limour</div>
        </div>
      
      
        <div class="license-meta-item license-meta-date">
          <div>Posted on</div>
          <div>October 4, 2021</div>
        </div>
      
      
        <div class="license-meta-item">
          <div>Licensed under</div>
          <div>
            
              
                <a class="print-no-link" target="_blank" href="https://creativecommons.org/licenses/by-nc-sa/4.0/">
                  <span class="hint--top hint--rounded" aria-label="BY - Attribution">
                    <i class="iconfont icon-by"></i>
                  </span>
                </a>
              
                <a class="print-no-link" target="_blank" href="https://creativecommons.org/licenses/by-nc-sa/4.0/">
                  <span class="hint--top hint--rounded" aria-label="NC - Non-commercial">
                    <i class="iconfont icon-nc"></i>
                  </span>
                </a>
              
                <a class="print-no-link" target="_blank" href="https://creativecommons.org/licenses/by-nc-sa/4.0/">
                  <span class="hint--top hint--rounded" aria-label="SA - Share-alike">
                    <i class="iconfont icon-sa"></i>
                  </span>
                </a>
              
            
          </div>
        </div>
      
    </div>
    <div class="license-icon iconfont"></div>
  </div>


                <div class="post-prevnext my-3">
                  <article class="post-prev col-6">
                    
                    
                      <a href="/892.html" title="TCGA (三) 两组间DEGs分析">
                        <i class="iconfont icon-arrowleft"></i>
                        <span class="hidden-mobile">TCGA (三) 两组间DEGs分析</span>
                        <span class="visible-mobile">Previous</span>
                      </a>
                    
                  </article>
                  <article class="post-next col-6">
                    
                    
                      <a href="/873.html" title="Seurat (四) 差异基因分析">
                        <span class="hidden-mobile">Seurat (四) 差异基因分析</span>
                        <span class="visible-mobile">Next</span>
                        <i class="iconfont icon-arrowright"></i>
                      </a>
                    
                  </article>
                </div>
              
            </div>

            
    <article id="comments" lazyload>
      
  <div id="waline"></div>
  <script type="text/javascript">
    Fluid.utils.loadComments('#waline', function() {
      Fluid.utils.createCssLink('https://cdn.staticfile.org/waline/2.15.5/waline.min.css')
      Fluid.utils.createScript('https://cdn.staticfile.org/waline/2.15.5/waline.min.js', function() {
        var options = Object.assign(
          {"serverURL":"https://comments.limour.top","path":"window.location.pathname","meta":["nick","mail","link"],"requiredMeta":["nick"],"lang":"zh-CN","emoji":["https://jscdn.limour.top/gh/walinejs/emojis/weibo"],"dark":"html[data-user-color-scheme=\"dark\"]","wordLimit":0,"pageSize":10},
          {
            el: '#waline',
            path: window.location.pathname
          }
        )
        Waline.init(options);
        Fluid.utils.waitElementVisible('#waline .vcontent', () => {
          var imgSelector = '#waline .vcontent img:not(.vemoji)';
          Fluid.plugins.imageCaption(imgSelector);
          Fluid.plugins.fancyBox(imgSelector);
        })
      });
    });
  </script>
  <noscript>Please enable JavaScript to view the comments</noscript>


    </article>
  

          </article>
        </div>
      </div>
    </div>

    <div class="side-col d-none d-lg-block col-lg-2">
      
  <aside class="sidebar" style="margin-left: -1rem">
    <div id="toc">
  <p class="toc-header">
    <i class="iconfont icon-list"></i>
    <span>Table of Contents</span>
  </p>
  <div class="toc-body" id="toc-body"></div>
</div>


  </aside>


    </div>
  </div>
</div>


      <a id="scroll-top-button" aria-label="TOP" href="#" role="button">
        <i class="iconfont icon-arrowup" aria-hidden="true"></i>
      </a>
    

      <div class="modal fade" id="modalSearch" tabindex="-1" role="dialog" aria-labelledby="ModalLabel"
     aria-hidden="true">
  <div class="modal-dialog modal-dialog-scrollable modal-lg" role="document">
    <div class="modal-content">
      <div class="modal-header text-center">
        <h4 class="modal-title w-100 font-weight-bold">Search</h4>
        <button type="button" id="local-search-close" class="close" data-dismiss="modal" aria-label="Close">
          <span aria-hidden="true">&times;</span>
        </button>
      </div>
      <div class="modal-body mx-3">
        <div class="md-form mb-5">
          <input type="text" id="local-search-input" class="form-control validate">
          <label data-error="x" data-success="v" for="local-search-input">Keyword</label>
        </div>
        <div class="list-group" id="local-search-result"></div>
      </div>
    </div>
  </div>
</div>

    
  </main>

  <footer>
    <div class="footer-inner">
  
    <div class="footer-content">
       <a target="_blank" rel="nofollow noopener" href="http://www.beian.gov.cn/portal/registerSystemInfo?recordcode=43130202000203"><img src="https://img.limour.top/2023/08/27/64eadeb81d6a0.webp" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload>湘公网安备 43130202000203号  </a> <a target="_blank" rel="nofollow noopener" href="https://beian.miit.gov.cn/">湘ICP备20008299号 </a> <a target="_blank" rel="nofollow noopener" href="https://icp.gov.moe/?keyword=20210128">萌ICP备20210128号</a> <br> <a href="https://www.foreverblog.cn/" target="_blank"> <img src="https://img.foreverblog.cn/logo_en_default.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload alt="" style="width:auto;height:24px"> </a> <br> <a href="https://hexo.io" target="_blank" rel="nofollow noopener"><span>Hexo</span></a> <i class="iconfont icon-love"></i> <a href="https://github.com/fluid-dev/hexo-theme-fluid" target="_blank" rel="nofollow noopener"><span>Fluid</span></a> <i class="iconfont icon-love"></i> <a href="https://github.com/limour-blog/archives-b" target="_blank" rel="nofollow noopener"><span>SRC</span></a> 
    </div>
  
  
</div>

  </footer>

  <!-- Scripts -->
  
  <script  src="https://jscdn.limour.top/npm/nprogress@0.2.0/nprogress.min.js" ></script>
  <link  rel="stylesheet" href="https://jscdn.limour.top/npm/nprogress@0.2.0/nprogress.min.css" />

  <script>
    NProgress.configure({"showSpinner":false,"trickleSpeed":100})
    NProgress.start()
    window.addEventListener('load', function() {
      NProgress.done();
    })
  </script>


<script  src="https://jscdn.limour.top/npm/jquery@3.6.4/dist/jquery.min.js" ></script>
<script  src="https://jscdn.limour.top/npm/bootstrap@4.6.1/dist/js/bootstrap.min.js" ></script>
<script  src="/js/events.js" ></script>
<script  src="/js/plugins.js" ></script>


  <script  src="https://lib.baomitu.com/typed.js/2.0.12/typed.min.js" ></script>
  <script>
    (function (window, document) {
      var typing = Fluid.plugins.typing;
      var subtitle = document.getElementById('subtitle');
      if (!subtitle || !typing) {
        return;
      }
      var text = subtitle.getAttribute('data-typed-text');
      
        typing(text);
      
    })(window, document);
  </script>


    <script  src="/js/img-lazyload.js" ></script>
  

<script>
  Fluid.utils.createScript('https://jscdn.limour.top/npm/tocbot@4.20.1/dist/tocbot.min.js', function() {
    var toc = jQuery('#toc');
    if (toc.length === 0 || !window.tocbot) { return; }
    var boardCtn = jQuery('#board-ctn');
    var boardTop = boardCtn.offset().top;

    window.tocbot.init(Object.assign({
      tocSelector     : '#toc-body',
      contentSelector : '.markdown-body',
      linkClass       : 'tocbot-link',
      activeLinkClass : 'tocbot-active-link',
      listClass       : 'tocbot-list',
      isCollapsedClass: 'tocbot-is-collapsed',
      collapsibleClass: 'tocbot-is-collapsible',
      scrollSmooth    : true,
      includeTitleTags: true,
      headingsOffset  : -boardTop,
    }, CONFIG.toc));
    if (toc.find('.toc-list-item').length > 0) {
      toc.css('visibility', 'visible');
    }

    Fluid.events.registerRefreshCallback(function() {
      if ('tocbot' in window) {
        tocbot.refresh();
        var toc = jQuery('#toc');
        if (toc.length === 0 || !tocbot) {
          return;
        }
        if (toc.find('.toc-list-item').length > 0) {
          toc.css('visibility', 'visible');
        }
      }
    });
  });
</script>


  <script src=https://lib.baomitu.com/clipboard.js/2.0.11/clipboard.min.js></script>

  <script>Fluid.plugins.codeWidget();</script>


<script>
  Fluid.utils.createScript('https://jscdn.limour.top/npm/anchor-js@4.3.1/anchor.min.js', function() {
    window.anchors.options = {
      placement: CONFIG.anchorjs.placement,
      visible  : CONFIG.anchorjs.visible
    };
    if (CONFIG.anchorjs.icon) {
      window.anchors.options.icon = CONFIG.anchorjs.icon;
    }
    var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
    var res = [];
    for (var item of el) {
      res.push('.markdown-body > ' + item.trim());
    }
    if (CONFIG.anchorjs.placement === 'left') {
      window.anchors.options.class = 'anchorjs-link-left';
    }
    window.anchors.add(res.join(', '));

    Fluid.events.registerRefreshCallback(function() {
      if ('anchors' in window) {
        anchors.removeAll();
        var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
        var res = [];
        for (var item of el) {
          res.push('.markdown-body > ' + item.trim());
        }
        if (CONFIG.anchorjs.placement === 'left') {
          anchors.options.class = 'anchorjs-link-left';
        }
        anchors.add(res.join(', '));
      }
    });
  });
</script>


<script>
  Fluid.utils.createScript('https://lib.baomitu.com/fancybox/3.5.7/jquery.fancybox.min.js', function() {
    Fluid.plugins.fancyBox();
  });
</script>


  <script>Fluid.plugins.imageCaption();</script>

  <script  src="/js/local-search.js" ></script>


<!-- 主题的启动项，将它保持在最底部 -->
<!-- the boot of the theme, keep it at the bottom -->
<script  src="/js/boot.js" ></script>


  <noscript>
    <div class="noscript-warning">Blog works best with JavaScript enabled</div>
  </noscript>
<!-- hexo injector body_end start -->
  <script defer src="/theme-inject/timeliness.js"></script>
<!-- hexo injector body_end end --></body>
</html>