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            <h1 id="seo-header">CSOmap (一) 分析流程</h1>
            
            
              <div class="markdown-body">
                
                <h2 id="第一步-明确CSOmap所需的数据"><a href="#第一步-明确CSOmap所需的数据" class="headerlink" title="第一步 明确CSOmap所需的数据"></a>第一步 明确CSOmap所需的数据</h2><ul>
<li>先读readme，里面描述了输入数据的格式</li>
</ul>
<p><a target="_blank" rel="noopener" href="https://img-cdn.limour.top/blog_wp/2021/09/image-17.png"><img src="https://img-cdn.limour.top/blog_wp/2021/09/image-17.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload></a></p>
<ul>
<li>label.txt：细胞标注表，格式如图</li>
</ul>
<p><a target="_blank" rel="noopener" href="https://img-cdn.limour.top/blog_wp/2021/09/image-13.png"><img src="https://img-cdn.limour.top/blog_wp/2021/09/image-13.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload></a></p>
<ul>
<li>LR_pairs.txt：受体配体表，格式如图，用CSOmap自带的也行</li>
</ul>
<p><a target="_blank" rel="noopener" href="https://img-cdn.limour.top/blog_wp/2021/09/image-11.png"><img src="https://img-cdn.limour.top/blog_wp/2021/09/image-11.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload></a></p>
<ul>
<li>TPM.txt：TPM标注化的表达矩阵，格式如图，第一行得用<code>\t</code>开头</li>
</ul>
<p><a target="_blank" rel="noopener" href="https://img-cdn.limour.top/blog_wp/2021/09/image-18.png"><img src="https://img-cdn.limour.top/blog_wp/2021/09/image-18.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload></a></p>
<h2 id="第二步-导出CSOmap所需的数据"><a href="#第二步-导出CSOmap所需的数据" class="headerlink" title="第二步 导出CSOmap所需的数据"></a>第二步 导出CSOmap所需的数据</h2><figure class="highlight nsis"><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></pre></td><td class="code"><pre><code class="hljs nsis"><span class="hljs-comment"># 0、加载程辑包</span><br>library(Seurat)<br>library(dplyr)<br>library(patchwork)<br><br><span class="hljs-comment"># 配置数据路径</span><br>root_path = <span class="hljs-string">&quot;~/zlliu/R_data/21.07.15.IntegrateData&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;~/CSOmap/data/zlliu_IntegrateData_region&quot;</span><br>if (!<span class="hljs-keyword">file</span>.exists(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><br><span class="hljs-comment"># 1、读取数据</span><br>sn = readRDS(<span class="hljs-keyword">file</span>.path(root_path, <span class="hljs-string">&#x27;hBLA_scRNAs.rds&#x27;</span>))<br><br><span class="hljs-comment"># 合并对象</span><br>scRNA &lt;- merge(sn<span class="hljs-variable">$BA213</span>, y=c(sn<span class="hljs-variable">$BA04</span>, sn<span class="hljs-variable">$BA06</span>, sn<span class="hljs-variable">$BA09</span>, sn<span class="hljs-variable">$BA21</span>,<br>                                   sn<span class="hljs-variable">$BA22</span>, sn<span class="hljs-variable">$BA37</span>, sn<span class="hljs-variable">$BA39</span>, sn<span class="hljs-variable">$BA40</span>,<br>                                   sn<span class="hljs-variable">$BA41</span>, sn<span class="hljs-variable">$BA42</span>, sn<span class="hljs-variable">$BA44</span>, sn<span class="hljs-variable">$BA45</span>))<br><br><span class="hljs-comment"># 保存脑区信息</span><br>scRNA[[<span class="hljs-string">&quot;Region&quot;</span>]] &lt;- Idents(scRNA)<br><br><span class="hljs-comment"># 导出label.txt</span><br>labels &lt;- scRNA[[<span class="hljs-string">&quot;Region&quot;</span>]]<br>labels<span class="hljs-variable">$cells</span> &lt;- gsub(<span class="hljs-string">&quot;-&quot;</span>, <span class="hljs-string">&quot;.&quot;</span> ,rownames(labels)) <span class="hljs-comment"># TPM的colnames 不知为何导出时被替换了，这里也替换一下</span><br>labels<span class="hljs-variable">$labels</span> &lt;- as.character(labels<span class="hljs-variable">$Region</span>)<br>rownames(labels) &lt;- NULL<br>labels = labels[,c(<span class="hljs-string">&quot;cells&quot;</span>, <span class="hljs-string">&quot;labels&quot;</span>)]<br>write.table(labels, <span class="hljs-string">&quot;label.txt&quot;</span>, row.names = F, sep = <span class="hljs-string">&quot;\t&quot;</span>, quote = F) <span class="hljs-comment"># 不要引号</span><br><br></code></pre></td></tr></table></figure>

<ul>
<li>对TPM.txt的格式进行小修补：</li>
</ul>
<figure class="highlight gradle"><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 gradle"><span class="hljs-keyword">import</span> mmap, os<br><br><span class="hljs-keyword">def</span> mapfile(filename, *args, <span class="hljs-keyword">size</span>=None, **kwargs):<br>    <span class="hljs-keyword">file</span> = open(filename, *args, **kwargs)<br>    <span class="hljs-keyword">if</span> <span class="hljs-keyword">size</span> is None: <span class="hljs-keyword">size</span> = os.path.getsize(filename)<br>    <span class="hljs-keyword">return</span> mmap.mmap(<span class="hljs-keyword">file</span>.fileno(), <span class="hljs-keyword">size</span>)<br><br>f = mapfile(<span class="hljs-string">&quot;data/zlliu_V1C/TPM.txt&quot;</span>,<span class="hljs-string">&#x27;r+&#x27;</span>, <span class="hljs-keyword">size</span>=<span class="hljs-number">10</span>)<br><br>f[<span class="hljs-number">0</span>:<span class="hljs-number">1</span>] = b<span class="hljs-string">&quot;\t&quot;</span><br><br></code></pre></td></tr></table></figure>

<h2 id="第三步-激活fat节点的matlab"><a href="#第三步-激活fat节点的matlab" class="headerlink" title="第三步 激活fat节点的matlab"></a>第三步 激活fat节点的matlab</h2><ul>
<li><a target="_blank" rel="noopener" href="https://ww2.mathworks.cn/matlabcentral/answers/130613-internet">如何在无法连接 Internet 的电脑上进行产品的安装和激活?</a></li>
<li><a target="_blank" rel="noopener" href="https://ww2.mathworks.cn/matlabcentral/answers/101892-what-is-a-host-id-how-do-i-find-my-host-id-in-order-to-activate-my-license">What is a Host ID? How do I find my Host ID in order to activate my license?</a></li>
<li>运行 <code>matlab -nojvm</code></li>
</ul>
<p><a target="_blank" rel="noopener" href="https://img-cdn.limour.top/blog_wp/2021/09/image-14.png"><img src="https://img-cdn.limour.top/blog_wp/2021/09/image-14.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload></a></p>
<ul>
<li>hostid中选一个， 比如 <code>6c:92:bf:ee:06:d6</code></li>
<li><a target="_blank" rel="noopener" href="https://ww2.mathworks.cn/licensecenter">获得离线许可证</a></li>
</ul>
<p><a target="_blank" rel="noopener" href="https://img-cdn.limour.top/blog_wp/2021/09/image-15.png"><img src="https://img-cdn.limour.top/blog_wp/2021/09/image-15.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload></a></p>
<ul>
<li>将许可证放入用户目录的License path，并修改后缀为 <code>.lic</code></li>
<li>测试：<code>matlab **-nodisplay**</code></li>
</ul>
<p><a target="_blank" rel="noopener" href="https://img-cdn.limour.top/blog_wp/2021/09/image-16.png"><img src="https://img-cdn.limour.top/blog_wp/2021/09/image-16.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload></a></p>
<h2 id="第四步-测试CSOmap分析"><a href="#第四步-测试CSOmap分析" class="headerlink" title="第四步 测试CSOmap分析"></a>第四步 测试CSOmap分析</h2><figure class="highlight awk"><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 awk">cd <span class="hljs-regexp">/home/</span>rqzhang<span class="hljs-regexp">/CSOmap/</span>code<br>matlab -nodisplay<br>runme(<span class="hljs-string">&#x27;demo&#x27;</span>);<br></code></pre></td></tr></table></figure>

<h2 id="第五步-进行CSOmap分析"><a href="#第五步-进行CSOmap分析" class="headerlink" title="第五步 进行CSOmap分析"></a>第五步 进行CSOmap分析</h2><ul>
<li>直接分析，不推荐，断网气死：</li>
</ul>
<figure class="highlight isbl"><table><tr><td class="gutter"><pre><span class="line">1</span><br></pre></td><td class="code"><pre><code class="hljs isbl"><span class="hljs-function"><span class="hljs-title">runme</span>(<span class="hljs-string">&#x27;zlliu_IntegrateData_region&#x27;</span>);</span><br></code></pre></td></tr></table></figure>

<ul>
<li>创建 <code>21.09.21.CSOmap.pbs</code></li>
</ul>
<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></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=8</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_IntegrateData_region&#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>

<ul>
<li>提交任务：<code>qsub /home/rqzhang/zlliu/PBS/CSOmap/21.09.21.CSOmap.pbs</code></li>
</ul>

                
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