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            <span id="subtitle">【记录】使用 circacompare 分析生物节律</span>
          
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            <h1 id="seo-header">【记录】使用 circacompare 分析生物节律</h1>
            
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                    Last updated on November 12, 2024 pm
                  
                
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                <p>circacompare 是一个专为分析生物节律数据而设计的 R 包。它的主要功能是比较不同条件下的节律参数，例如振幅、周期和相位。circacompare 使用非线性混合效应模型来拟合节律数据，这使得它在处理具有重复测量和复杂实验设计的数据时表现出色。与 circacompare 相比，<a href="./shi-yong--JTK-CYCLE--suan-fa-fen-xi-sheng-wu-jie-lv">MetaCycle</a> 是另一个流行的 R 包，用于生物节律分析。MetaCycle 提供了多种算法（如 ARSER、JTK_CYCLE 和 Lomb-Scargle）来检测时间序列数据中的周期性信号。它的优势在于能够处理大规模数据集，并且适用于各种不同的实验条件。</p>
<h2 id="conda安装包">conda安装包</h2>
<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></pre></td><td class="code"><pre><code class="hljs bash">conda create -n zct conda-forge::r-tidyverse conda-forge::r-irkernel<br>conda run -n zct Rscript -e <span class="hljs-string">&quot;IRkernel::installspec(name=&#x27;zct&#x27;, displayname=&#x27;zct&#x27;)&quot;</span><br>conda run -n zct Rscript -e <span class="hljs-string">&quot;install.packages(&#x27;circacompare&#x27;)&quot;</span><br></code></pre></td></tr></table></figure>
<h2 id="导入包和数据">导入包和数据</h2>
<figure class="highlight r"><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></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>tidyverse<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>circacompare<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>ggplot2<span class="hljs-punctuation">)</span><br><br>dt <span class="hljs-operator">&lt;-</span> readr<span class="hljs-operator">::</span>read_csv<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;./circacompare.CSV&#x27;</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span> <br>mutate<span class="hljs-punctuation">(</span>group <span class="hljs-operator">=</span> factor<span class="hljs-punctuation">(</span>group<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span> <br>mutate<span class="hljs-punctuation">(</span>organ <span class="hljs-operator">=</span> factor<span class="hljs-punctuation">(</span>organ<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span> <br>mutate<span class="hljs-punctuation">(</span>project <span class="hljs-operator">=</span> factor<span class="hljs-punctuation">(</span>project<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
<h2 id="两组比较">两组比较</h2>
<figure class="highlight r"><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></pre></td><td class="code"><pre><code class="hljs R">s_symbol <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;Bmal1&#x27;</span> <br>s_organ <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;Heart&#x27;</span><br>s_project <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;compare1&#x27;</span><br><br><span class="hljs-comment"># 根据参数选择数据</span><br>dt_s <span class="hljs-operator">&lt;-</span> dt <span class="hljs-operator">%&gt;%</span> <br>subset<span class="hljs-punctuation">(</span>symbol <span class="hljs-operator">==</span> s_symbol <span class="hljs-operator">&amp;</span> organ <span class="hljs-operator">==</span> s_organ <span class="hljs-operator">&amp;</span> project <span class="hljs-operator">==</span> s_project<span class="hljs-punctuation">)</span>  <span class="hljs-operator">%&gt;%</span> <br>mutate<span class="hljs-punctuation">(</span>group <span class="hljs-operator">=</span> factor<span class="hljs-punctuation">(</span>group<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment"># 进行比较</span><br>result <span class="hljs-operator">&lt;-</span> circacompare<span class="hljs-punctuation">(</span>x <span class="hljs-operator">=</span> dt_s<span class="hljs-punctuation">,</span> col_time <span class="hljs-operator">=</span> <span class="hljs-string">&quot;time&quot;</span><span class="hljs-punctuation">,</span> col_group <span class="hljs-operator">=</span> <span class="hljs-string">&quot;group&quot;</span><span class="hljs-punctuation">,</span> col_outcome <span class="hljs-operator">=</span> <span class="hljs-string">&quot;measure&quot;</span><span class="hljs-punctuation">,</span> alpha_threshold <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br><br><span class="hljs-comment"># 查看绘图</span><br>save_plot <span class="hljs-operator">&lt;-</span> result<span class="hljs-operator">$</span>plot <span class="hljs-operator">+</span> <br>theme_minimal<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span>  <br>ggtitle<span class="hljs-punctuation">(</span>paste<span class="hljs-punctuation">(</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>s_symbol<span class="hljs-punctuation">,</span> s_organ<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> collapse <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;_&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span><br>theme<span class="hljs-punctuation">(</span>plot.title <span class="hljs-operator">=</span> element_text<span class="hljs-punctuation">(</span>hjust <span class="hljs-operator">=</span> <span class="hljs-number">0.5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><br><span class="hljs-comment"># 查看统计汇总</span><br>result<span class="hljs-operator">$</span>summary<br>tmp <span class="hljs-operator">&lt;-</span> circacompare<span class="hljs-operator">:::</span>extract_model_coefs<span class="hljs-punctuation">(</span>result<span class="hljs-operator">$</span>fit<span class="hljs-punctuation">)</span><br>tmp<br>tmp<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;phi&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;estimate&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;std_error&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;phi&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;estimate&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;std_error&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">/</span> <span class="hljs-punctuation">(</span><span class="hljs-number">2</span> <span class="hljs-operator">*</span> <span class="hljs-built_in">pi</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">*</span> save_plot<span class="hljs-operator">$</span>plot_env<span class="hljs-operator">$</span>V<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;tau&#x27;</span><span class="hljs-punctuation">]</span><br>tmp<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;phi1&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;estimate&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;std_error&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;phi1&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;estimate&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;std_error&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">/</span> <span class="hljs-punctuation">(</span><span class="hljs-number">2</span> <span class="hljs-operator">*</span> <span class="hljs-built_in">pi</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">*</span> save_plot<span class="hljs-operator">$</span>plot_env<span class="hljs-operator">$</span>V<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;tau&#x27;</span><span class="hljs-punctuation">]</span><br>tmp<br><br>save_plot<br><br><span class="hljs-comment"># 保存图为 pdf</span><br><span class="hljs-punctuation">&#123;</span>pdf<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;pdf/&#x27;</span><span class="hljs-punctuation">,</span> paste<span class="hljs-punctuation">(</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>s_symbol<span class="hljs-punctuation">,</span> s_organ<span class="hljs-punctuation">,</span> s_project<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> collapse <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;_&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;.pdf&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">6</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">6</span><span class="hljs-punctuation">)</span><br> print<span class="hljs-punctuation">(</span>save_plot<span class="hljs-punctuation">)</span><br>dev.off<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>
<figure class="highlight r"><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></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-comment"># 导出拟合的数据</span><br>save_plot<br>x <span class="hljs-operator">&lt;-</span> seq<span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span> <span class="hljs-number">24</span><span class="hljs-punctuation">,</span> by <span class="hljs-operator">=</span> <span class="hljs-number">0.01</span><span class="hljs-punctuation">)</span><br>newdf <span class="hljs-operator">&lt;-</span> data.frame<span class="hljs-punctuation">(</span>time <span class="hljs-operator">=</span> x<span class="hljs-punctuation">,</span> g1 <span class="hljs-operator">=</span> save_plot<span class="hljs-operator">$</span>plot_env<span class="hljs-operator">$</span>eq_1<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> g2 <span class="hljs-operator">=</span> save_plot<span class="hljs-operator">$</span>plot_env<span class="hljs-operator">$</span>eq_2<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>write.csv<span class="hljs-punctuation">(</span>newdf<span class="hljs-punctuation">,</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;csv/&#x27;</span><span class="hljs-punctuation">,</span> paste<span class="hljs-punctuation">(</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>s_symbol<span class="hljs-punctuation">,</span> s_organ<span class="hljs-punctuation">,</span> s_project<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> collapse <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;_&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;.csv&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> row.names <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
<h2 id="单组绘图">单组绘图</h2>
<figure class="highlight r"><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></pre></td><td class="code"><pre><code class="hljs R">s_symbol <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;Rev-erbα&#x27;</span> <br>s_organ <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;Kidney&#x27;</span><br>s_project <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;KO-AL&#x27;</span><br><br><span class="hljs-comment"># 根据参数选择数据</span><br>dt_s <span class="hljs-operator">&lt;-</span> dt <span class="hljs-operator">%&gt;%</span> <br>subset<span class="hljs-punctuation">(</span>symbol <span class="hljs-operator">==</span> s_symbol <span class="hljs-operator">&amp;</span> organ <span class="hljs-operator">==</span> s_organ <span class="hljs-operator">&amp;</span> project <span class="hljs-operator">==</span> s_project<span class="hljs-punctuation">)</span>  <span class="hljs-operator">%&gt;%</span> <br>mutate<span class="hljs-punctuation">(</span>group <span class="hljs-operator">=</span> factor<span class="hljs-punctuation">(</span>group<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><br><span class="hljs-comment"># 进行统计分析</span><br>options<span class="hljs-punctuation">(</span>show.error.messages <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">,</span> warn <span class="hljs-operator">=</span> <span class="hljs-operator">-</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>result <span class="hljs-operator">&lt;-</span> try<span class="hljs-punctuation">(</span><span class="hljs-punctuation">&#123;</span><br>  circa_single<span class="hljs-punctuation">(</span><br>    x <span class="hljs-operator">=</span> dt_s<span class="hljs-punctuation">,</span> col_time <span class="hljs-operator">=</span> <span class="hljs-string">&quot;time&quot;</span><span class="hljs-punctuation">,</span> col_outcome <span class="hljs-operator">=</span> <span class="hljs-string">&quot;measure&quot;</span><span class="hljs-punctuation">,</span> period <span class="hljs-operator">=</span> <span class="hljs-number">24</span><span class="hljs-punctuation">,</span> alpha_threshold <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span><br>    timeout_n <span class="hljs-operator">=</span> <span class="hljs-number">100000</span><span class="hljs-punctuation">,</span><br>    control <span class="hljs-operator">=</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><br>      main_params <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;k&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;alpha&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;phi&quot;</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">)</span><br>  <span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><span class="hljs-punctuation">,</span> silent <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span><br>options<span class="hljs-punctuation">(</span>show.error.messages <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> warn <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment"># “k”表示中值，“alpha”表示振幅，“phi”表示相位。引入的额外参数是“tau”表示周期。</span><br><br><span class="hljs-comment"># 查看绘图</span><br>save_plot <span class="hljs-operator">&lt;-</span> result<span class="hljs-operator">$</span>plot <span class="hljs-operator">+</span> <br>theme_minimal<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span>  <br>ggtitle<span class="hljs-punctuation">(</span>paste<span class="hljs-punctuation">(</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>s_symbol<span class="hljs-punctuation">,</span> s_organ<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> collapse <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;_&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span><br>theme<span class="hljs-punctuation">(</span>plot.title <span class="hljs-operator">=</span> element_text<span class="hljs-punctuation">(</span>hjust <span class="hljs-operator">=</span> <span class="hljs-number">0.5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><br><span class="hljs-comment"># 查看统计汇总</span><br>result<span class="hljs-operator">$</span>summary<br>tmp <span class="hljs-operator">&lt;-</span> circacompare<span class="hljs-operator">:::</span>extract_model_coefs<span class="hljs-punctuation">(</span>result<span class="hljs-operator">$</span>fit<span class="hljs-punctuation">)</span><br>tmp<br>tmp<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;phi&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;estimate&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;std_error&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;phi&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;estimate&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;std_error&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">/</span> <span class="hljs-punctuation">(</span><span class="hljs-number">2</span> <span class="hljs-operator">*</span> <span class="hljs-built_in">pi</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">*</span> save_plot<span class="hljs-operator">$</span>plot_env<span class="hljs-operator">$</span>V<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;tau&#x27;</span><span class="hljs-punctuation">]</span><br>tmp<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;phi1&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;estimate&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;std_error&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;phi1&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;estimate&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;std_error&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">/</span> <span class="hljs-punctuation">(</span><span class="hljs-number">2</span> <span class="hljs-operator">*</span> <span class="hljs-built_in">pi</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">*</span> save_plot<span class="hljs-operator">$</span>plot_env<span class="hljs-operator">$</span>V<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;tau&#x27;</span><span class="hljs-punctuation">]</span><br>tmp<br><br>save_plot<br><br><span class="hljs-comment"># 保存图为 pdf</span><br><span class="hljs-punctuation">&#123;</span>pdf<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;pdf/&#x27;</span><span class="hljs-punctuation">,</span> paste<span class="hljs-punctuation">(</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>s_symbol<span class="hljs-punctuation">,</span> s_organ<span class="hljs-punctuation">,</span> s_project<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> collapse <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;_&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;.pdf&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">6</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">6</span><span class="hljs-punctuation">)</span><br> print<span class="hljs-punctuation">(</span>save_plot<span class="hljs-punctuation">)</span><br>dev.off<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>
<h2 id="周期和衰减参数">周期和衰减参数</h2>
<figure class="highlight r"><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></pre></td><td class="code"><pre><code class="hljs R">s_symbol <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;Bmal1&#x27;</span> <br>s_organ <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;Heart&#x27;</span><br>s_project <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;compare1&#x27;</span><br><br><span class="hljs-comment"># 根据参数选择数据</span><br>dt_s <span class="hljs-operator">&lt;-</span> dt <span class="hljs-operator">%&gt;%</span> <br>subset<span class="hljs-punctuation">(</span>symbol <span class="hljs-operator">==</span> s_symbol <span class="hljs-operator">&amp;</span> organ <span class="hljs-operator">==</span> s_organ <span class="hljs-operator">&amp;</span> project <span class="hljs-operator">==</span> s_project<span class="hljs-punctuation">)</span>  <span class="hljs-operator">%&gt;%</span> <br>mutate<span class="hljs-punctuation">(</span>group <span class="hljs-operator">=</span> factor<span class="hljs-punctuation">(</span>group<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><br><span class="hljs-comment"># 进行统计分析</span><br>options<span class="hljs-punctuation">(</span>show.error.messages <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">,</span> warn <span class="hljs-operator">=</span> <span class="hljs-operator">-</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>result <span class="hljs-operator">&lt;-</span> try<span class="hljs-punctuation">(</span><span class="hljs-punctuation">&#123;</span><br>  circacompare<span class="hljs-punctuation">(</span><br>    x <span class="hljs-operator">=</span> dt_s<span class="hljs-punctuation">,</span> col_time <span class="hljs-operator">=</span> <span class="hljs-string">&quot;time&quot;</span><span class="hljs-punctuation">,</span> col_group <span class="hljs-operator">=</span> <span class="hljs-string">&quot;group&quot;</span><span class="hljs-punctuation">,</span> col_outcome <span class="hljs-operator">=</span> <span class="hljs-string">&quot;measure&quot;</span><span class="hljs-punctuation">,</span> period <span class="hljs-operator">=</span> <span class="hljs-number">24</span><span class="hljs-punctuation">,</span> alpha_threshold <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span><br>    timeout_n <span class="hljs-operator">=</span> <span class="hljs-number">100000</span><span class="hljs-punctuation">,</span><br>    control <span class="hljs-operator">=</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><br>      main_params <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;k&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;alpha&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;phi&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>      decay_params <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;alpha&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>      grouped_params <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;alpha&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;alpha_decay&quot;</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">)</span><br>  <span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><span class="hljs-punctuation">,</span> silent <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span><br>options<span class="hljs-punctuation">(</span>show.error.messages <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> warn <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment"># “k”表示中值，“alpha”表示振幅，“phi”表示相位。引入的额外参数是“tau”表示周期。</span><br><br><span class="hljs-comment"># 查看绘图</span><br>save_plot <span class="hljs-operator">&lt;-</span> result<span class="hljs-operator">$</span>plot <span class="hljs-operator">+</span> <br>theme_minimal<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span>  <br>ggtitle<span class="hljs-punctuation">(</span>paste<span class="hljs-punctuation">(</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>s_symbol<span class="hljs-punctuation">,</span> s_organ<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> collapse <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;_&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span><br>theme<span class="hljs-punctuation">(</span>plot.title <span class="hljs-operator">=</span> element_text<span class="hljs-punctuation">(</span>hjust <span class="hljs-operator">=</span> <span class="hljs-number">0.5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><br><span class="hljs-comment"># 查看统计汇总</span><br>result<span class="hljs-operator">$</span>summary<br>tmp <span class="hljs-operator">&lt;-</span> circacompare<span class="hljs-operator">:::</span>extract_model_coefs<span class="hljs-punctuation">(</span>result<span class="hljs-operator">$</span>fit<span class="hljs-punctuation">)</span><br>tmp<br>tmp<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;phi&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;estimate&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;std_error&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;phi&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;estimate&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;std_error&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">/</span> <span class="hljs-punctuation">(</span><span class="hljs-number">2</span> <span class="hljs-operator">*</span> <span class="hljs-built_in">pi</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">*</span> save_plot<span class="hljs-operator">$</span>plot_env<span class="hljs-operator">$</span>V<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;tau&#x27;</span><span class="hljs-punctuation">]</span><br>tmp<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;phi1&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;estimate&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;std_error&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;phi1&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;estimate&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;std_error&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">/</span> <span class="hljs-punctuation">(</span><span class="hljs-number">2</span> <span class="hljs-operator">*</span> <span class="hljs-built_in">pi</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">*</span> save_plot<span class="hljs-operator">$</span>plot_env<span class="hljs-operator">$</span>V<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;tau&#x27;</span><span class="hljs-punctuation">]</span><br>tmp<br><br>save_plot<br><br><span class="hljs-comment"># 保存图为 pdf</span><br><span class="hljs-punctuation">&#123;</span>pdf<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;pdf/&#x27;</span><span class="hljs-punctuation">,</span> paste<span class="hljs-punctuation">(</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>s_symbol<span class="hljs-punctuation">,</span> s_organ<span class="hljs-punctuation">,</span> s_project<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> collapse <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;_&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;_decay.pdf&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">6</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">6</span><span class="hljs-punctuation">)</span><br> print<span class="hljs-punctuation">(</span>save_plot<span class="hljs-punctuation">)</span><br>dev.off<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>
                
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