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  133. <h1 id="seo-header">复旦高性能计算 (七) Python调用R</h1>
  134. <div class="markdown-body">
  135. <h2 id="前置要求"><a href="#前置要求" class="headerlink" title="前置要求"></a>前置要求</h2><ul>
  136. <li><a target="_blank" rel="noopener" href="https://limour.top/631.html">复旦高性能计算 (一) Linux无root权限安装软件:以R为示例</a> 这里编译时开启了–enable-R-shlib</li>
  137. <li><a target="_blank" rel="noopener" href="https://limour.top/1098.html">复旦高性能计算 (六) jupyter启用R内核</a> 确保不出奇怪的问题</li>
  138. <li>install.packages(c(‘RJSONIO’, ‘httr’), repos&#x3D;”<a target="_blank" rel="noopener" href="http://mirrors.tuna.tsinghua.edu.cn/CRAN/">http://mirrors.tuna.tsinghua.edu.cn/CRAN/</a>“ )</li>
  139. </ul>
  140. <h2 id="第一步-安装rpy2"><a href="#第一步-安装rpy2" class="headerlink" title="第一步 安装rpy2"></a>第一步 安装rpy2</h2><figure class="highlight awk"><table><tr><td class="gutter"><pre><span class="line">1</span><br></pre></td><td class="code"><pre><code class="hljs awk">pip3.<span class="hljs-number">8</span> install rpy2 -i https:<span class="hljs-regexp">//</span>pypi.tuna.tsinghua.edu.cn/simple<br></code></pre></td></tr></table></figure>
  141. <ul>
  142. <li>查看rpy2的安装路径</li>
  143. </ul>
  144. <figure class="highlight elm"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br></pre></td><td class="code"><pre><code class="hljs elm"><span class="hljs-keyword">import</span> sys<br><span class="hljs-title">sys</span>.path<br></code></pre></td></tr></table></figure>
  145. <ul>
  146. <li>配置环境变量 每次启动先运行</li>
  147. </ul>
  148. <figure class="highlight moonscript"><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 moonscript"><span class="hljs-keyword">import</span> <span class="hljs-built_in">os</span><br><span class="hljs-built_in">os</span>.environ[<span class="hljs-string">&#x27;R_HOME&#x27;</span>] = <span class="hljs-string">&#x27;/home/rqzhang/zlliu/dev/R/R_s/lib64/R&#x27;</span> # R的安装后含SVN-REVISION的目录 非bin目录<br><span class="hljs-built_in">os</span>.environ[<span class="hljs-string">&#x27;R_USER&#x27;</span>] = <span class="hljs-string">&#x27;/home/rqzhang/zlliu/dev/python38/lib/python3.8/site-packages/rpy2&#x27;</span> # rpy2的安装目录<br></code></pre></td></tr></table></figure>
  149. <p><a target="_blank" rel="noopener" href="http://www.lfd.uci.edu/~gohlke/pythonlibs">冷门编译好的python库</a></p>
  150. <h2 id="第二步-调用方法一(不推荐)"><a href="#第二步-调用方法一(不推荐)" class="headerlink" title="第二步 调用方法一(不推荐)"></a>第二步 调用方法一(不推荐)</h2><figure class="highlight coffeescript"><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 coffeescript"><span class="hljs-keyword">from</span> rpy2.robjects <span class="hljs-keyword">import</span> r <span class="hljs-keyword">as</span> Rcode<br><span class="hljs-keyword">from</span> rpy2.robjects.packages <span class="hljs-keyword">import</span> importr <span class="hljs-keyword">as</span> Rrequire<br>Rrequire(<span class="hljs-string">&#x27;ggplot2&#x27;</span>) <span class="hljs-comment"># 导入R包</span><br><span class="hljs-built_in">print</span>(Rcode(<span class="hljs-string">&quot;pi&quot;</span>)) <span class="hljs-comment"># 运行R语句</span><br><br><span class="hljs-comment">#rx()相当于”[“操作(注意取出的是R的list对象),而rx2()相当于”[[“操作</span><br></code></pre></td></tr></table></figure>
  151. <p><a target="_blank" rel="noopener" href="https://pandas.pydata.org/pandas-docs/stable/getting_started/comparison/comparison_with_r.html">pandas.py: Comparison with R &#x2F; R libraries</a></p>
  152. <h2 id="第三步-调用方法二(推荐)"><a href="#第三步-调用方法二(推荐)" class="headerlink" title="第三步 调用方法二(推荐)"></a>第三步 调用方法二(推荐)</h2><ul>
  153. <li>开启 %R 支持</li>
  154. </ul>
  155. <figure class="highlight haml"><table><tr><td class="gutter"><pre><span class="line">1</span><br></pre></td><td class="code"><pre><code class="hljs haml"><span class="hljs-tag">%<span class="hljs-selector-tag">load_ext</span></span> rpy2.ipython<br></code></pre></td></tr></table></figure>
  156. <ul>
  157. <li>测试数据集</li>
  158. </ul>
  159. <figure class="highlight apache"><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 apache"><span class="hljs-attribute">import</span> pandas as pd<br><span class="hljs-attribute">data</span> = pd.DataFrame(&#123;&#x27;x&#x27;:[<span class="hljs-number">1</span>,<span class="hljs-number">2</span>,<span class="hljs-number">3</span>,<span class="hljs-number">4</span>,<span class="hljs-number">5</span>,<span class="hljs-number">6</span>],&#x27;y&#x27;:[<span class="hljs-number">1</span>,<span class="hljs-number">2</span>,<span class="hljs-number">3</span>,<span class="hljs-number">4</span>,<span class="hljs-number">5</span>,<span class="hljs-number">6</span>]&#125;)<br><span class="hljs-attribute">px</span> = <span class="hljs-number">1</span><br><span class="hljs-attribute">py</span> = <span class="hljs-number">2</span><br></code></pre></td></tr></table></figure>
  160. <ul>
  161. <li>cell内调用R</li>
  162. </ul>
  163. <figure class="highlight haskell"><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 haskell">%%<span class="hljs-type">R</span> -i <span class="hljs-class"><span class="hljs-keyword">data</span> -o colN</span><br><span class="hljs-title">require</span>(ggplot2)<br><span class="hljs-title">colN</span> = colnames(<span class="hljs-class"><span class="hljs-keyword">data</span>)</span><br><span class="hljs-title">ggplot</span>(<span class="hljs-class"><span class="hljs-keyword">data</span>=<span class="hljs-keyword">data</span>) + geom_point(<span class="hljs-title">aes</span>(<span class="hljs-title">x</span>=<span class="hljs-title">x</span>,<span class="hljs-title">y</span>=<span class="hljs-title">y</span>))</span><br></code></pre></td></tr></table></figure>
  164. <ul>
  165. <li>一行内调用R</li>
  166. </ul>
  167. <figure class="highlight perl"><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 perl">%R <span class="hljs-keyword">require</span>(ggplot2)<br>%R -i px,py<br>z = %R px*py<br><span class="hljs-keyword">print</span>(colN, z[<span class="hljs-number">0</span>]<br></code></pre></td></tr></table></figure>
  168. <p><a target="_blank" rel="noopener" href="https://zhuanlan.zhihu.com/p/139032905">如何优雅地在Jupyter Notebook中同时运行R和IPython</a></p>
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  241. <script type="text/javascript">
  242. Fluid.utils.loadComments('#waline', function() {
  243. Fluid.utils.createCssLink('https://cdn.staticfile.org/waline/2.15.5/waline.min.css')
  244. Fluid.utils.createScript('https://cdn.staticfile.org/waline/2.15.5/waline.min.js', function() {
  245. var options = Object.assign(
  246. {"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},
  247. {
  248. el: '#waline',
  249. path: window.location.pathname
  250. }
  251. )
  252. Waline.init(options);
  253. Fluid.utils.waitElementVisible('#waline .vcontent', () => {
  254. var imgSelector = '#waline .vcontent img:not(.vemoji)';
  255. Fluid.plugins.imageCaption(imgSelector);
  256. Fluid.plugins.fancyBox(imgSelector);
  257. })
  258. });
  259. });
  260. </script>
  261. <noscript>Please enable JavaScript to view the comments</noscript>
  262. </article>
  263. </article>
  264. </div>
  265. </div>
  266. </div>
  267. <div class="side-col d-none d-lg-block col-lg-2">
  268. <aside class="sidebar" style="margin-left: -1rem">
  269. <div id="toc">
  270. <p class="toc-header">
  271. <i class="iconfont icon-list"></i>
  272. <span>Table of Contents</span>
  273. </p>
  274. <div class="toc-body" id="toc-body"></div>
  275. </div>
  276. </aside>
  277. </div>
  278. </div>
  279. </div>
  280. <a id="scroll-top-button" aria-label="TOP" href="#" role="button">
  281. <i class="iconfont icon-arrowup" aria-hidden="true"></i>
  282. </a>
  283. <div class="modal fade" id="modalSearch" tabindex="-1" role="dialog" aria-labelledby="ModalLabel"
  284. aria-hidden="true">
  285. <div class="modal-dialog modal-dialog-scrollable modal-lg" role="document">
  286. <div class="modal-content">
  287. <div class="modal-header text-center">
  288. <h4 class="modal-title w-100 font-weight-bold">Search</h4>
  289. <button type="button" id="local-search-close" class="close" data-dismiss="modal" aria-label="Close">
  290. <span aria-hidden="true">&times;</span>
  291. </button>
  292. </div>
  293. <div class="modal-body mx-3">
  294. <div class="md-form mb-5">
  295. <input type="text" id="local-search-input" class="form-control validate">
  296. <label data-error="x" data-success="v" for="local-search-input">Keyword</label>
  297. </div>
  298. <div class="list-group" id="local-search-result"></div>
  299. </div>
  300. </div>
  301. </div>
  302. </div>
  303. </main>
  304. <footer>
  305. <div class="footer-inner">
  306. <div class="footer-content">
  307. <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>
  308. </div>
  309. </div>
  310. </footer>
  311. <!-- Scripts -->
  312. <script src="https://jscdn.limour.top/npm/nprogress@0.2.0/nprogress.min.js" ></script>
  313. <link rel="stylesheet" href="https://jscdn.limour.top/npm/nprogress@0.2.0/nprogress.min.css" />
  314. <script>
  315. NProgress.configure({"showSpinner":false,"trickleSpeed":100})
  316. NProgress.start()
  317. window.addEventListener('load', function() {
  318. NProgress.done();
  319. })
  320. </script>
  321. <script src="https://jscdn.limour.top/npm/jquery@3.6.4/dist/jquery.min.js" ></script>
  322. <script src="https://jscdn.limour.top/npm/bootstrap@4.6.1/dist/js/bootstrap.min.js" ></script>
  323. <script src="/js/events.js" ></script>
  324. <script src="/js/plugins.js" ></script>
  325. <script src="https://lib.baomitu.com/typed.js/2.0.12/typed.min.js" ></script>
  326. <script>
  327. (function (window, document) {
  328. var typing = Fluid.plugins.typing;
  329. var subtitle = document.getElementById('subtitle');
  330. if (!subtitle || !typing) {
  331. return;
  332. }
  333. var text = subtitle.getAttribute('data-typed-text');
  334. typing(text);
  335. })(window, document);
  336. </script>
  337. <script src="/js/img-lazyload.js" ></script>
  338. <script>
  339. Fluid.utils.createScript('https://jscdn.limour.top/npm/tocbot@4.20.1/dist/tocbot.min.js', function() {
  340. var toc = jQuery('#toc');
  341. if (toc.length === 0 || !window.tocbot) { return; }
  342. var boardCtn = jQuery('#board-ctn');
  343. var boardTop = boardCtn.offset().top;
  344. window.tocbot.init(Object.assign({
  345. tocSelector : '#toc-body',
  346. contentSelector : '.markdown-body',
  347. linkClass : 'tocbot-link',
  348. activeLinkClass : 'tocbot-active-link',
  349. listClass : 'tocbot-list',
  350. isCollapsedClass: 'tocbot-is-collapsed',
  351. collapsibleClass: 'tocbot-is-collapsible',
  352. scrollSmooth : true,
  353. includeTitleTags: true,
  354. headingsOffset : -boardTop,
  355. }, CONFIG.toc));
  356. if (toc.find('.toc-list-item').length > 0) {
  357. toc.css('visibility', 'visible');
  358. }
  359. Fluid.events.registerRefreshCallback(function() {
  360. if ('tocbot' in window) {
  361. tocbot.refresh();
  362. var toc = jQuery('#toc');
  363. if (toc.length === 0 || !tocbot) {
  364. return;
  365. }
  366. if (toc.find('.toc-list-item').length > 0) {
  367. toc.css('visibility', 'visible');
  368. }
  369. }
  370. });
  371. });
  372. </script>
  373. <script src=https://lib.baomitu.com/clipboard.js/2.0.11/clipboard.min.js></script>
  374. <script>Fluid.plugins.codeWidget();</script>
  375. <script>
  376. Fluid.utils.createScript('https://jscdn.limour.top/npm/anchor-js@4.3.1/anchor.min.js', function() {
  377. window.anchors.options = {
  378. placement: CONFIG.anchorjs.placement,
  379. visible : CONFIG.anchorjs.visible
  380. };
  381. if (CONFIG.anchorjs.icon) {
  382. window.anchors.options.icon = CONFIG.anchorjs.icon;
  383. }
  384. var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
  385. var res = [];
  386. for (var item of el) {
  387. res.push('.markdown-body > ' + item.trim());
  388. }
  389. if (CONFIG.anchorjs.placement === 'left') {
  390. window.anchors.options.class = 'anchorjs-link-left';
  391. }
  392. window.anchors.add(res.join(', '));
  393. Fluid.events.registerRefreshCallback(function() {
  394. if ('anchors' in window) {
  395. anchors.removeAll();
  396. var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
  397. var res = [];
  398. for (var item of el) {
  399. res.push('.markdown-body > ' + item.trim());
  400. }
  401. if (CONFIG.anchorjs.placement === 'left') {
  402. anchors.options.class = 'anchorjs-link-left';
  403. }
  404. anchors.add(res.join(', '));
  405. }
  406. });
  407. });
  408. </script>
  409. <script>
  410. Fluid.utils.createScript('https://lib.baomitu.com/fancybox/3.5.7/jquery.fancybox.min.js', function() {
  411. Fluid.plugins.fancyBox();
  412. });
  413. </script>
  414. <script>Fluid.plugins.imageCaption();</script>
  415. <script src="/js/local-search.js" ></script>
  416. <!-- 主题的启动项,将它保持在最底部 -->
  417. <!-- the boot of the theme, keep it at the bottom -->
  418. <script src="/js/boot.js" ></script>
  419. <noscript>
  420. <div class="noscript-warning">Blog works best with JavaScript enabled</div>
  421. </noscript>
  422. <!-- hexo injector body_end start -->
  423. <script defer src="/theme-inject/timeliness.js"></script>
  424. <!-- hexo injector body_end end --></body>
  425. </html>