make package document updates

xieguigang · Jun 27, 2024 · dacc9ae · dacc9ae
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diff --git a/vignettes/mzkit_hpc/hpc/deconvolution.html b/vignettes/mzkit_hpc/hpc/deconvolution.html
@@ -0,0 +1,95 @@
+<!DOCTYPE html><html lang="zh-CN">
+  <head>
+    <meta http-equiv="content-type" content="text/html; charset=UTF-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, minimum-scale=1.0, maximum-scale=1.0" />
+    <title>deconvolution</title>
+    <meta name="author" content="[email protected]" />
+    <meta name="copyright" content="SMRUCC genomics Copyright (c) 2022" />
+    <meta name="keywords" content="R#; deconvolution; hpc" />
+    <meta name="generator" content="https://github.com/rsharp-lang" />
+    <meta name="theme-color" content="#333" />
+    <meta name="description" content="..." />
+    <meta class="foundation-data-attribute-namespace" />
+    <meta class="foundation-mq-xxlarge" />
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+    <meta class="foundation-mq-medium" />
+    <meta class="foundation-mq-small" />
+    <meta class="foundation-mq-topbar" />
+    <style>
+
+.table-three-line {
+border-collapse:collapse; /* 关键属性：合并表格内外边框(其实表格边框有2px，外面1px，里面还有1px哦) */
+border:solid #000000; /* 设置边框属性；样式(solid=实线)、颜色(#999=灰) */
+border-width:2px 0 2px 0px; /* 设置边框状粗细：上 右 下 左 = 对应：1px 0 0 1px */
+}
+.left-1{
+    border:solid #000000;border-width:1px 1px 2px 0px;padding:2px;
+    font-weight:bolder;
+}
+.right-1{
+    border:solid #000000;border-width:1px 0px 2px 1px;padding:2px;
+    font-weight:bolder;
+}
+.mid-1{
+    border:solid #000000;border-width:1px 1px 2px 1px;padding:2px;
+    font-weight:bolder;
+}
+.left{
+    border:solid #000000;border-width:1px 1px 1px 0px;padding:2px;
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+.right{
+    border:solid #000000;border-width:1px 0px 1px 1px;padding:2px;
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+.mid{
+    border:solid #000000;border-width:1px 1px 1px 1px;padding:2px;
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+table caption {font-size:14px;font-weight:bolder;}
+</style>
+  </head>
+  <body>
+    <table width="100%" summary="page for {deconvolution}">
+      <tbody>
+        <tr>
+          <td>{deconvolution}</td>
+          <td style="text-align: right;">R# Documentation</td>
+        </tr>
+      </tbody>
+    </table>
+    <h1>deconvolution</h1>
+    <hr />
+    <p style="     font-size: 1.125em;     line-height: .8em;     margin-left: 0.5%;     background-color: #fbfbfb;     padding: 24px; ">
+      <code>
+        <span style="color: blue;">require</span>(<span style="color: black; font-weight: bold;">mzkit_hpc</span>);
+                               <br /><br /><span style="color: green;">{$desc_comments}</span><br /><span style="color: blue;">imports</span><span style="color: brown"> "deconvolution"</span><span style="color: blue;"> from</span><span style="color: brown"> "hpc"</span>;
+                           </code>
+    </p>
+    <p></p>
+    <blockquote>
+      <p style="font-style: italic; font-size: 0.9em;">
+
+                           </p>
+    </blockquote>
+    <div id="main-wrapper">
+      <table class="table-three-line" style="display: none">
+        <caption>.NET clr type export</caption>
+        <tbody></tbody>
+      </table>
+      <br />
+      <br />
+      <table class="table-three-line">
+        <caption>.NET clr function exports</caption>
+        <tbody><tr>
+  <td id="peak_alignments">
+    <a href="./deconvolution/peak_alignments.html">peak_alignments</a>
+  </td>
+  <td><p>Make peak group alignments and export peaktable</p></td>
+</tr></tbody>
+      </table>
+    </div>
+    <hr />
+    <div style="text-align: center;">[<a href="../index.html">Document Index</a>]</div>
+  </body>
+</html>
diff --git a/vignettes/mzkit_hpc/hpc/deconvolution/peak_alignments.html b/vignettes/mzkit_hpc/hpc/deconvolution/peak_alignments.html
@@ -0,0 +1,79 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>Make peak group alignments and export peaktable</title>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
+    <link rel="stylesheet" type="text/css" href="https://mzkit.org/assets/js/page.css">
+</head>
+
+<body>
+    <div class="container">
+
+        <table style="width: 100%;">
+            <tr>
+                <td>peak_alignments {deconvolution}</td>
+                <td style="text-align: right;">R Documentation</td>
+            </tr>
+        </table>
+
+        <h2>Make peak group alignments and export peaktable</h2>
+
+        <h3>Description</h3>
+
+
+
+        <h3>Usage</h3>
+
+        <div style="width: 100%; padding-left: 3%; color: black;">
+            <pre><code class='language-R' style="color: black; font-weight:normal;"><strong>peak_alignments</strong>(<i>peak.groups</i>, <i>features.mz</i>,
+    <i>tolerance</i> = <span style='color: brown;'><strong>"da:0.005"</strong></span>,
+    <i>peak.width</i> = <span style='color: brown;'><strong>"3,15"</strong></span>,
+    <i>baseline</i> = <span style='color: green;'>0.65</span>,
+    <i>joint</i> = <span style='color: blue !important;'>FALSE</span>,
+    <i>dtw</i> = <span style='color: blue !important;'>FALSE</span>);</code></pre>
+        </div>
+
+        <h3>Arguments</h3>
+
+        <table>
+
+<dt>peak.groups</dt>
+<dd><p>[as <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/XICPool.html">XICPool</a>]</p></dd>
+
+
+<dt>features.mz</dt>
+<dd><p>[as double]</p></dd>
+
+        </table>
+
+
+        <h3 style="display: none;">Details</h3>
+
+
+
+        <h3 style="display: block">Authors</h3>
+
+        hpc
+
+        <h3>Value</h3>
+
+        this function returns data object of type <i>any</i> kind.<h4>clr value class</h4><ul><li><i>any</i> kind</li></ul>
+
+        <h3 style="display: none;">Examples</h3>
+
+
+
+        <hr />
+        <div style="text-align: center;">[Package <em>deconvolution</em> version 1.0.0.0 <a
+                href="../deconvolution.html">Index</a>]
+        </div>
+    </div>
+</body>
+
+<script type="text/javascript" src="https://mzkit.org/assets/js/R_syntax.js"></script>
+<script type="text/javascript" src="https://mzkit.org/assets/js/highlights.js"></script>
+<script type="text/javascript">r_highlights("example_r");</script>
+
+</html>
diff --git a/vignettes/mzkit_hpc/index.html b/vignettes/mzkit_hpc/index.html
@@ -5,17 +5,21 @@
 Author: xieguigang
 Maintainer: xieguigang &lt;[email protected]>
 Description: Build high performance computing mzkit algorithm library 
-    based on Darwinism HPC runtime.
+    based on Darwinism HPC runtime. An engineering practice of processing 
+    ultra massive lc-ms mass spectrometry rawdata, ms-imaging rawdata 
+    and single-cells metabolomics rawdata.
 License: MIT
 Encoding: UTF-8
 LazyData: true
 </pre>
 <br />
+<a href="./keywords.html">View package by keywords.</a>
 <h2>R Package Symbols</h2>
 <ul>
 <li><a href="./R/docs/.onLoad.html">.onLoad</a></li>
 </ul>
 <h2>Library: hpc.dll</h2>
 <ul>
+<li><a href="./hpc/deconvolution.html">deconvolution</a></li>
 <li><a href="./hpc/MsImaging.html">MsImaging</a></li>
 </ul>
diff --git a/vignettes/mzkit_hpc/keywords.html b/vignettes/mzkit_hpc/keywords.html
@@ -0,0 +1,16 @@
+<h2>lc-ms</h2>
+<p><a href="./hpc/deconvolution/peak_alignments.html">peak_alignments</a></p>
+
+<h2>single cells</h2>
+<p><a href="./hpc/MsImaging/SCMs_ionStat_parallel.html">SCMs_ionStat_parallel</a></p>
+
+<h2>parallel</h2>
+<p><a href="./hpc/MsImaging/SCMs_ionStat_parallel.html">SCMs_ionStat_parallel</a>, <a href="./hpc/MsImaging/MSI_ionStat_parallel.html">MSI_ionStat_parallel</a></p>
+
+<h2>features</h2>
+<p><a href="./hpc/MsImaging/SCMs_ionStat_parallel.html">SCMs_ionStat_parallel</a>, <a href="./hpc/MsImaging/MSI_ionStat_parallel.html">MSI_ionStat_parallel</a></p>
+
+<h2>spatial</h2>
+<p><a href="./hpc/MsImaging/MSI_ionStat_parallel.html">MSI_ionStat_parallel</a></p>
+
+