update package documents

xieguigang · Jun 17, 2024 · 27765f8 · 27765f8
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diff --git a/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/IonStat.html b/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/IonStat.html
@@ -38,6 +38,7 @@ <h3>Declare</h3>
    basePixelY: integer;
    # the average spatial density
    density: double;
+   entropy: double;
    # the max intensity value of current ion across all pixels
    maxIntensity: double;
    # Moran-I index value of current ion layer geometry data
@@ -65,6 +66,8 @@ <h3>Declare</h3>
    Q2Intensity: double;
    # the intensity value of quartile Q3 level(75% quantile)
    Q3Intensity: double;
+   rsd: double;
+   sparsity: double;
 }
 </code>
         </pre>

diff --git a/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SingleCells/MatrixReader.html b/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SingleCells/MatrixReader.html
@@ -30,6 +30,7 @@ <h3>Declare</h3>
             <code id="clr_ts">
 # namespace BioNovoGene.Analytical.MassSpectrometry.SingleCells
 export class MatrixReader {
+   dim_size: <a href="/vignettes/clr/System/Drawing/Size.html">Size</a>;
    # number of the ion features
    featureSize: integer;
    # A numeric vector of the ion features m/z
@@ -47,6 +48,7 @@ <h3>Declare</h3>
         <h3>.NET clr type reference tree</h3>
 
         <ol>
+<li>use by <i>property</i> member <code>dim_size</code>: <a href="/vignettes/clr/System/Drawing/Size.html">Size</a></li>
 <li>use by <i>property</i> member <code>matrixType</code>: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/mzData/mzWebCache/FileApplicationClass.html">FileApplicationClass</a></li>
 </ol>
 

diff --git a/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SingleCells/SingleCellIonStat.html b/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SingleCells/SingleCellIonStat.html
@@ -34,15 +34,20 @@ <h3>Declare</h3>
    baseCell: string;
    # the cell numbers that contains this ion feature.
    cells: integer;
+   entropy: double;
    # the max intensity value of current ion feature.
    maxIntensity: double;
    # the ion feature m/z value
    mz: double;
+   mz_error: string;
+   mzmax: double;
+   mzmin: double;
    Q1Intensity: double;
    Q2Intensity: double;
    Q3Intensity: double;
    # RSD value of the intensity value of current ion feature across multiple cells
    RSD: double;
+   sparsity: double;
 }
 </code>
         </pre>

diff --git a/vignettes/clr/BioNovoGene/BioDeep/Chemistry/MetaLib/RefMet.html b/vignettes/clr/BioNovoGene/BioDeep/Chemistry/MetaLib/RefMet.html
@@ -0,0 +1,92 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>BioNovoGene.BioDeep.Chemistry.MetaLib.RefMet</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>RefMet {BioNovoGene.BioDeep.Chemistry.MetaLib}</td>
+                <td style="text-align: right;">.NET clr documentation</td>
+            </tr>
+        </table>
+
+        <h2>RefMet</h2>
+
+        <h3>Description</h3>
+
+        <p>RefMet: A Reference set of Metabolite names</p>
+
+<p>RefMet Naming Conventions
+
+ The names used in RefMet are generally based on common, officially accepted terms and 
+ incorporate notations which are appropriate for the type of analytical technique used.
+ In general, high-throughput untargeted MS experiments are not capable of deducing 
+ stereochemistry, double bond position/geometry and sn position (for glycerolipids/
+ lycerophospholipids). Secondly, the type of MS technique employed, as well as the mass
+ accuacy of the instrument will produce identifications at different levels of detail. 
+ For example, MS/MS methods are capable of identifying acyl chain substituents in lipids 
+ (e.g. PC 16:0/20:4) whereas MS methods only using precursor ion information might report 
+ these ions as "sum-composition" species (e.g. PC 36:4). RefMet covers both types of 
+ notations in an effort to enable data-sharing and comparative analysis of metabolomics 
+ data, using an analytical chemistry-centric approach.
+
+ The "sum-composition" lipid species indicate the number Of carbons And number Of "double
+ bond equivalents" (DBE), but Not chain positions Or Double bond regiochemistry And geometry.
+ The concept Of a Double bond equivalent unites a range Of chemical functionality which 
+ gives rise To isobaric features by mass spectometry. For example a chain containing a ring 
+ results In loss Of 2 hydrogen atoms (compared To a linear Structure) And thus has 1 DBE 
+ since the mass And molecular formula Is identical To a linear Structure With one Double bond.
+ Similarly, conversion Of a hydroxyl group To ketone results In loss Of 2 hydrogen atoms,
+ therefore the ketone Is assigned 1 DBE. Where applicable, the number Of oxygen atoms Is added 
+ To the abbreviation, separated by a semi-colon. Oxygen atoms In the Class-specific functional
+ group (e.g. the carboxylic acid group For fatty acids Or the phospholcholine group For PC) 
+ are excluded. In the Case Of sphingolipids, all oxygen atoms apart from the amide oxygen are
+ included, In order To discrminate, For example, between 1-deoxyceramides (;O), ceramides (;O2) 
+ And phytoceramides (;O3).
+
+ Some notes pertaining To different metabolite classes are outlined below.</p>
+
+        <h3>Declare</h3>        
+
+        <pre>
+            <code id="clr_ts">
+# namespace BioNovoGene.BioDeep.Chemistry.MetaLib
+export class RefMet {
+   exactmass: string;
+   formula: string;
+   inchi_key: string;
+   main_class: string;
+   pubchem_cid: string;
+   refmet_name: string;
+   smiles: string;
+   sub_class: string;
+   super_class: string;
+}
+</code>
+        </pre>
+
+        <h3>.NET clr type reference tree</h3>
+
+        this clr type has no other .net clr type reference.
+
+
+        <hr />
+        <div style="text-align: center;">[Package <em>{$package}</em> version {$version} <a
+                href="../{$package}.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("clr_ts");</script>
+
+</html>
diff --git a/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/Compound.html b/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/Compound.html
@@ -33,6 +33,7 @@ <h3>Declare</h3>
    category: <a href="/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/BriteHEntry/BriteTerm.html">BriteTerm[]</a>;
    # the metabolite common names
    commonNames: string;
+   # the database cross reference links
    DbLinks: <a href="/vignettes/clr/SMRUCC/genomics/ComponentModel/DBLinkBuilder/DBLink.html">DBLink[]</a>;
    # KEGG compound ID: <code>cpd:C\d+</code>
    entry: string;

diff --git a/vignettes/mzkit/mzkit/SingleCells.html b/vignettes/mzkit/mzkit/SingleCells.html
@@ -173,6 +173,18 @@ <h1>SingleCells</h1>
     <a href="./SingleCells/spatial_labels.html">spatial_labels</a>
   </td>
   <td><p>get the labels based on the spatial information of each spot</p></td>
+</tr>
+<tr>
+  <td id="singleCell_labels">
+    <a href="./SingleCells/singleCell_labels.html">singleCell_labels</a>
+  </td>
+  <td></td>
+</tr>
+<tr>
+  <td id="total_peaksum">
+    <a href="./SingleCells/total_peaksum.html">total_peaksum</a>
+  </td>
+  <td><p>do matrix data normalization via total peak sum</p></td>
 </tr></tbody>
       </table>
     </div>

diff --git a/vignettes/mzkit/mzkit/SingleCells/singleCell_labels.html b/vignettes/mzkit/mzkit/SingleCells/singleCell_labels.html
@@ -0,0 +1,67 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>singleCell_labels</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>singleCell_labels {SingleCells}</td>
+                <td style="text-align: right;">R Documentation</td>
+            </tr>
+        </table>
+
+        <h2>singleCell_labels</h2>
+
+        <h3>Description</h3>
+
+        singleCell_labels
+
+        <h3>Usage</h3>
+
+        <div style="width: 100%; padding-left: 3%; color: black;">
+            <pre><code class='language-R' style="color: black; font-weight:normal;"><strong>singleCell_labels</strong>(<i>x</i>);</code></pre>
+        </div>
+
+        <h3>Arguments</h3>
+
+        <table>
+
+        </table>
+
+
+        <h3 style="display: none;">Details</h3>
+
+
+
+        <h3 style="display: block">Authors</h3>
+
+        BioNovoGene
+
+        <h3>Value</h3>
+
+        this function returns data object of type string.<h4>clr value class</h4><ul><li>string</li></ul>
+
+        <h3 style="display: none;">Examples</h3>
+
+
+
+        <hr />
+        <div style="text-align: center;">[Package <em>SingleCells</em> version 1.0.0.0 <a
+                href="../SingleCells.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/mzkit/SingleCells/total_peaksum.html b/vignettes/mzkit/mzkit/SingleCells/total_peaksum.html
@@ -0,0 +1,75 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>do matrix data normalization via total peak sum</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>total_peaksum {SingleCells}</td>
+                <td style="text-align: right;">R Documentation</td>
+            </tr>
+        </table>
+
+        <h2>do matrix data normalization via total peak sum</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>total_peaksum</strong>(<i>x</i>,
+    <i>scale</i> = <span style='color: green;'>1000000</span>);</code></pre>
+        </div>
+
+        <h3>Arguments</h3>
+
+        <table>
+
+<dt>x</dt>
+<dd><p>[as <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SingleCells/Deconvolute/MzMatrix.html">MzMatrix</a>]</p></dd>
+
+
+<dt>scale</dt>
+<dd><p>[as double]</p></dd>
+
+        </table>
+
+
+        <h3 style="display: none;">Details</h3>
+
+
+
+        <h3 style="display: block">Authors</h3>
+
+        BioNovoGene
+
+        <h3>Value</h3>
+
+        this function returns data object of type <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SingleCells/Deconvolute/MzMatrix.html">MzMatrix</a>.<h4>clr value class</h4><ul><li><a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SingleCells/Deconvolute/MzMatrix.html">MzMatrix</a></li></ul>
+
+        <h3 style="display: none;">Examples</h3>
+
+
+
+        <hr />
+        <div style="text-align: center;">[Package <em>SingleCells</em> version 1.0.0.0 <a
+                href="../SingleCells.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/mzkit/massbank.html b/vignettes/mzkit/mzkit/massbank.html
@@ -86,6 +86,12 @@ <h1>massbank</h1>
     <a href="/vignettes/clr/BioNovoGene/BioDeep/Chemistry/MetaLib/Models/MetaLib.html">metalib: MetaLib</a>
   </td>
   <td><p>对<code>chebi/kegg/pubchem/HMDB/metlin</code>的物质注释信息整合库，这个数据库只要为了生成编号，名称之类的注释信息而构建的</p></td>
+</tr>
+<tr>
+  <td id="refmet">
+    <a href="/vignettes/clr/BioNovoGene/BioDeep/Chemistry/MetaLib/RefMet.html">refmet: RefMet</a>
+  </td>
+  <td><p>RefMet: A Reference set of Metabolite names</p></td>
 </tr></tbody>
       </table>
       <br />
@@ -104,6 +110,12 @@ <h1>massbank</h1>
   </td>
   <td><p>Extract the annotation metadata from the MONA comment data</p></td>
 </tr>
+<tr>
+  <td id="read.RefMet">
+    <a href="./massbank/read.RefMet.html">read.RefMet</a>
+  </td>
+  <td><p>read the csv table of refmet</p></td>
+</tr>
 <tr>
   <td id="read.MoNA">
     <a href="./massbank/read.MoNA.html">read.MoNA</a>