update math documents

xieguigang · Jun 26, 2024 · 0899547 · 0899547
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diff --git a/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/IonStat.html b/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/IonStat.html
@@ -22,29 +22,49 @@ <h2>IonStat</h2>
 
         <h3>Description</h3>
 
-
+        <p>Stats the ion features inside a MSI raw data slide</p>
 
         <h3>Declare</h3>        
 
         <pre>
             <code id="clr_ts">
 # namespace BioNovoGene.Analytical.MassSpectrometry.MsImaging
 export class IonStat {
+   # the average intensity value of current ion across all pixels
    averageIntensity: double;
+   # the x axis position of the pixel which has the max intensity value of current ion layer
    basePixelX: integer;
+   # the y axis position of the pixel which has the max intensity value of current ion layer
    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
+   #  
+   #  In statistics, Moran's I is a measure of spatial autocorrelation developed by Patrick Alfred Pierce Moran.
+   #  Spatial autocorrelation is characterized by a correlation in a signal among nearby locations in space. 
+   #  Spatial autocorrelation is more complex than one-dimensional autocorrelation because spatial correlation 
+   #  is multi-dimensional (i.e. 2 or 3 dimensions of space) and multi-directional.
    moran: double;
+   # the ion m/z value of current ms-imaging layer feature
    mz: double;
+   # the max range value of current ion m/z
    mzmax: double;
+   # the min range value of current ion m/z
    mzmin: double;
+   # the description text of the mz range: mzmax - mzmin
    mzwidth: string;
+   # the total pixel number of current ion m/z occurs.
    pixels: integer;
+   # the Moran-I test p-value
    pvalue: double;
+   # the intensity value of quartile Q1 level(25% quantile)
    Q1Intensity: double;
+   # the intensity value of quartile Q2 level(median value, 50% quantile)
    Q2Intensity: double;
+   # the intensity value of quartile Q3 level(75% quantile)
    Q3Intensity: double;
    rsd: double;
    sparsity: double;

diff --git a/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SingleCells/File/MatrixHeader.html b/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SingleCells/File/MatrixHeader.html
@@ -0,0 +1,73 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>BioNovoGene.Analytical.MassSpectrometry.SingleCells.File.MatrixHeader</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>MatrixHeader {BioNovoGene.Analytical.MassSpectrometry.SingleCells.File}</td>
+                <td style="text-align: right;">.NET clr documentation</td>
+            </tr>
+        </table>
+
+        <h2>MatrixHeader</h2>
+
+        <h3>Description</h3>
+
+
+
+        <h3>Declare</h3>        
+
+        <pre>
+            <code id="clr_ts">
+# namespace BioNovoGene.Analytical.MassSpectrometry.SingleCells.File
+export class MatrixHeader {
+   # get count of the ion feature size under current mass <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SingleCells/File/MatrixHeader.html">MatrixHeader</a>.<a href="#">tolerance</a>
+   featureSize: integer;
+   # the matrix data type of current object, value of this property could be one of the flag value:
+   #  
+   #  1. <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/mzData/mzWebCache/FileApplicationClass.html">FileApplicationClass</a>.<a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/mzData/mzWebCache/FileApplicationClass.html">MSImaging</a> 2d spatial data
+   #  2. <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/mzData/mzWebCache/FileApplicationClass.html">FileApplicationClass</a>.<a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/mzData/mzWebCache/FileApplicationClass.html">MSImaging3D</a> 3d spatial data
+   #  3. <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/mzData/mzWebCache/FileApplicationClass.html">FileApplicationClass</a>.<a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/mzData/mzWebCache/FileApplicationClass.html">SingleCellsMetabolomics</a> single cell matrix data
+   matrixType: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/mzData/mzWebCache/FileApplicationClass.html">FileApplicationClass</a>;
+   # m/z vector in numeric format of round to digit 4, this ion m/z 
+   #  feature list is generated under the current mass 
+   #  <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SingleCells/File/MatrixHeader.html">MatrixHeader</a>.<a href="#">tolerance</a>.
+   mz: double;
+   mzmax: double;
+   mzmin: double;
+   # number of the spots
+   numSpots: integer;
+   # the script string of the mz diff tolerance for <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SingleCells/File/MatrixHeader.html">MatrixHeader</a>.<a href="#">mz</a>
+   tolerance: string;
+}
+</code>
+        </pre>
+
+        <h3>.NET clr type reference tree</h3>
+
+        <ol>
+<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>
+
+
+        <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/BioNovoGene/Analytical/MassSpectrometry/SingleCells/File/MatrixReader.html b/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SingleCells/File/MatrixReader.html
@@ -0,0 +1,67 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>BioNovoGene.Analytical.MassSpectrometry.SingleCells.File.MatrixReader</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>MatrixReader {BioNovoGene.Analytical.MassSpectrometry.SingleCells.File}</td>
+                <td style="text-align: right;">.NET clr documentation</td>
+            </tr>
+        </table>
+
+        <h2>MatrixReader</h2>
+
+        <h3>Description</h3>
+
+        <p>A lazy binary data matrix reader for the singlecells/spatial data</p>
+
+        <h3>Declare</h3>        
+
+        <pre>
+            <code id="clr_ts">
+# namespace BioNovoGene.Analytical.MassSpectrometry.SingleCells.File
+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
+   ionSet: double;
+   # <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SingleCells/Deconvolute/MzMatrix.html">MzMatrix</a>.<a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/mzData/mzWebCache/FileApplicationClass.html">matrixType</a>
+   matrixType: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/mzData/mzWebCache/FileApplicationClass.html">FileApplicationClass</a>;
+   # the number of the single cells or spatial spot data
+   spots: integer;
+   # the description text of the mass tolerance error
+   tolerance: string;
+}
+</code>
+        </pre>
+
+        <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>
+
+
+        <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/BioNovoGene/Analytical/MassSpectrometry/SingleCells/SingleCellIonStat.html b/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SingleCells/SingleCellIonStat.html
@@ -46,7 +46,7 @@ <h3>Declare</h3>
    Q2Intensity: double;
    Q3Intensity: double;
    # RSD value of the intensity value of current ion feature across multiple cells
-   RSD: double;
+   rsd: double;
    sparsity: double;
 }
 </code>

diff --git a/vignettes/clr/BioNovoGene/BioDeep/Chemistry/MetaLib/RefMet.html b/vignettes/clr/BioNovoGene/BioDeep/Chemistry/MetaLib/RefMet.html
@@ -60,7 +60,7 @@ <h3>Declare</h3>
             <code id="clr_ts">
 # namespace BioNovoGene.BioDeep.Chemistry.MetaLib
 export class RefMet {
-   exactmass: string;
+   exactmass: double;
    formula: string;
    inchi_key: string;
    main_class: string;

diff --git a/vignettes/clr/BioNovoGene/BioDeep/Chemistry/SpectraInfo.html b/vignettes/clr/BioNovoGene/BioDeep/Chemistry/SpectraInfo.html
@@ -0,0 +1,74 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>BioNovoGene.BioDeep.Chemistry.SpectraInfo</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>SpectraInfo {BioNovoGene.BioDeep.Chemistry}</td>
+                <td style="text-align: right;">.NET clr documentation</td>
+            </tr>
+        </table>
+
+        <h2>SpectraInfo</h2>
+
+        <h3>Description</h3>
+
+        <p>The reference spectra data which is parsed from the MoNA database</p>
+
+<p>is a collection of the mass spectrum <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/ms2.html">ms2</a> data.</p>
+
+        <h3>Declare</h3>        
+
+        <pre>
+            <code id="clr_ts">
+# namespace BioNovoGene.BioDeep.Chemistry
+export class SpectraInfo {
+   collision_energy: string;
+   column: string;
+   flow_gradient: string;
+   flow_rate: string;
+   fragmentation_mode: string;
+   instrument: string;
+   instrument_type: string;
+   ion_mode: string;
+   ionization: string;
+   MassPeaks: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/ms2.html">ms2[]</a>;
+   MsLevel: string;
+   mz: double;
+   precursor_type: string;
+   resolution: string;
+   retention_time: string;
+   solvent_a: string;
+   solvent_b: string;
+}
+</code>
+        </pre>
+
+        <h3>.NET clr type reference tree</h3>
+
+        <ol>
+<li>use by <i>property</i> member <code>MassPeaks</code>: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/ms2.html">ms2</a></li>
+</ol>
+
+
+        <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/BioNovoGene/BioDeep/Chemistry/SpectraSection.html b/vignettes/clr/BioNovoGene/BioDeep/Chemistry/SpectraSection.html
@@ -0,0 +1,85 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>BioNovoGene.BioDeep.Chemistry.SpectraSection</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>SpectraSection {BioNovoGene.BioDeep.Chemistry}</td>
+                <td style="text-align: right;">.NET clr documentation</td>
+            </tr>
+        </table>
+
+        <h2>SpectraSection</h2>
+
+        <h3>Description</h3>
+
+        <p>Union of the spectrum data and the metabolite annotation metadata</p>
+
+<p>this data object used for union the metabolite annotation <a href="/vignettes/clr/BioNovoGene/BioDeep/Chemistry/MetaData.html">MetaData</a> and 
+ the spectrum data(<a href="/vignettes/clr/BioNovoGene/BioDeep/Chemistry/SpectraSection.html">SpectraSection</a>.<a href="/vignettes/clr/BioNovoGene/BioDeep/Chemistry/SpectraInfo.html">SpectraInfo</a>).</p>
+
+        <h3>Declare</h3>        
+
+        <pre>
+            <code id="clr_ts">
+# namespace BioNovoGene.BioDeep.Chemistry
+export class SpectraSection extends <a href="/vignettes/clr/BioNovoGene/BioDeep/Chemistry/MetaLib/Models/MetaInfo.html">MetaInfo</a> {
+   # should contains the necessary header data for @<code>M:BioNovoGene.BioDeep.Chemistry.SchemaMapper.FillData(System.Collections.Specialized.NameValueCollection)</code>
+   Comment: <a href="/vignettes/clr/System/Collections/Specialized/NameValueCollection.html">NameValueCollection</a>;
+   description: string;
+   exact_mass: double;
+   formula: string;
+   GetSpectrumPeaks: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/PeakMs2.html">PeakMs2</a>;
+   ID: string;
+   IUPACName: string;
+   libtype: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Ms1/PrecursorType/IonModes.html">IonModes</a>;
+   # MoNA里面都主要是将注释的信息放在<a href="/vignettes/clr/BioNovoGene/BioDeep/Chemistry/SpectraSection.html">SpectraSection</a>.<a href="/vignettes/clr/System/Collections/Specialized/NameValueCollection.html">Comment</a>字段里面的。
+   #  物质的注释信息主要是放在这个结构体之中，这个属性是对<a href="/vignettes/clr/BioNovoGene/BioDeep/Chemistry/SpectraSection.html">SpectraSection</a>.<a href="/vignettes/clr/System/Collections/Specialized/NameValueCollection.html">Comment</a>
+   #  属性的解析结果
+   MetaDB: <a href="/vignettes/clr/BioNovoGene/BioDeep/Chemistry/MetaData.html">MetaData</a>;
+   MetaReader: <a href="/vignettes/clr/BioNovoGene/BioDeep/Chemistry/UnionReader.html">UnionReader</a>;
+   ms_level: integer;
+   name: string;
+   # The reference spectrum data
+   SpectraInfo: <a href="/vignettes/clr/BioNovoGene/BioDeep/Chemistry/SpectraInfo.html">SpectraInfo</a>;
+   synonym: string;
+   xref: <a href="/vignettes/clr/BioNovoGene/BioDeep/Chemistry/MetaLib/CrossReference/xref.html">xref</a>;
+}
+</code>
+        </pre>
+
+        <h3>.NET clr type reference tree</h3>
+
+        <ol>
+<li>this class extends from <a href="/vignettes/clr/BioNovoGene/BioDeep/Chemistry/MetaLib/Models/MetaInfo.html">MetaInfo</a> class: <a href="/vignettes/clr/BioNovoGene/BioDeep/Chemistry/MetaLib/Models/MetaInfo.html">MetaInfo</a></li>
+<li>use by <i>property</i> member <code>Comment</code>: <a href="/vignettes/clr/System/Collections/Specialized/NameValueCollection.html">NameValueCollection</a></li>
+<li>use by <i>property</i> member <code>GetSpectrumPeaks</code>: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/PeakMs2.html">PeakMs2</a></li>
+<li>use by <i>property</i> member <code>libtype</code>: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Ms1/PrecursorType/IonModes.html">IonModes</a></li>
+<li>use by <i>property</i> member <code>MetaDB</code>: <a href="/vignettes/clr/BioNovoGene/BioDeep/Chemistry/MetaData.html">MetaData</a></li>
+<li>use by <i>property</i> member <code>MetaReader</code>: <a href="/vignettes/clr/BioNovoGene/BioDeep/Chemistry/UnionReader.html">UnionReader</a></li>
+<li>use by <i>property</i> member <code>SpectraInfo</code>: <a href="/vignettes/clr/BioNovoGene/BioDeep/Chemistry/SpectraInfo.html">SpectraInfo</a></li>
+<li>use by <i>property</i> member <code>xref</code>: <a href="/vignettes/clr/BioNovoGene/BioDeep/Chemistry/MetaLib/CrossReference/xref.html">xref</a></li>
+</ol>
+
+
+        <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>