make updates of the help documents

xieguigang · Dec 22, 2023 · c3bd0c0 · c3bd0c0
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diff --git a/.../BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/MsImaging/Correction.html b/.../BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/MsImaging/Correction.html
@@ -22,7 +22,7 @@ <h2>Correction</h2>
 
         <h3>Description</h3>
 
-
+        An abstract data model for make scan x correction
 
         <h3>Declare</h3>        
 

diff --git a/...lr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/MsImaging/Metadata.html b/...lr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/MsImaging/Metadata.html
@@ -30,14 +30,20 @@ <h3>Declare</h3>
             <code id="clr_ts">
 # namespace BioNovoGene.Analytical.MassSpectrometry.Assembly.Comprehensive.MsImaging
 export class Metadata {
+   # the max scan number in x axis
    scan_x: integer;
+   # the max rows in y axis
    scan_y: integer;
+   # the spatial resolution
    resolution: double;
+   # the ion m/z value range of the scan result.
    mass_range: <a href="/vignettes/clr/Microsoft/VisualBasic/ComponentModel/Ranges/Model/DoubleRange.html">DoubleRange</a>;
    # the string name of @``T:BioNovoGene.Analytical.MassSpectrometry.Assembly.mzData.mzWebCache.FileApplicationClass``, 
    #  not the description id value
    class: string;
+   # the calculated physical width of the sample slider data
    physical_width: double;
+   # the calculated physical height of the sample slider data
    physical_height: double;
 }
 </code>

diff --git a/...tes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/MSISummary.html b/...tes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/MSISummary.html
@@ -34,7 +34,9 @@ <h3>Declare</h3>
    rowScans: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/iPixelIntensity[].html">iPixelIntensity[][]</a>;
    # the MALDI scan dimension size
    size: <a href="/vignettes/clr/System/Drawing/Size.html">Size</a>;
+   # the range of the x axis: [min, max]
    x: double;
+   # the range of the y axis: [min, max]
    y: double;
 }
 </code>

diff --git a/...ettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/ScanData.html b/...ettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/ScanData.html
@@ -0,0 +1,57 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.imzML.ScanData</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>ScanData {BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.imzML}</td>
+                <td style="text-align: right;">.NET clr documentation</td>
+            </tr>
+        </table>
+
+        <h2>ScanData</h2>
+
+        <h3>Description</h3>
+
+        a 2D single pixel pointer data in the generated image
+
+        <h3>Declare</h3>        
+
+        <pre>
+            <code id="clr_ts">
+# namespace BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.imzML
+export class ScanData {
+   MzPtr: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/ibdPtr.html">ibdPtr</a>;
+   IntPtr: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/ibdPtr.html">ibdPtr</a>;
+   spotID: integer;
+   polarity: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Ms1/PrecursorType/IonModes.html">IonModes</a>;
+   # [lowest observed m/z, highest observed m/z]
+   mass: <a href="/vignettes/clr/Microsoft/VisualBasic/ComponentModel/Ranges/Model/DoubleRange.html">DoubleRange</a>;
+   totalIon: double;
+   x: integer;
+   y: integer;
+}
+</code>
+        </pre>
+
+        <hr />
+        <div style="text-align: center;">[Package <em>{$package}</em> version {$version} <a
+                href="../{$package}.html">Index</a>]
+        </div>
+    </div>
+</body>
+
+<script type="text/javascript" src="https://mzkit.org/assets/js/R_syntax.js"></script>
+<script type="text/javascript" src="https://mzkit.org/assets/js/highlights.js"></script>
+<script type="text/javascript">r_highlights("clr_ts");</script>
+
+</html>
diff --git a/...ttes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/ibdReader.html b/...ttes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/ibdReader.html
@@ -0,0 +1,54 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.imzML.ibdReader</title>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
+    <link rel="stylesheet" type="text/css" href="https://mzkit.org/assets/js/page.css">
+</head>
+
+<body>
+    <div class="container">
+
+        <table style="width: 100%;">
+            <tr>
+                <td>ibdReader {BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.imzML}</td>
+                <td style="text-align: right;">.NET clr documentation</td>
+            </tr>
+        </table>
+
+        <h2>ibdReader</h2>
+
+        <h3>Description</h3>
+
+        the binary data reader of the mass spectrum data
+
+        <h3>Declare</h3>        
+
+        <pre>
+            <code id="clr_ts">
+# namespace BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.imzML
+export class ibdReader {
+   # Universal Unique Identifier
+   UUID: string;
+   # the original source file name
+   fileName: string;
+   # the ibd file size
+   size: integer;
+}
+</code>
+        </pre>
+
+        <hr />
+        <div style="text-align: center;">[Package <em>{$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/MsImaging/IonStat.html b/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/IonStat.html
@@ -30,20 +30,34 @@ <h3>Declare</h3>
             <code id="clr_ts">
 # namespace BioNovoGene.Analytical.MassSpectrometry.MsImaging
 export class IonStat {
+   # the ion m/z value of current ms-imaging layer feature
    mz: double;
+   # the min range value of current ion m/z
    mzmin: double;
+   # the max range value of current ion m/z
    mzmax: double;
+   # the description text of the mz range: mzmax - mzmin
    mzwidth: string;
+   # the average spatial density
    pixels: integer;
    density: double;
    maxIntensity: double;
    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;
    Q1Intensity: double;
    Q2Intensity: double;
    Q3Intensity: 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 Moran-I test p-value
    pvalue: double;
 }
 </code>

diff --git a/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SingleCells/MatrixReader.html b/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SingleCells/MatrixReader.html
@@ -0,0 +1,52 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>BioNovoGene.Analytical.MassSpectrometry.SingleCells.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}</td>
+                <td style="text-align: right;">.NET clr documentation</td>
+            </tr>
+        </table>
+
+        <h2>MatrixReader</h2>
+
+        <h3>Description</h3>
+
+
+
+        <h3>Declare</h3>        
+
+        <pre>
+            <code id="clr_ts">
+# namespace BioNovoGene.Analytical.MassSpectrometry.SingleCells
+export class MatrixReader {
+   tolerance: string;
+   featureSize: integer;
+   ionSet: double;
+   spots: integer;
+}
+</code>
+        </pre>
+
+        <hr />
+        <div style="text-align: center;">[Package <em>{$package}</em> version {$version} <a
+                href="../{$package}.html">Index</a>]
+        </div>
+    </div>
+</body>
+
+<script type="text/javascript" src="https://mzkit.org/assets/js/R_syntax.js"></script>
+<script type="text/javascript" src="https://mzkit.org/assets/js/highlights.js"></script>
+<script type="text/javascript">r_highlights("clr_ts");</script>
+
+</html>
diff --git a/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SpatialMatrixReader.html b/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SpatialMatrixReader.html
@@ -0,0 +1,48 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>BioNovoGene.Analytical.MassSpectrometry.SpatialMatrixReader</title>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
+    <link rel="stylesheet" type="text/css" href="https://mzkit.org/assets/js/page.css">
+</head>
+
+<body>
+    <div class="container">
+
+        <table style="width: 100%;">
+            <tr>
+                <td>SpatialMatrixReader {BioNovoGene.Analytical.MassSpectrometry}</td>
+                <td style="text-align: right;">.NET clr documentation</td>
+            </tr>
+        </table>
+
+        <h2>SpatialMatrixReader</h2>
+
+        <h3>Description</h3>
+
+        The wrapper of the spatial matrix to R# language
+
+        <h3>Declare</h3>        
+
+        <pre>
+            <code id="clr_ts">
+# namespace BioNovoGene.Analytical.MassSpectrometry
+export class SpatialMatrixReader {
+}
+</code>
+        </pre>
+
+        <hr />
+        <div style="text-align: center;">[Package <em>{$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/Chemoinformatics/Formula/FormulaComposition.html b/vignettes/clr/BioNovoGene/BioDeep/Chemoinformatics/Formula/FormulaComposition.html
@@ -30,7 +30,9 @@ <h3>Declare</h3>
             <code id="clr_ts">
 # namespace BioNovoGene.BioDeep.Chemoinformatics.Formula
 export class FormulaComposition {
+   # the charge value of current formula
    charge: double;
+   # the ppm error between the theriocal mass value and the input mass value
    ppm: double;
    massdiff: double;
    # Hydrogen/Carbon element ratio

diff --git a/vignettes/clr/BioNovoGene/BioDeep/Chemoinformatics/SDF/SDF.html b/vignettes/clr/BioNovoGene/BioDeep/Chemoinformatics/SDF/SDF.html
@@ -44,6 +44,7 @@ <h3>Declare</h3>
    name: string;
    Comment: string;
    Structure: <a href="/vignettes/clr/BioNovoGene/BioDeep/Chemoinformatics/SDF/Models/Structure.html">Structure</a>;
+   # the metadata that could be used as the annotation information of current molecule.
    MetaData: list;
 }
 </code>

diff --git a/vignettes/clr/Microsoft/VisualBasic/ComponentModel/Ranges/Model/DoubleRange.html b/vignettes/clr/Microsoft/VisualBasic/ComponentModel/Ranges/Model/DoubleRange.html
@@ -36,6 +36,7 @@ <h3>Declare</h3>
    Max: double;
    # Length of the range (deffirence between maximum and minimum values)
    Length: double;
+   # A vector with 2 elements: [min, max]
    MinMax: double;
 }
 </code>

diff --git a/vignettes/clr/SMRUCC/genomics/Analysis/HTS/DataFrame/DataFrameRow.html b/vignettes/clr/SMRUCC/genomics/Analysis/HTS/DataFrame/DataFrameRow.html
@@ -0,0 +1,54 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>SMRUCC.genomics.Analysis.HTS.DataFrame.DataFrameRow</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>DataFrameRow {SMRUCC.genomics.Analysis.HTS.DataFrame}</td>
+                <td style="text-align: right;">.NET clr documentation</td>
+            </tr>
+        </table>
+
+        <h2>DataFrameRow</h2>
+
+        <h3>Description</h3>
+
+        The gene expression data samples file.(基因的表达数据样本)
+
+        <h3>Declare</h3>        
+
+        <pre>
+            <code id="clr_ts">
+# namespace SMRUCC.genomics.Analysis.HTS.DataFrame
+export class DataFrameRow {
+   # The unique reference id of current expression data vector
+   geneID: string;
+   # This gene's expression value in the different experiment condition.(同一个基因在不同实验之下的表达值)
+   experiments: double;
+   # Gets the sample counts of current gene expression data.(获取基因表达数据样本数目)
+   samples: integer;
+}
+</code>
+        </pre>
+
+        <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>