update package documents

xieguigang · Jun 21, 2024 · 276cee8 · 276cee8
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diff --git a/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/IonStat.html b/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/IonStat.html
@@ -22,49 +22,29 @@ <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/mzkit_hpc/hpc/MsImaging.html b/vignettes/mzkit_hpc/hpc/MsImaging.html
@@ -85,7 +85,13 @@ <h1>MsImaging</h1>
   <td id="SCMs_ionStat_parallel">
     <a href="./MsImaging/SCMs_ionStat_parallel.html">SCMs_ionStat_parallel</a>
   </td>
-  <td><p>run measure of the ion features in IPC parallel</p></td>
+  <td><p>run measure of the ion features in IPC parallel for a huge single cells rawdata matrix</p></td>
+</tr>
+<tr>
+  <td id="MSI_ionStat_parallel">
+    <a href="./MsImaging/MSI_ionStat_parallel.html">MSI_ionStat_parallel</a>
+  </td>
+  <td><p>run measure of the ion features in IPC parallel for a huge ms-imaging rawdata matrix</p></td>
 </tr></tbody>
       </table>
     </div>

diff --git a/vignettes/mzkit_hpc/hpc/MsImaging/MSI_ionStat_parallel.html b/vignettes/mzkit_hpc/hpc/MsImaging/MSI_ionStat_parallel.html
@@ -0,0 +1,75 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>run measure of the ion features in IPC parallel for a huge ms-imaging rawdata matrix</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>MSI_ionStat_parallel {MsImaging}</td>
+                <td style="text-align: right;">R Documentation</td>
+            </tr>
+        </table>
+
+        <h2>run measure of the ion features in IPC parallel for a huge ms-imaging rawdata matrix</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>MSI_ionStat_parallel</strong>(<i>x</i>,
+    <i>grid.size</i> = <span style='color: green;'>5</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>grid.size</dt>
+<dd><p>[as integer]</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 <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/IonStat.html">IonStat</a>.<h4>clr value class</h4><ul><li><a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/IonStat.html">IonStat</a></li></ul>
+
+        <h3 style="display: none;">Examples</h3>
+
+
+
+        <hr />
+        <div style="text-align: center;">[Package <em>MsImaging</em> version 1.0.0.0 <a
+                href="../MsImaging.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/hpc/MsImaging/SCMs_ionStat_parallel.html b/vignettes/mzkit_hpc/hpc/MsImaging/SCMs_ionStat_parallel.html
@@ -2,7 +2,7 @@
 <html>
 
 <head>
-    <title>run measure of the ion features in IPC parallel</title>
+    <title>run measure of the ion features in IPC parallel for a huge single cells rawdata matrix</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">
@@ -18,7 +18,7 @@
             </tr>
         </table>
 
-        <h2>run measure of the ion features in IPC parallel</h2>
+        <h2>run measure of the ion features in IPC parallel for a huge single cells rawdata matrix</h2>
 
         <h3>Description</h3>