update help documents

xieguigang · Feb 4, 2024 · eb82cd9 · eb82cd9
1 parent e3c9968
commit eb82cd9
Show file tree

Hide file tree

Showing 121 changed files with 2,826 additions and 189 deletions.
diff --git a/vignettes/MSImaging/MSImaging/MSIfilter.html b/vignettes/MSImaging/MSImaging/MSIfilter.html
@@ -82,6 +82,12 @@ <h1>MSIfilter</h1>
       <table class="table-three-line">
         <caption>.NET clr function exports</caption>
         <tbody><tr>
+  <td id="intensity_cut">
+    <a href="./MSIfilter/intensity_cut.html">intensity_cut</a>
+  </td>
+  <td><p>removes low intensity spots</p></td>
+</tr>
+<tr>
   <td id="log_scale">
     <a href="./MSIfilter/log_scale.html">log_scale</a>
   </td>

diff --git a/vignettes/MSImaging/MSImaging/MSIfilter/intensity_cut.html b/vignettes/MSImaging/MSImaging/MSIfilter/intensity_cut.html
@@ -0,0 +1,76 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>removes low intensity spots</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>intensity_cut {MSIfilter}</td>
+                <td style="text-align: right;">R Documentation</td>
+            </tr>
+        </table>
+
+        <h2>removes low intensity spots</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>intensity_cut</strong>(
+    <i>threshold</i> = <span style='color: green;'>0.05</span>,
+    <i>quantile</i> = <span style='color: blue !important;'>FALSE</span>);</code></pre>
+        </div>
+
+        <h3>Arguments</h3>
+
+        <table>
+
+<dt>threshold</dt>
+<dd><p><p>-</p></p></dd>
+
+
+<dt>quantile</dt>
+<dd><p><p>-</p></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/MsImaging/Blender/Scaler/IntensityCutScaler.html">IntensityCutScaler</a>.<h4>clr value class</h4><ul><li><a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/IntensityCutScaler.html">IntensityCutScaler</a></li></ul>
+
+        <h3 style="display: none;">Examples</h3>
+
+
+
+        <hr />
+        <div style="text-align: center;">[Package <em>MSIfilter</em> version 1.0.0.0 <a
+                href="../MSIfilter.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/MSImaging/MSImaging/ggplot.html b/vignettes/MSImaging/MSImaging/ggplot.html
@@ -121,7 +121,7 @@ <h1>ggplot</h1>
   <td id="raster_blending">
     <a href="./ggplot/raster_blending.html">raster_blending</a>
   </td>
-  <td></td>
+  <td><p>rendering a gdi+ heatmap for create raster annotation in ggplot layer</p></td>
 </tr>
 <tr>
   <td id="geom_msimaging">

diff --git a/vignettes/MSImaging/MSImaging/ggplot/geom_MSIbackground.html b/vignettes/MSImaging/MSImaging/ggplot/geom_MSIbackground.html
@@ -50,7 +50,12 @@ <h3 style="display: block">Authors</h3>
 
         <h3>Value</h3>
 
-        this function returns data object in these one of the listed data types: <a href="/vignettes/clr/ggplotMSImaging/MSIBackgroundOption.html">MSIBackgroundOption</a>, <a href="/vignettes/clr/ggplotMSImaging/layers/MSITICOverlap.html">MSITICOverlap</a>.<h4>clr value class</h4><ul><li><a href="/vignettes/clr/ggplotMSImaging/MSIBackgroundOption.html">MSIBackgroundOption</a></li><li><a href="/vignettes/clr/ggplotMSImaging/layers/MSITICOverlap.html">MSITICOverlap</a></li></ul>
+        <p>this function returns clr object in types based on the <strong><code>background</code></strong> parameter:</p>
+
+<ol>
+<li>"TIC" or "BPC": <a href="/vignettes/clr/ggplotMSImaging/layers/MSITICOverlap.html">MSITICOverlap</a></li>
+<li>html color code: <a href="/vignettes/clr/ggplotMSImaging/MSIBackgroundOption.html">MSIBackgroundOption</a></li>
+</ol><h4>clr value class</h4><ul><li><a href="/vignettes/clr/ggplotMSImaging/MSIBackgroundOption.html">MSIBackgroundOption</a></li><li><a href="/vignettes/clr/ggplotMSImaging/layers/MSITICOverlap.html">MSITICOverlap</a></li></ul>
 
         <h3 style="display: none;">Examples</h3>
 

diff --git a/vignettes/MSImaging/MSImaging/ggplot/geom_color.html b/vignettes/MSImaging/MSImaging/ggplot/geom_color.html
@@ -68,7 +68,7 @@ <h3 style="display: block">Authors</h3>
 
         <h3>Value</h3>
 
-        this function returns data object of type <a href="/vignettes/clr/ggplot/layers/ggplotLayer.html">ggplotLayer</a>.<h4>clr value class</h4><ul><li><a href="/vignettes/clr/ggplot/layers/ggplotLayer.html">ggplotLayer</a></li></ul>
+        this function returns data object in these one of the listed data types: <a href="/vignettes/clr/ggplot/layers/ggplotLayer.html">ggplotLayer</a>, <a href="/vignettes/clr/ggplotMSImaging/layers/MSIChannelLayer.html">MSIChannelLayer</a>.<h4>clr value class</h4><ul><li><a href="/vignettes/clr/ggplot/layers/ggplotLayer.html">ggplotLayer</a></li><li><a href="/vignettes/clr/ggplotMSImaging/layers/MSIChannelLayer.html">MSIChannelLayer</a></li></ul>
 
         <h3 style="display: none;">Examples</h3>
 

diff --git a/vignettes/MSImaging/MSImaging/ggplot/geom_msimaging.html b/vignettes/MSImaging/MSImaging/ggplot/geom_msimaging.html
@@ -88,7 +88,7 @@ <h3 style="display: block">Authors</h3>
 
         <h3>Value</h3>
 
-        this function returns data object of type <a href="/vignettes/clr/ggplot/layers/ggplotLayer.html">ggplotLayer</a>.<h4>clr value class</h4><ul><li><a href="/vignettes/clr/ggplot/layers/ggplotLayer.html">ggplotLayer</a></li></ul>
+        this function returns data object in these one of the listed data types: <a href="/vignettes/clr/ggplot/layers/ggplotLayer.html">ggplotLayer</a>, <a href="/vignettes/clr/ggplotMSImaging/layers/MSImagingLayer.html">MSImagingLayer</a>.<h4>clr value class</h4><ul><li><a href="/vignettes/clr/ggplot/layers/ggplotLayer.html">ggplotLayer</a></li><li><a href="/vignettes/clr/ggplotMSImaging/layers/MSImagingLayer.html">MSImagingLayer</a></li></ul>
 
         <h3 style="display: none;">Examples</h3>
 

diff --git a/vignettes/MSImaging/MSImaging/ggplot/raster_blending.html b/vignettes/MSImaging/MSImaging/ggplot/raster_blending.html
@@ -2,7 +2,7 @@
 <html>
 
 <head>
-    <title>raster_blending</title>
+    <title>rendering a gdi+ heatmap for create raster annotation in ggplot layer</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">
@@ -18,11 +18,11 @@
             </tr>
         </table>
 
-        <h2>raster_blending</h2>
+        <h2>rendering a gdi+ heatmap for create raster annotation in ggplot layer</h2>
 
         <h3>Description</h3>
 
-        raster_blending
+
 
         <h3>Usage</h3>
 
@@ -36,6 +36,25 @@ <h3>Arguments</h3>
 
         <table>
 
+<dt>pixels</dt>
+<dd><p><p>the pixels data</p></p></dd>
+
+
+<dt>dims</dt>
+<dd><p><p>the spatial dimension size of the sample data</p></p></dd>
+
+
+<dt>scale</dt>
+<dd><p><p>the color palette name</p></p></dd>
+
+
+<dt>levels</dt>
+<dd><p><p>the color scaler levels</p></p></dd>
+
+
+<dt>env</dt>
+<dd><p><p>-</p></p></dd>
+
         </table>
 
 
@@ -49,7 +68,7 @@ <h3 style="display: block">Authors</h3>
 
         <h3>Value</h3>
 
-        this function returns data object of type <a href="/vignettes/clr/System/Drawing/Bitmap.html">Bitmap</a>.<h4>clr value class</h4><ul><li><a href="/vignettes/clr/System/Drawing/Bitmap.html">Bitmap</a></li></ul>
+        <p>a gdi+ raster image</p><h4>clr value class</h4><ul><li><a href="/vignettes/clr/System/Drawing/Bitmap.html">Bitmap</a></li></ul>
 
         <h3 style="display: none;">Examples</h3>
 

diff --git a/vignettes/MSImaging/R/docs/PlotMSIMatrixHeatmap.html b/vignettes/MSImaging/R/docs/PlotMSIMatrixHeatmap.html
@@ -43,7 +43,7 @@ <h3>Arguments</h3>
         <table>
 
 <dt>ions.data</dt>
-<dd><p><p>a list of MSI layers data, each element in this list should also be a list object that contains data slots: 1. type  precursor type information string 2. title   the ion metabolite name 3. layer   the MSI ion layer data</p></p></dd>
+<dd><p><p>a list of MSI layers data, each element in this list should also be a list object that contains data slots: 1. type  precursor type information string 2. title   the ion metabolite name 3. layer   the MSI ion layer data 4. mz      the target ion m/z value</p></p></dd>
 
         </table>
 

diff --git a/vignettes/MSImaging/_assets/R_syntax.js b/vignettes/MSImaging/_assets/R_syntax.js
diff --git a/vignettes/MSImaging/ggplot/ggplot2.html b/vignettes/MSImaging/ggplot/ggplot2.html
@@ -266,6 +266,12 @@ <h1>ggplot2</h1>
   </td>
   <td></td>
 </tr>
+<tr>
+  <td id="geom_tile">
+    <a href="./ggplot2/geom_tile.html">geom_tile</a>
+  </td>
+  <td></td>
+</tr>
 <tr>
   <td id="annotation_raster">
     <a href="./ggplot2/annotation_raster.html">annotation_raster</a>
@@ -402,6 +408,12 @@ <h1>ggplot2</h1>
   </td>
   <td></td>
 </tr>
+<tr>
+  <td id="scale_fill_distiller">
+    <a href="./ggplot2/scale_fill_distiller.html">scale_fill_distiller</a>
+  </td>
+  <td></td>
+</tr>
 <tr>
   <td id="scale_x_continuous">
     <a href="./ggplot2/scale_x_continuous.html">scale_x_continuous</a>

diff --git a/vignettes/MSImaging/ggplot/ggplot2/geom_tile.html b/vignettes/MSImaging/ggplot/ggplot2/geom_tile.html
@@ -0,0 +1,68 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>geom_tile</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>geom_tile {ggplot2}</td>
+                <td style="text-align: right;">R Documentation</td>
+            </tr>
+        </table>
+
+        <h2>geom_tile</h2>
+
+        <h3>Description</h3>
+
+        geom_tile
+
+        <h3>Usage</h3>
+
+        <div style="width: 100%; padding-left: 3%; color: black;">
+            <pre><code class='language-R' style="color: black; font-weight:normal;"><strong>geom_tile</strong>(
+    <i>mapping</i> = <span style='color: blue !important;'>NULL</span>);</code></pre>
+        </div>
+
+        <h3>Arguments</h3>
+
+        <table>
+
+        </table>
+
+
+        <h3 style="display: none;">Details</h3>
+
+
+
+        <h3 style="display: block">Authors</h3>
+
+        SMRUCC
+
+        <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>ggplot2</em> version 1.0.0.0 <a
+                href="../ggplot2.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/MSImaging/ggplot/ggplot2/scale_fill_distiller.html b/vignettes/MSImaging/ggplot/ggplot2/scale_fill_distiller.html
@@ -0,0 +1,70 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>scale_fill_distiller</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>scale_fill_distiller {ggplot2}</td>
+                <td style="text-align: right;">R Documentation</td>
+            </tr>
+        </table>
+
+        <h2>scale_fill_distiller</h2>
+
+        <h3>Description</h3>
+
+        scale_fill_distiller
+
+        <h3>Usage</h3>
+
+        <div style="width: 100%; padding-left: 3%; color: black;">
+            <pre><code class='language-R' style="color: black; font-weight:normal;"><strong>scale_fill_distiller</strong>(
+    <i>palette</i> = <span style='color: brown;'><strong>"YlGnBu"</strong></span>,
+    <i>direction</i> = <span style='color: green;'>1</span>,
+    <i>alpha</i> = <span style='color: green;'>1</span>);</code></pre>
+        </div>
+
+        <h3>Arguments</h3>
+
+        <table>
+
+        </table>
+
+
+        <h3 style="display: none;">Details</h3>
+
+
+
+        <h3 style="display: block">Authors</h3>
+
+        SMRUCC
+
+        <h3>Value</h3>
+
+        this function returns data object of type <a href="/vignettes/clr/ggplot/options/ggplotColorProfile.html">ggplotColorProfile</a>.<h4>clr value class</h4><ul><li><a href="/vignettes/clr/ggplot/options/ggplotColorProfile.html">ggplotColorProfile</a></li></ul>
+
+        <h3 style="display: none;">Examples</h3>
+
+
+
+        <hr />
+        <div style="text-align: center;">[Package <em>ggplot2</em> version 1.0.0.0 <a
+                href="../ggplot2.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/MSImaging/ggplot/ggplot2/theme.html b/vignettes/MSImaging/ggplot/ggplot2/theme.html
@@ -40,6 +40,7 @@ <h3>Usage</h3>
     <i>plot.title</i> = <span style='color: blue !important;'>NULL</span>,
     <i>panel.background</i> = <span style='color: blue !important;'>NULL</span>,
     <i>panel.grid</i> = <span style='color: brown;'><strong>"stroke: lightgray; stroke-width: 2px; stroke-dash: dash;"</strong></span>,
+    <i>panel.grid.major</i> = <span style='color: brown;'><strong>"stroke: lightgray; stroke-width: 2px; stroke-dash: dash;"</strong></span>,
     <i>panel.border</i> = <span style='color: blue !important;'>NULL</span>);</code></pre>
         </div>