R/html_psf_analysis.r
In hloefflerwirth/oposSOM: Comprehensive analysis of transcriptome data
Defines functions
pipeline.htmlPsfAnalysis
pipeline.htmlPsfAnalysis <- function(env)
{
if (!env$preferences$activated.modules$psf.analysis)
{
return()
}
data("kegg.collection")
folders <- dir( "PSF Analysis" )
if(length(folders)>0)
for( x in folders )
{
filename <- file.path("PSF Analysis", x, "0verview.html" )
util.info("Writing:", filename)
outfile <- file(filename, "w")
cat("<!DOCTYPE html>
<html>
<head>
<title>PSF Analysis Summary of ", env$files.name, " dataset</title>
<style>
body {
margin: 0;
padding: 0;
color: #333;
background-color: #fff;
font: normal normal normal 14px/180% sans-serif;
}
#wrapper {
width: 90%;
min-width: 400px;
max-width: 800px;
margin: 20px auto;
}
h1, h2 {
clear: both;
margin: 30px 0 0 0;
line-height: 210%;
border-bottom: 1px solid #eee;
}
dl {
line-height: 180%;
}
dl dt {
width: 50%;
float: left;
color: #111;
}
dl dt:after {
content: ':';
}
dl dd {
margin-left: 50%;
}
a {
color: #4183C4;
text-decoration: none;
}
table {
width: 100%;
margin: 24px 0;
border-collapse: collapse;
}
table th,
table td {
text-align: left;
padding: 4px 6px;
}
table thead tr,
table tbody tr:nth-child(2n) {
background-color: #f0f0f0;
}
table td a {
display: block;
}
#toc {
float: left;
width: 100%;
}
#toc li {
float: left;
width: 33%;
}
</style>
</head>
<body>
<div id=\"wrapper\">
<h1>General Information</h1>
<dl>
<dt>Number of Pathways</dt>
<dd>", length(kegg.collection), "</dd>
</dl>
<ul>
<li>
<a href=\"0verview Heatmaps.pdf\" target=\"_blank\">
PSF signal Heatmaps (PDF)
</a>
</li>
</ul>
<ul id=\"toc\">", sep="", file=outfile)
cat("
</ul>
<h1>Pathways</h1>
<p>
Population maps of the node and of the sink genes, and profile plots
of the mean and maximum sink node signals are shown.
Additionally the signal flow in each sample is given for the pathways.
</p>", sep="", file=outfile)
cat("
<table>
<thead>
<tr>
<th>Pathway</th>
<th>Report sheet</th>
</tr>
</thead>
<tbody>", sep="", file=outfile)
for (ii in seq_along(kegg.collection))
{
cat("
<tr>
<td>", names(kegg.collection)[ii], "</td>
<td><a href=\"", substring(make.names(names(kegg.collection)[ii]), 1, 100),
".pdf\" target=\"_blank\">PDF</a></td>
</tr>", sep="", file=outfile)
}
cat("
</tbody>
</table>", sep="", file=outfile)
cat("
</div>
</body>
</html>", sep="", file=outfile)
close(outfile)
}
}
hloefflerwirth/oposSOM documentation built on April 30, 2024, 1:07 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions pipeline.htmlPsfAnalysis
pipeline.htmlPsfAnalysis <- function(env)
{
if (!env$preferences$activated.modules$psf.analysis)
{
return()
}
data("kegg.collection")
folders <- dir( "PSF Analysis" )
if(length(folders)>0)
for( x in folders )
{
filename <- file.path("PSF Analysis", x, "0verview.html" )
util.info("Writing:", filename)
outfile <- file(filename, "w")
cat("<!DOCTYPE html>
<html>
<head>
<title>PSF Analysis Summary of ", env$files.name, " dataset</title>
<style>
body {
margin: 0;
padding: 0;
color: #333;
background-color: #fff;
font: normal normal normal 14px/180% sans-serif;
}
#wrapper {
width: 90%;
min-width: 400px;
max-width: 800px;
margin: 20px auto;
}
h1, h2 {
clear: both;
margin: 30px 0 0 0;
line-height: 210%;
border-bottom: 1px solid #eee;
}
dl {
line-height: 180%;
}
dl dt {
width: 50%;
float: left;
color: #111;
}
dl dt:after {
content: ':';
}
dl dd {
margin-left: 50%;
}
a {
color: #4183C4;
text-decoration: none;
}
table {
width: 100%;
margin: 24px 0;
border-collapse: collapse;
}
table th,
table td {
text-align: left;
padding: 4px 6px;
}
table thead tr,
table tbody tr:nth-child(2n) {
background-color: #f0f0f0;
}
table td a {
display: block;
}
#toc {
float: left;
width: 100%;
}
#toc li {
float: left;
width: 33%;
}
</style>
</head>
<body>
<div id=\"wrapper\">
<h1>General Information</h1>
<dl>
<dt>Number of Pathways</dt>
<dd>", length(kegg.collection), "</dd>
</dl>
<ul>
<li>
<a href=\"0verview Heatmaps.pdf\" target=\"_blank\">
PSF signal Heatmaps (PDF)
</a>
</li>
</ul>
<ul id=\"toc\">", sep="", file=outfile)
cat("
</ul>
<h1>Pathways</h1>
<p>
Population maps of the node and of the sink genes, and profile plots
of the mean and maximum sink node signals are shown.
Additionally the signal flow in each sample is given for the pathways.
</p>", sep="", file=outfile)
cat("
<table>
<thead>
<tr>
<th>Pathway</th>
<th>Report sheet</th>
</tr>
</thead>
<tbody>", sep="", file=outfile)
for (ii in seq_along(kegg.collection))
{
cat("
<tr>
<td>", names(kegg.collection)[ii], "</td>
<td><a href=\"", substring(make.names(names(kegg.collection)[ii]), 1, 100),
".pdf\" target=\"_blank\">PDF</a></td>
</tr>", sep="", file=outfile)
}
cat("
</tbody>
</table>", sep="", file=outfile)
cat("
</div>
</body>
</html>", sep="", file=outfile)
close(outfile)
}
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.