Mercurial > repos > dereeper > cytoscape

diff Cytoscape.pl @ 0:e3beb33f88f0 draft

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planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
author dereeper
date Tue, 14 Aug 2018 08:02:10 -0400
parents
children 0e43c52e2449
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line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Cytoscape.pl	Tue Aug 14 08:02:10 2018 -0400
@@ -0,0 +1,115 @@
+#!/usr/bin/perl
+
+use strict;
+#use Switch;
+use Getopt::Long;
+use Bio::SeqIO;
+
+use Cwd;
+my $dir = getcwd;
+
+
+my $usage = qq~Usage:$0 <args> [<opts>]
+where <args> are:
+    -i, --input         <input>
+    -h, --html          <html_output>
+~;
+$usage .= "\n";
+
+my ($infile,$htmlout);
+
+
+GetOptions(
+	"input=s"    => \$infile,
+	"html=s"     => \$htmlout,
+);
+
+
+die $usage
+  if ( !$infile);
+
+
+my $datain = "";
+open(I,$infile);
+while(<I>){
+	my $line = $_;
+	$datain.=$line;
+}
+close(I);
+chomp($datain);chomp($datain);
+# remove brackets at the beginning and end of JSON
+my $new_datain = substr($datain,1,length($datain)-2);
+$datain = $new_datain;
+	
+my @colors = ("#ed292a","#ed292a","#82ABA0","#2255a6","#6ebe43","#e76599","#662e91","#c180ff","#ea8b2f","#fff100","#666666","#01ffff","#bfbfbf","#2ac966","#666666");
+
+
+my $pie_block = "";
+for (my $i = 0; $i <= scalar @colors; $i++){
+        $pie_block .= "'pie-$i-background-color': '$colors[$i]',\n";
+        $pie_block .= "'pie-$i-background-size': 'mapData(group$i, 0, 10, 0, 100)',\n";
+}
+
+open(HTML_CYTOSCAPE,">$htmlout");
+                        my $html = qq~<!DOCTYPE html>
+<html><head>
+<meta http-equiv="content-type" content="text/html; charset=UTF-8">
+<link href="http://sniplay.southgreen.fr/cytoscape/Pie_style/style.css" rel="stylesheet">
+<meta charset="utf-8">
+<meta name="viewport" content="user-scalable=no, initial-scale=1.0, minimum-scale=1.0, maximum-scale=1.0, minimal-ui">
+<title>Pie style</title>
+<script src="http://sniplay.southgreen.fr/cytoscape/Pie_style/jquery.js"></script>
+<script src="http://sniplay.southgreen.fr/cytoscape/Pie_style/cytoscape.js"></script>
+<script type="text/javascript">
+\$(function(){ // on dom ready
+
+\$('#cy').cytoscape({
+
+  style: cytoscape.stylesheet()
+    .selector(':selected')
+      .css({
+        'background-color': 'black',
+        'line-color': 'black',
+        'opacity': 1
+      })
+    .selector('.faded')
+      .css({
+        'opacity': 0.25,
+        'text-opacity': 0
+      })
+    .selector('edge')
+      .css({
+                'width': 1,
+                'line-color': 'black',
+      })
+    .selector('node')
+      .css({
+        'width': 'mapData(width, 0, 10, 0, 100)',
+        'height': 'mapData(width, 0, 10, 0, 100)',
+        'content': 'data(id)',
+        'pie-size': '98%',
+        $pie_block
+      }),
+$datain
+  ,
+layout: {
+        name: 'cose',
+    padding: 10
+  },
+
+  ready: function(){
+    window.cy = this;
+  }
+});
+
+});
+
+</script>
+</head>
+<body>
+<div id="cy">
+</div>
+~;
+print HTML_CYTOSCAPE $html;
+close(HTML_CYTOSCAPE);
+