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绘制最简单的基因组图

已有 2792 次阅读 2014-4-30 16:41 |个人分类:|系统分类:科研笔记

应同学要求帮忙绘制 一个简单的基因组图(在圆圈中标上基因的其实位置)

刚开始上网查了下,有个软件叫circos非常厉害,perl写的,好呆也用perl3年多了,应该没问题。

但折腾了好长时间,发现karotype文件太复杂,而且自身携带的API 不是基础API。

于是我想用R完成这个基因组图,在R中找到了Rcircos还是用不了。

我了解到了一个SVG的东西,里面都是一些基本的API ,怎么画点 画线 等

借助于perl创建SVG文件 一切迎刃而解

#############################createsvg.pl#####################

#!/usr/bin/perl -w

#author:  chen zhaoqiang
#function: 绘制自定义圈图,产生svg文件


use strict;

open FH,"xb.txt";
my @text=<FH>;
chomp(@text);
#@text=(0,90,180,270,360);



#print $text[0];
my $start=$text[0];
print "\n";
my $end=$text[-1];

my $long=$end-$start;



my $radius=300;

my $center_x=500;
my $center_y=400;
#<circle  cx="" cy="450" r="200"></circle>
print '<circle  cx="'.$center_x.'" cy="'.$center_y.'" r="'.$radius.'" stroke = "black"  stroke-width = "1" fill="none"></circle> ';
print "\n";



my $radius_in=$radius-10;
my $radius_out=$radius+10;

foreach my $line(@text)
{
     
      my $nowlong=$line-$start;
      my $angle=$nowlong/$long*3.14159265*2;    #弧度
     # print "$angle  \n";
   #  $angle=3.141592653589793238462643383279502884197/2;
   
      my $x1=$radius_in*cos($angle)+$center_x;
      my $y1=$radius_in*sin($angle)+$center_y;
     
     
        my $x2=$radius_out*cos($angle)+$center_x;
      my $y2=$radius_out*sin($angle)+$center_y;
     
   
      print '<line x1="'.$x1.'" y1="'.$y1.'" x2="'.$x2.'" y2="'.$y2.'" style="stroke:rgb(99,99,99);stroke-width:2" />';
      print "n";
     
   
}


########################################最后的svg文件###########################



<?xml version="1.0" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
"http://www./Graphics/SVG/1.1/DTD/svg11.dtd">
<svg width="100%" height="100%" version="1.1"
xmlns="http://www./2000/svg">




<circle  cx="500" cy="400" r="300" stroke = "black"  stroke-width = "1" fill="none"></circle>
<line x1="790" y1="400" x2="810" y2="400" style="stroke:rgb(99,99,99);stroke-width:2" />
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