igraph is a free software package for creating and manipulating undirected and directed graphs. It includes implementations for classic graph theory problems like minimum spanning trees and network flow, and also implements algorithms for some recent network analysis methods, like community structure search.

igraph contains functions for generating regular and random graphs, manipulating graphs, assigning attributes to vertices and edges. It can calculate various structural properties, graph isomorphism, includes heuristics for community structure detection, supports many file formats. The R and Python interfaces support visualization.

igraph runs on most modern machines and operating systems, and it is tested on MS Windows, Mac OSX and various Linux versions. The software you need for installing igraph depends on whether you want to use the C library, the R package or the Python extension; and may vary depending on your platform.

实际问题：大鼠（rat）中转录因子与其靶基因之间的调控网络。
原始数据：Integrated Transcription Factor Platform
中间数据：经整理后得到2个文件，如下所示：
node.txt——节点（转录因子与基因）数据；
relation.txt——连线（转录因子与其调控的靶基因）数据。
最终网络：

PS1：这种一张图片中包含成百上千个节点与连线的网络图除了忽悠忽悠人，真的有什么实际用途吗？
PS2：这张图还是蛮漂亮的：弯弯的月亮、头戴两朵小花……
简单注释：绿色的节点是转录因子，蓝色的节点是基因；红色的连线表示转录因子调控（表达）转录因子（的基因），黑色的连线表示转录因子调控一般的基因。

官网主页（The igraph library）
Network Analysis with igraph（Creating Graphs）
Experiments with igraph
Plotting texts as graphs with R and igraph

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