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Cytoscape的“傻瓜式”教程

在这个世界,一个人的颜值和内涵很重要;在科研界中,优秀的科研论文除了创新的研究内容外,也需要“高颜值”的数据结果图。今天小编就和大家分享一个常用的网络图编辑软件—Cytoscape。

Cytoscape是一款可图形化显示网络并进行分析和编辑的软件。支持多种网络描述格式,也可以用以Tab制表符分隔的文本或Microsoft Excel文件作为输入,或利用软件本身的编辑器模块直接构建网络。它具体可以做什么?直接上图告诉你!

 

没错,这都是用Cytoscape完成的网络图,展示遗传关系或者生物学过程中的互作关系。有么有眼馋这些“高颜值”的图?心动不如行动,赶紧按接下来的Cytoscape使用教程学起来。

1. 安装并打开Cytoscape_v3.4.0

Java安装

Cytoscape的使用需要依赖Java环境,Cytoscape 3.4.0使用Java8,不再支持Java6和Java7。如果计算机上还没有安装Java,或者当前使用版本较低,需要重新下载安装Java8(网址链接见文末)。不同操作系统选择相应的Java版本下载安装。

Cytoscape安装

Cytoscape 同样有适用于不同操作平台的版本,安装方法不尽相同。所有的版本都可以从http://cytoscape.org/网站下载。Windows系统下双击exe应用程序开始安装;Linux和Mac OS X系统运行sh文件安装。

2. 导入蛋白质互作网络数据库中参考物种的蛋白互作网络

网络文件格式包括:TXT、SIF、GML等,在Cytoscape安装目录下有Sample Data,是部分网络文件的示例。

本地导入参考物种的蛋白互作网络:

 

Cytoscape默认将文件第一行作为列名。如果文件第一行是基因,在导入网络时要在Advanced Options中取消用第一行作为列名。

然后选择每一列数据的属性,包括Source Node、Interaction Type、Target Node、Edge Attribution、Source Attribution、Target Attribution等,同时对应不同颜色和图标标记。

导入后,右上部窗口内展示蛋白互作网络图,右下部为网络图的相关节点 (Node) 及边 (Edge) 的数据信息。左侧为导入的网络目录和网络属性 (Style) 设置菜单。

从公共数据库中获得参考物种的蛋白互作网络:

例如要导入某个物种的蛋白质互作网络:选择物种和想要查看的数据库,搜索包含该物种蛋白互作网络的数据库,导入数据(时间稍长)。

3. 在Layout选项下可以选择方便观测的布局(默认导入的布局方式为Perfuse Force Directed Layout)。

4. 设置网络节点和边的风格 (Style)

在Style选项卡下Node设置中对点的形状、颜色、大小等进行设置。例如:选择Shape为圆形、Fill Color为灰色、节点的高度 (Meight) 和宽度 (Width) 为50.0。

 

在Style选项卡下Edge设置中对边的形状、颜色、大小等进行设置。例如,将连线的颜色设置为蓝色,同时设置到Target方向的箭头同样为蓝色。

5. 导入差异表达基因及其属性列,映射到互作网络中作为各节点的拓扑性质。

选取目标网络、设置关键列 (Column1)、选择需要的节点属性列(可以选取多列,本例选取Column2,并重命名为Label,其中为up/down数据)。

6. 根据上下调基因 (up/down) 标示网络,定义上调基因 (up) 为红色,下调基因 (down) 为蓝色。

7. 导出数据

导出图像Export Network as Graphics。

导出数据 Export Table。

可导出数据面板中的网络节点、边和整体网络的信息。

在弹出窗口编辑导出文件名。

以上就是Cytoscape的“傻瓜式”教程,其实一款软件的应用从入门到精通,是需要时间的。希望大家多多尝试,其实鼠标点点点就能做到的,不用大家写代码哒!祝大家早日画出自己满意的网络图~

Java8下载地址:http://www.oracle.com/technetwork/java/javase/downloads/index.html

OpenJDK7网址:http://openjdk.java.net/

Cytoscape下载地址:http://www.cytoscape.org/download.php

参考手册:http://manual.cytoscape.org/en/stable/

发文章用Cytoscape作图记得引用文献哦:
ShannonP, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks[J]. Genome Research, 2003, 13(11): 2498-2504.

作者: genome.cn

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