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How to use dagre layout in cytoscape.js to draw a simple tree. I am putting
layout{ name: 'dagre'} and added dagre.js file from .
It is not working.
closed as unclear what you're asking by , , , ,
Please clarify your specific problem or add additional details to highlight exactly what you need.
As it's currently written, it’s hard to tell exactly what you're asking. See the
page for help clarifying this question. If this question can be reworded to fit the rules in the , please .
I had the similar problem. I've used dagre.js from cytoscape package () and its working fine.
It seems like cytoscape dagre layout is not compatible with latest dagre.js () or something like this. It throws error on that line:
var g = new dagre.Digraph();
Use the dagre library bundled with the distribution in the lib folder hosted on GitHub.
Please post an example.
It works on the debug page and in the docs, so I suspect there's an issue with your code.
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Stack Overflow works best with JavaScript enabled【看图说话】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。上次给大家介绍了一下Cytoscape的使用，小伙伴们意犹未尽，今天小编就继续和大家分享这个常用的网络图编辑软件。
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（这点很关键......）
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, ): .
中科新生命，成立于2004年，专注于质谱技术方法在科技服务、生物医药、精准医疗领域的应用开发。12年质谱服务经验，每年处理本数超万例，通过与中科院的技术合作及企业研发团队的自主创新，致力成为您最具价值的生物技术合作伙伴。
中科新生命 · 质谱系统解决方案领航者
生物医药结构确证
蛋白质组 - 修饰蛋白质组 - 代谢组 - 脂质组
公众号 · 行业动态
www.aptbiotech.com T: 021- E: info_apt@sibs.ac.cn Q:
责任编辑：
声明：该文观点仅代表作者本人，搜狐号系信息发布平台，搜狐仅提供信息存储空间服务。
今日搜狐热点o Published a year agocytoscape-cytoscape-ngraph.forcelayout
Description
cytoscape-ngraph.forcelayout
Dependencies
Cytoscape.js &=x.y.z
Usage instructions
Download the library:
via npm: npm install cytoscape-ngraph.forcelayout,
via bower: bower install cytoscape-ngraph.forcelayout, or
via direct download in the repository (probably from a tag).
require() the library as appropriate for your project:
var cytoscape = require('cytoscape');var cyforcelayout = require('cytoscape-ngraph.forcelayout'); cyforcelayout( cytoscape );
register extension
require(['cytoscape', 'cytoscape-ngraph.forcelayout'], function( cytoscape, cyforcelayout ){
cyforcelayout( cytoscape );
register extension});
Plain HTML/JS has the extension registered for you automatically, because no require() is needed.
Please briefly describe your API here:
cy.cyforcelayout({
tell layout that we want to compute all at once:
maxIterations: 1000,
stepsPerCycle: 30,
Run it till the end:
waitForStep: false
physics: {
springLength: 100,
springCoeff: 0.0008,
gravity: -1.2,
theta: 0.8,
dragCoeff: 0.02,
timeStep: 20,
iterations: 10000,
fit: true,
stableThreshold: 0.000009
iterations: 10000,
refreshInterval: 16,
refreshIterations: 10,
iterations until thread sends an update
stableThreshold: 2,
animate: true,
fit: true});
Publishing instructions
This project is set up to automatically be published to npm and bower.
To publish:
Set the version number environment variable: export VERSION=1.2.3
Publish: gulp publish
If publishing to bower for the first time, you'll need to run bower register cytoscape-ngraph.forcelayout https://github.com/nickoasmv/cytoscape-ngraph.forcelayout.git}