Download Cytoscape User Manual PDF

TitleCytoscape User Manual
File Size20.0 MB
Total Pages259
Table of Contents
Launching Cytoscape
	System Requirements
	Getting Started
Command Line Arguments
Quick Tour of Cytoscape
	Starter Panel
	Basic Features
	The Menus
	Network Management
	Network View Tools
Creating Networks
	Import Fixed-Format Network Files
	Import Networks from Unformatted Table Files
	Import Networks from Public Databases
	Create a New Network or Edit One Manually
Nested Networks
	Creating Nested Networks
	Visualization of Nested Networks
Supported Network File Formats
	SIF Format
	GML Format
	XGMML Format
	SBML (Systems Biology Markup Language) Format
	BioPAX (Biological PAthways eXchange) Format
	Delimited Text Table and Excel Workbook
	Cytoscape.js JSON
	Cytoscape CX
Node and Edge Column Data
	Import Data Table Files
	Legacy Cytoscape Attributes Format
	Import Data Table from Public Databases
	Mapping Identifiers
Column Data Functions and Equations
	Column Formulas
	The Formula Builder
	A Note for App Writers
Finding and Filtering Nodes and Edges
	Search Bar
	The Select Menu
Navigation and Layout
	Basic Network Navigation
	Other Mouse Behaviors
	Manual Layout
	Node Layout Tools
	Edge Bend and Automatic Edge Bundling
	Automatic Layout Algorithms
	yFiles Layouts
	Layout Parameters
	What are Styles?
	Introduction to the Style Interface
	Introduction to Style
	Images, Charts and Gradients
	Styles Tutorials
	Advanced Topics
	Managing Styles
Network Annotations
	Types of Annotations
	The Annotation Panel
	Creating Annotations
	Selecting Annotations
	Moving Annotations Backwards and Forwards
	Renaming Annotations
	Editing Annotations
	Deleting Annotations
	Grouping Annotations
App Manager
	What are Apps?
	Installing Apps
	Managing your Installed Apps
Automation Panel
Cytoscape Web Browser
	CyBrowser Window
	CyBrowser in Results Panel
	Why CyBrowser?
	Merge Networks
	Network Analysis
	NetworkAnalyzerDemo: Computation and Visualization of Topological Parameters and Centrality Measures for Biological Networks
Cytoscape Preferences
	Managing Properties
	Managing Bookmarks
	Managing Proxy Servers
	Managing Group Settings
	Managing OpenCL Settings
	Adding and Removing Links
	Managing Panels
	Other Features
Rendering Engine
	What is Level of Detail (LOD)?
Export Your Data
	Raw Data Export
	Exporting for Publication
Cytoscape and OpenCL (Computing on the GPU)
	What it is for?
	Setup & Configuration
	OpenCL/GPU Troubleshooting
Cytoscape.js and Cytoscape
	What is Cytoscape.js?
	Data Exchange between Cytoscape and Cytoscape.js
	Export Styles to Cytoscape.js
	Build Your Own Web Application with Cytoscape.js
Cytoscape Automation
	R and Python Packages
	CyREST Interface Layer
Cytoscape Privacy Policy
Basic Expression Analysis Tutorial
Document Text Contents
Page 1

Cytoscape User Manual
Release 3.8.0

The Cytoscape Consortium

Apr 17, 2020

Page 129

Cytoscape User Manual, Release 3.8.0

Step 2. Switch between different styles

You can change the style by making a selection from the Current Style drop-down list, found at the top of the Style

For example, if you select Sample1, a new style will be applied to your network, and you will see a white background
and round blue nodes. If you zoom in closer, you can see that protein-DNA interactions (specified with the label “pd”)
are drawn with dashed edges, whereas protein-protein interactions (specified with the label “pp”) are drawn with solid
edges (see sample screenshot below).

Finally, if you select Solid, you can see the graphics below:

12.3. Introduction to Style 123

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Cytoscape User Manual, Release 3.8.0

This style does not have mappings except node/edge labels, but you can modify the network graphics by editing the
Default Value for any property.

Additional sample styles are available in the sampleStyles.xml file in the sampleData directory. You can import
the sample file from File → Import → Styles from File. . . .

12.3.1 List of Node, Edge and Network Properties

Cytoscape allows a wide variety of properties to be controlled. These are summarized in the tables below.

12.3.2 Available Shapes and Line Styles

12.3.3 How Mappings Work

For each property, you can specify a default value or define a dynamic mapping. Cytoscape currently supports three
different types of mappings:

1. Passthrough Mapping

• The values of network column data are passed directly through to properties. A passthrough mapping is
typically used to specify node/edge labels. For example, a passthrough mapping can label all nodes with
their common gene names.

2. Discrete Mapping

• Discrete column data are mapped to discrete properties. For example, a discrete mapping can map dif-
ferent types of molecules to different node shapes, such as rectangles for gene products and ellipses for

3. Continuous Mapping

• Continuous data are mapped to properties. Depending on the property, there are three kinds of continuous

124 Chapter 12. Styles

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Cytoscape User Manual, Release 3.8.0

252 Chapter 27. Cytoscape Privacy Policy

Page 259


Basic Expression Analysis Tutorial

The Cytoscape Basic Data Visualization tutorial is now available here.

The complete set of Cytoscape tutorials is available at


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