Cytoscape

Cytoscape oper-source

(Plug in)

 Cytoscape
Cytoscape
Linux Windows Mac OS X
Java SE 5
6 Cytoscape

The Menus

.sif .pvals .xml .txt .cys .excel Java

VizMapper

The Menus

Layout

Plugin

File
sif .pvals .xml .txt .cys .excel
sif File->Import->Network->Select>Sampledata->(ex : galFiltered.sif)->Import

File
Import Import Network From Table

Edit
View
Linkout
Linkout:
Cytoscape
(ID) Ex
m001 LinkOut

Edit Preferences Properties...

Property Name nodelinkouturl.
LinkOut Value
%ID%

Ex Yahoo Edit
Preferences Properties...
Property Name nodelinkouturl.Yahoo
Value

http://tw.search.yahoo.com/search?fr=fp-tab-
web-t&ei=UTF-8&p=%ID%

Yahoo m000

View
CytoPanel1 CytoPanel2 Network Overview
VizMapper

VizMapper introduction visual styles

VizMapper

New
Duplicate
Rename
Delete
Create Legend
Close
Define

Introduction Define
Define VizMapper VizMapper
(NodeAttribute) (Edge Attribute) (GlobalDefaults)

NodeAttribute Define
Border Color
Node Label Color
Node Label Position

NodeAttribute
Border Color
Node Label Color
Node Label Position

Node
Node
Node
Node
Node
Node

Shape
Size
Label
Font
Color
Line Type

New
(Discrete Mapper)
(Passthrough Mapper)
(Continuous Mapper)

 new

Map Attribute Node_Color_Shape

2
2 2 2

Apply to Network

EdgeAttribute
Edge Target Arrow

Edge Label

Edge Font

Edge Label Color

Edge Color

Edge Line Type

Edge Source Arrow

 Edge
Color Mapping BasicDiscrete
Map Attribute
interaction Apply
to
Network

Global Defaults
Background Color

Selected Node Color 1

Selected Node Color 2

CytoPanel

Selected Edge Color 1

Selected Edge Color 2

CytoPanel

Select

File

Search
Cytoscape

ID m123

Search m123

m123

(interaction)
pp

 Cytoscape

Select Index Type

Select Attribute

Attribute Description

Sample Attribute Values

Filters
Cytoscape

Cytoscape


1 . Numeric Filter
> = <
2 . String Filter
*

Ex m m*
3 . Topology Filter

4 . Boolean Meta-Filter

Layout
Layout

Plugin

http://chianti.ucsd.edu/Cyto-2_4_0/javadoc/
Cytoscape JAVA Plugin


HelloWorld JAVA
Cytoscape

import javax.swing.JOptionPane;
import cytoscape.plugin.CytoscapePlugin;
import cytoscape.Cytoscape;
public class HelloWorld extends CytoscapePlugin{
public HelloWorld() {
String message="== ==";
System.out.println(message);
JOptionPane.showMessageDialog(Cytoscape.getDesktop(
), message);
}
}

 JAVA JOptionPane showMessageDialog

CytoscapePlugin
Cytoscape.getDesktop
import
JAVA
JAVA cytoscape
JAVA
CytoscapePlugin Cytoscape
\Cytoscape_v2.4.0\ cytoscape.jar
C:\Program Files\Java\jdk1.6.0\jre\lib\ext\

 Cytoscape Plugin
jar
Step1: JAVA HellowWorld.class
Step2:
manifest.mf
Main-Class:< >
< >
Step3: HellowWorld.class manifest.mf jdk
bin
Step4: jdk bin
jar cvfm hi.jar manifest.mf *.class bin
hi.jar
.class .class

jar cvfm myJAR.jar manifest.mf A.class B.class

C.class ..... .class A B C

.class

.jar

 jar
..\Cytoscape_v2.4.0\plugins\
Cytoscape

 Plugin level

Plugin prefuse.jar cerebral-v1.0.1.jar

..\ Cytoscape_v2.4.0\plugins\ Cytoscape
localization Plugin Cytoscape

PluginsCreate Cerebral view

 Allow placement in any layer

level unknown
Localization level
Create Layout