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Cytoscape oper-source
(Plug in)
Cytoscape
Cytoscape
Linux Windows Mac OS X
Java SE 5
6 Cytoscape
The Menus
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
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
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
Apply to Network
EdgeAttribute
Edge Target Arrow
Edge Label
Edge Font
Edge Label Color
Edge Color
Edge Line Type
Edge
Color Mapping BasicDiscrete
Map Attribute
interaction Apply
to
Network
Global Defaults
Background Color
Select
File
Search
Cytoscape
ID m123
Search m123
m123
(interaction)
pp
Cytoscape
Select Attribute
Attribute Description
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);
}
}
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
.class
.jar
jar
..\Cytoscape_v2.4.0\plugins\
Cytoscape
Plugin level