DEMA

Introduction
DEMA is a plugin for data visualization. By generating a layout according to the network information, data analyst can use the layout to perceive the data relations.
- You need to have the latest version of Cytoscape (3.4.0)
- Install the DEMA plugin from the Cytoscape plugin manager. If you install it manually (e.g. the version isn’t in the plugin manager yet), then it must be in the CytoscapeConfiguration\3\apps\installed
Descriptions of files that DEMA needs

DEMA provides three kinds of layouts as the above table shows. Layout with blue frame is the most basic layout. There are two files as inputs for DEMA. One is an edge text file (necessary) that describes a network composed of edges. The other one is node text file (optional) that describes the properties of nodes in the network. The information provided by the blue frame is necessary and used to compose a network. Also, according to the information from the blue frame, basic layout is generated by DEMA. The information in the green frame is optional and used to generate weighted edge layout. The information in the red frame is optional and used to generate grouping layout.
Instructions
Tutorial video (5 mins): https://youtu.be/N9EhWbZGSg4
1. install the .jar file library downloaded from the website
click "Apps" -> select "App Manager" -> click "Install from File..." -> choose file directory and select the .jar file -> click "open"

2. import the Protein-Protein Interaction file (.txt)
click "import network" button -> select file and configure the "source","target" and "IC" (import as decimal format) columns -> click "ok"

3. import the gene's attribute file (.txt)
click "import attribute" button -> select file and configure the "set" (import as string format) columns -> click "ok"

4. generate the layout
click "Layout" button -> select "DEMA" and configure the parameters -> click "ok"

Introduction