Graph construction and visualization

Methodological Material

Elena Nikolaeva, Egon Elbre

MTAT.03.251 Graph Mining

Hedi Peterson, Bioinformatics, fall 2010

Import network filesFile formats

• Simple interaction file (SIF or .sif format) • Nested network format (NNF or .nnf format) • Graph Markup Language (GML or .gml format) • XGMML (extensible graph markup and

modelling language). • SBML • BioPAX • PSI-MI Level 1 and 2.5 • Delimited text • Excel Workbook (.xls)

MTAT.03.251 Graph Mining

Import network files Fixed-Format Network Files

(SIF, GML, XGMML, etc.)• File → Import → Network (multiple file

types)

MTAT.03.251 Graph Mining

Import network filesFree-Format Table Files

File → Import → Network from Table (Text/MS Excel)

MTAT.03.251 Graph Mining

Imported Network Example

MTAT.03.251 Graph Mining

Layout

MTAT.03.251 Graph Mining

Spring Embedded

MTAT.03.251 Graph Mining

Create sub network• Select a group of nodes

• Press icon MTAT.03.251 Graph Mining

Useful tips• Select→ Edges→ Select adjacent edges• Select→ Nodes→ First neighbors of selected nodes

MTAT.03.251 Graph Mining

Finding Node• Quick Find feature, which enables you to quickly find nodes

and edges• Start typing in the text box. The search box will

automatically display a list of all matching nodes. • Select a matching node. Cytoscape will automatically zoom

in on the selected node.

MTAT.03.251 Graph Mining

Delete Node, Edge• Select Node or Edge

• Edit→ Delete Selected Nodes and Edges

MTAT.03.251 Graph Mining

Connect Nodes• Edit→ Connect Selected Nodes

MTAT.03.251 Graph Mining

Add node• Select the Editor tab in CytoPanel• Drag and drop a node shape from the

palette onto the canvas• To connect two nodes with an edge,

drag and drop a line shape onto a node on the canvas

MTAT.03.251 Graph Mining

Visual styles• Can be created or edited using the Cytoscape

VizMapperVisual Attributes Associated with Nodes

Visual Attributes Associated with Edges

Node Color Edge Color Node Opacity Edge Opacity

Node Border Color Edge Line Style. Solid or dashed lines are supported.Node Border Opacity Edge Line Width

Node Border Line Style. Solid and dashed lines are supported.

Edge Source and Target Arrow Shape: The following options are available:

Node Border Line Width Edge Source and Target Arrow Color Node Shape. The following options are available:

Edge Source and Target Arrow Opacity

Node Size: the width and height of each node.

Edge Label: the text label for each edge.

Node Label: the text label for each node. Edge Label Color

Node Label Color Edge Label Opacity

Node Label Opacity Edge Font: edge label font and size. Node Label Position: the position of the label relative to the node. Node Font: node label font and size.

MTAT.03.251 Graph Mining

Create a Basic Visual Style. Set Default Values

• Open the VizMapper• Click the Options button , and select Create new visual style• Edit default values• Change the default node shape and filling color

• Apply your settings

MTAT.03.251 Graph Mining

Graph construction and visualization Methodological MaterialSlide 2Import network filesSlide 4Slide 5Imported Network ExampleLayoutSpring EmbeddedCreate sub networkUseful tipsFinding NodeDelete Node, EdgeConnect NodesAdd nodeVisual stylesCreate a Basic Visual Style. Set Default Values