Network Visualization: Cytoscape

Transcription

1 Network Visualization: Cytoscape Ritchie Lab Center for Systems Genomics Pennsylvania State University September 13, 2014

2 What is Cytoscape? Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. cytoscape.org

3 Cytoscape Platforms- Mac OS X, Windows 32bit, Windows 64bit (64bit JVM required), Linux System Requirements Small Network Visualization Large Network Analysis/ Visualization Processor 1GHz As fast as possible Memory 512MB 2GB+ Graphics Card On board Video High end Graphics Card Monitor XGA (1024X768) Wide or Dual Monitor Compatible with Java 6 or 7

4 Interface Windows (shown): Cytoscape.exe Command Line (Linux or Mac OS): cytoscape.sh

5 Brief Overview of Menus File Undo, Destroy, Remove, Delete selected nodes/ edges View Open, New, Save, Import, Export, Run, Print, Quit Edit Network management panels, Graphics manager, Arrange windows Select Select and hide options for nodes/edges, Filters Layout Cytoscape and yfiles layouts, Edge manipulations, Scale & rotate tools Apps Tools Help Browse user manual, Contact help desk, Developer s log console, Report bugs

6 Tools Menu Analyze network Create subnetworks, analyze statistics, create parameter plots Merge networks Workflow Analyze selected networks and create custom visual styles using amount of connectivity Edit or change visual style using Layout menu and VizMapper

7 Control Panel Float Panel Network Filters Navigator Create new network from selection VizMapper Modify attributes for Edge Color, Edge Line Style, Node Border, Node Color, Node Shape, Node Label, and others Choose mapping type for different column

8 Tips for using Cytoscape Think about what you want to see from the data Limit the number of networks that you have open If creating many visual styles via VizMapper, it is best to only work on one network at a time Copy visual style Large versus small networks Preserves default style and custom style Save network often Larger networks prone to memory leaks

9 Hands on Example Example network file found here: <Link to file on website>

10 Importing a network file Start New Session -> From Network File Under Advanced check Show Text File Import Options Check Transfer first line as column names Choose Source Interaction, Interaction Type, and Target Interaction

11 Supported File Formats Delimited text (eg. tab delimited,.csv,.txt) Excel Workbook (.xls) 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

12 What an input file should look like The file must have at least two columns You must specify each interaction directly One source column and one target column Ex. To get the network node1-node2-node3, you would need two rows of data node1,node2 node2,node3 Additional columns are listed as Edge Attributes Data must be numerical

13 Layouts and Visual Styles Create a Custom Style Hierarchical layout VizMapper Node Fill Color Name Discrete Mapping Node Shape Name Discrete Mapping

14 Phenotype Gene SNP

15 Exporting network to image Underneath the menu bar, click the Export Network Image to File icon Cick Save a File and browse to desired location Adjust zoom and/or DPI

16 Examples of More Complex Networks

17 Documentation and Resources Sample Workflow Cytoscape Methods Cline, M., Smoot, M., Cerami, E., Kuchinsky, A., Landys, N., et al., Integration of biological networks and gene expression data using Cytoscape. Nature Protocols 2, Salto, R., Smoot M.E., Ono K., Ruscheinski J., Wang P.L., Lotia S., Pico A.R., Bader G.D., Ideker T., A travel guide to Cytoscape plugins. Nature Methods 9, Tutorials Portal:Cytoscape3 App Store