Data Visualization with Cytoscape

Slides:
https://cytoscape.github.io/cytoscape-tutorials/presentations/data-visualization-2018-sib.html


John "Scooter" Morris

Swiss Institute of Bioinformatics
1 November 2018

Goals and Motivations

By the end of this workshop you should be able to:

  • Understand the major applications of network biology
  • Import your data into Cytoscape
  • Learn some approaches to effective network visualizations
  • Master network layouts and data visualization
  • Learn some of the advanced features of network visualization in Cytoscape
  • Know where to find relevant Cytoscape apps and tutorials
Introductions and Concepts Guided Tour of Cytoscape 10 Simple Rules... Network Visualization in Cytoscape Workflows Wrap up

Introductions

John "Scooter" Morris, UCSF
  • Executive director, Resource for Biocomputing, Visualization, and Informatics
  • Roving Engineer, National Resource for Network Biology
  • Cytoscape team since 2006
  • Author of over a dozen Cytoscape apps

Introductions

What about you?

  • Clinicians
  • Bench Biologists
  • Bioinformaticians
  • Computer Scientists
  • Chemists
  • Mathematicians
  • Other

Introductions

Prior Cytoscape or network analysis experience?

  • None -- that's what I'm here for!
  • Some network analysis, but what's Cytoscape?
  • I've played with Cytoscape, but still have a lot to learn.
  • I use Cytoscape all the time...
    (hey, I could probably teach this course!)
Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Analysis and Viz Hands-on Exercises Wrap up

Tour of Cytoscape


  1. Launch Cytoscape v3.7.0

Tour of Cytoscape


  1. Open CyBrowser
  2. Enter URL: tutorials.cytoscape.org

Tour of Cytoscape


  1. Click on Tour of Cytoscape
  2. Resize window to your preference

Tour of Cytoscape

Follow-along walkthrough:

  1. Loading networks
  2. Loading tables
  3. Selection and filtering
  4. Changing visual attributes
  5. Exporting images
  6. Saving sessions
Introductions and Concepts Guided Tour of Cytoscape 10 Simple Rules... Network Visualization in Cytoscape Workflows Wrap up
Introductions and Concepts Guided Tour of Cytoscape 10 Simple Rules... Network Visualization in Cytoscape Workflows Wrap up
Introductions and Concepts Guided Tour of Cytoscape 10 Simple Rules... Network Visualization in Cytoscape Workflows Wrap up

Workflows

The workflows are intended to be interactive and done mostly with Cytoscape directly

Transcriptomics Workflow

Sample data set: RCA.exp.547.med.txt: TCGA Breast Cancer expression data

Proteomics Workflow

Sample data set: JX_90min_prot.txt: Protein prospector output

Proteomics(PTM) Workflow

Introductions and Concepts Guided Tour of Cytoscape 10 Simple Rules... Network Visualization in Cytoscape Workflows Wrap up

Wrap up

Questions and Discussion

Thank You!

Here are additional resources you may find useful:

Thank You!




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