Data Visualization
with Cytoscape

Slides: http://tutorials.cytoscape.org


John "Scooter" Morris and Alex Pico

UCSF
09 March 2023

Goals and Motivations

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

  • 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 Advanced Visualization and Challenges Visualizing Groups in Cytoscape Hands-on Custom Graphics 10 Simple Rules... Your Visualization Challenges

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 30 Cytoscape apps

Introductions

Alex Pico, Gladstone Institutes
  • Director, Bioinformatics Core
  • Executive director, National Resource for Network Biology
  • Cytoscape team since 2006
  • Author of over a dozen Cytoscape apps

Introductions

Introductions

What are your network visualization challenges?

Introductions Advanced Visualization and Challenges Visualizing Groups in Cytoscape Hands-on Custom Graphics 10 Simple Rules... Your Visualization Challenges
Introductions Advanced Visualization and Challenges Visualizing Groups in Cytoscape Hands-on Custom Graphics 10 Simple Rules... Your Visualization Challenges
Introductions Advanced Visualization and Challenges Visualizing Groups in Cytoscape Hands-on Custom Graphics 10 Simple Rules... Your Visualization Challenges

Hands-on Custom Graphics

Custom Graphics Protocol
Introductions Advanced Visualization and Challenges Visualizing Groups in Cytoscape Hands-on Custom Graphics 10 Simple Rules... Your Visualization Challenges
Introductions Advanced Visualization and Challenges Visualizing Groups in Cytoscape Hands-on Custom Graphics 10 Simple Rules... Your Visualization Challenges

Visualization Challenges

Use these datasets or your own dataset to try out what you've learned!

Transcriptomics Dataset

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

Proteomics Dataset

Sample data set: JX_90min_prot.txt: Protein prospector output

Thank You!

Here are additional resources you may find useful:

Thank You!




surveymonkey.com/r/cytoscape