Data Visualization with Cytoscape

Slides:
https://cytoscape.github.io/cytoscape-tutorials/presentations/data-visualization-2019-ucsf.html

John "Scooter" Morris and Alex Pico

UCSF
19 February 2019

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 10 Simple Rules... Hands-on Custom Graphics Advanced Visualization and Challenges Visualizing Groups in Cytoscape 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 a dozen Cytoscape apps

Introductions

Alex Pico, Gladstone Institutes

Associate director, Bioinformatics Core
Executive director, National Resource for Network Biology
Cytoscape team since 2006
Author of half a dozen Cytoscape apps

Introductions

What about you?

Clinicians
Bench Biologists
Bioinformaticians
Computer Scientists
Chemists
Mathematicians
Other

Introductions

What are your network visualization challenges?

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

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

Hands-on Custom Graphics

Custom Graphics Protocol

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

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