Prince:Tools for Plotting Data

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(with an emphasis on example galleries and open source tools)

Simple-medium complexity plots

More complicated plots (especially multifactorial)

  • R
  • lattice multifactorial heaven
  • matplotlib very precise control of all plotting elements (you can use YAML to move data into it)

Organizing your data

  • Ruport (ruby reports) organize data into tabular form from almost any source (normal data, SQL tables, etc.)

Network Visualization

  • hive plots
  • gephi interactive network plotting (handles proteome scale interactions networks)
  • cytoscape
  • graphviz sfdp is okay for very large networks
  • lgl (someone needs to modernize it)