Prince:Tools for Plotting Data

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

Simple-medium complexity plots

 * gruff graphs (ruby) uses rmagick to produce svg plots. (gem install gruff)
 * ruby gnuplot (gem install gnuplot)
 * gnuplot

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)