Prince:Tools for Plotting Data

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(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)