ggplot2 Visualization

General thoughts on visualizing data

• Visualizing Data from Data Carpentry ⚠️
• Michael Deutsch Real-life Data Visualization

• http://gapminder.org

  GapMinder World

  GapMinderDev

  Hans Rosling TED Talk

• The Grammar of Graphics by Leland Wilkinson ⚠️

ggplot2

• ggplot2 Tutorial by Jenny Bryan
  • Jenny Bryan’s Graph Things
  • Graph Dos and Don’ts ⚠️

• bar charts

  position_dodge

  Layout panels in grid

ggplot2 examples

• Sarah Stevens plot | [ code ⚠️
• Graphics by Examples ⚠️: boxplot ⚠️

Interactive graphics

• plotly

  Plotly Book (Casper Sievert) ⚠️

• ggvis ⚠️)

• D3 HeatMap

  Shiny D3 Heatmap ⚠️

Multiple plots

• cowplot

  plots on grid ⚠️

• cowplot, gridExtra & Viewport tutorial
• GGally
• grid viewports
• ggplot2 workarounds
  • Mixing ggplot2 graphs with other graphical output
  • Editing raw grid objects from a ggplot

color palletes (particularly color blind)

• ColorBrewer

  scale_color_brewer() ⚠️

  Brewer Palettes Swatches ⚠️

• ggsci (several color pallettes modeled after NPG, AAAS, etc. Also includes two themes for Rick & Morty as well as The Simpsons)
• viridis (another set of color schemes that are logically selected to be color-blind friendly and have an even transition between colors.)

Other gg packages

• ggalt

• ggtree ⚠️

  ggdendro

• ggExtra
• vcfR

Heatmaps

• pretty heatmaps with pheatmap
• Gplots and heatmap.2 for heatmaps

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Dynamic & Scientific Graphics References

Visualization is the key to quick insights with data:

• Interactive Frameworks & D3:
  • d3: Data-Driven Documents
  • Interactive Graphics With D3 (Karl Broman) ⚠️
  • D3 Graphics Gallery & Tutorials
• Effective Presentation Principles:
  • How to Display Data Badly & Top 10 Worst Graphs (Karl Broman) ⚠️
  • Edward Tufte: Visual Explanations
  • Six Simple Techniques for Presenting Data (Hans Rosling)
• Biological & Network Visualization Tools:
  • Circos Circular Visualization ⚠️
  • Cytoscape Network Visualizer
  • igraph R Library