ggplot2

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 (usually need to be prettied up in inkscape/illustrator)