Bookmarks: R data visualization, ggplot2 plotting tips

Bookmarks for useful graphing tutorials in R. 

Types of plots possible with ggplot2

• "Be awesome in ggplot2" - a visually beautiful guide to see what is possible. Great to get ideas for data visualization.
  
  

Formatting in general

Themes available for ggplot2 graphs

• http://www.sthda.com/english/wiki/ggplot2-themes-and-background-colors-the-3-elements

Modifying color, font, text size in ggplot2

• http://www.sthda.com/english/wiki/ggplot2-title-main-axis-and-legend-titles

Creating custom themes for ggplot2

• https://rpubs.com/mclaire19/ggplot2-custom-themes

Add subscripts, Greek letters, and other special characters to graph legends

Useful to add subscripts in axes, e.g. log₁₀(FDR)

• https://rstudio-pubs-static.s3.amazonaws.com/136237_170402e5f0b54561bf7605bdea98267a.html

Adding annotations to plots

• annotate() function examples to add text at specific x,y locations, gray boxes
• Adding text with partial bolding to the string
• Alternative to main and sub variables in plot() - use mtext() to add text

Color palettes and gradients:

• The guide to gradients in R and ggplot2 including plot background gradients
• R color palettes [497 continuous]
• Top R Color Palettes to Know for Great Data Visualization

Formatting x- and y-axes

• Pretty axis breaks: https://bookdown.org/Maxine/ggplot2-maps/posts/2019-11-27-using-scales-package-to-modify-ggplot2-scale/
• Log transformations: https://www.datanovia.com/en/blog/ggplot-log-scale-transformation/

geom_tile() for matrix data - heatmap

Fix label spacing in ggplot2 with ggrepel -- install.packages("ggrepel")
Use the R package, ggrepel, to add point label text that doesn't overlap.
Use functions ggrepel::geom_label_repel for boxed labels
Use function ggrepel::geom_text_repel for just text, no background

Ideas with ggrepel:
https://stackoverflow.com/questions/15624656/label-points-in-geom-point

Make an animated gif to better see point labels, with ggrepel:
https://mran.microsoft.com/snapshot/2017-02-28/web/packages/ggrepel/vignettes/ggrepel.html

Making a color gradient to label points, and formatting the legend
https://stackoverflow.com/questions/24265652/label-minimum-and-maximum-of-scale-fill-gradient-legend-with-text-ggplot2

Color code outliers in a box and whisker plot by a specific variable

• https://stackoverflow.com/questions/57614343/geom-boxplot-how-to-specifically-color-only-outliers-based-on-group-and-keep-ev
  
  

Fix for long axis titles that run into each other: scale_x_discrete(guide = guide_axis(n.dodge = 2))

Formatting legends

• Horizontal discrete legends with text on the top or bottom
• ggplot2 legend : Easy steps to change the position and the appearance

Heatmaps

• Heatmap demystified (Ming Tang)
• Understand how to scale data in heatmaps (Ming Tang, "A Tale of Two Heatmaps")
• Triple (three) heatmaps in one figure: once center (XY) and other two at X and Y axis directions (U. R. Bhabuk)

Combining figures

Marginal plots: add histograms or boxplots around the axes to add summarized data

• https://www.r-graph-gallery.com/277-marginal-histogram-for-ggplot2.html
• https://stackoverflow.com/questions/47446458/ggextra-plot-format-similar-marginal-plots-for-different-plot-dimensions
• "Marginal rugs" to scatter plots
• Add density plots for each axis with gridExtra

Cowplot R package

• "Using cowplot to construct multi-panel figures entirely via code"

Making pdf files

• Compile png images into pdf files: https://jonkimanalyze.wordpress.com/2014/07/24/r-compile-png-files-into-pdf/
• Combine, split, extract pages from pdf files: https://www.r-bloggers.com/2019/04/join-split-and-compress-pdf-files-with-pdftools/

Interactive figures

• Interactive charts overview with ggplotly and ggplot2 - in R
• Similar overview - in Python
• Question about saving multiple html widgets together
• Different packages for interactive figures and tables

RMarkdown guide

• How to set up a table of contents
• Change how dataframes print
• RMarkdown themes

Ongoing bookmarks. Last edited Aug 4, 2022