README.md

In JLSteenwyk/ggpubfigs: ggpubfigs

ggpubfigs is a ggplot2 extension that helps create publication ready figures for the life sciences. Importantly, ggpubfigs implements themes and color palettes that are both aesthetically pleasing and colorblind friendly.

If you found ggpubfigs helpful, please cite: ggpubfigs: Colorblind-Friendly Color Palettes and ggplot2 Graphic System Extensions for Publication-Quality Scientific Figures. DOI: 10.1128/MRA.00871-21

Guide

Install Quick Start Color palettes Table of Hex Codes Themes FAQ Acknowledgements

Install

# execute this command only the first time you use ggpubfigs
devtools::install_github("JLSteenwyk/ggpubfigs")
# load ggpubfigs
library(ggpubfigs)

Quick Start

These quick start examples demonstrate how to implement two aesthetically pleasing themes and color palettes.

# using the "ito_seven" color palette and theme_big_simple()
ggplot(mtcars, aes(factor(carb), fill=factor(cyl))) + geom_bar() + scale_fill_manual(values = friendly_pal("ito_seven")) + theme_big_simple()

# using the "bright_seven" color palette and theme_big_grid()
ggplot(mtcars, aes(factor(carb), fill=factor(cyl))) + geom_bar() + scale_fill_manual(values = friendly_pal("bright_seven")) + theme_big_grid()

Color palettes

Color palettes are all colorblind friendly. Thus, your figures will be accessible to more people, which is inarguably better for your audience and you. Color palettes are named using the following scheme: identifier (underscore) number of colors in color palette.

To use these colorblind friendly color palettes, use the following command as an example for both discrete and continuous purposes:

ggplot(mtcars, aes(factor(carb), fill=factor(cyl))) + geom_bar() + scale_fill_manual(values = friendly_pal("contrast_three"))

pal <- friendly_pal("contrast_three", 50, type = "continuous")
image(volcano, col = pal)

Table of Hex Codes

| Palettes | Colors used | | -------------- | ------------------------------------------------------------------------------- | | bright_seven | #4477AA, #228833, #AA3377, #BBBBBB, #66CCEE, #CCBB44, #EE6677 | | contrast_three | #004488, #BB5566, #DDAA33 | | vibrant_seven | #0077BB, #EE7733, #33BBEE, #CC3311, #009988, #EE3377, #BBBBBB | | muted_nine | #332288, #117733, #CC6677, #88CCEE, #999933, #882255, #44AA99, #DDCC77, #AA4499 | | nickel_five | #648FFF, #FE6100, #785EF0, #FFB000, #DC267F | | ito_seven | #0072B2, #D55E00, #009E73, #CC79A7, #56B4E9, #E69F00, #F0E442 | | ibm_five | #648FFF, #785EF0, #DC267F, #FE6100, #FFB000 | | wong_eight | #E69F00, #56B4E9, #009E73, #F0E442, #0072B2, #D55E00, #CC79A7, #000000 | | tol_eight | #332288, #117733, #44AA99, #88CCEE, #DDCC77, #CC6677, #AA4499, #882255 | | zesty_four | #F5793A, #A95AA1, #85C0F9, #0F2080 | | retro_four | #601A4A, #EE442F, #63ACBE, #F9F4EC |

Themes

Publication-ready figures

theme_grid()

ggplot(iris, aes(Sepal.Length, Petal.Width, color = Species)) + geom_point() + theme_grid()

ggplot(iris, aes(Sepal.Length, fill = Species)) + geom_histogram() + theme_grid()

theme_big_grid()

ggplot(iris, aes(Sepal.Length, Petal.Width, color = Species)) + geom_point() + theme_big_grid()

ggplot(iris, aes(Sepal.Length, fill = Species)) + geom_histogram() + theme_big_grid()

theme_simple()

ggplot(iris, aes(Sepal.Length, Petal.Width, color = Species)) + geom_point() + theme_simple()

ggplot(iris, aes(Sepal.Length, fill = Species)) + geom_histogram() + theme_simple()

theme_big_simple()

ggplot(iris, aes(Sepal.Length, Petal.Width, color = Species)) + geom_point() + theme_big_simple()

ggplot(iris, aes(Sepal.Length, fill = Species)) + geom_histogram() + theme_big_simple()

theme_grey()

ggplot(iris, aes(Sepal.Length, Petal.Width, color = Species)) + geom_point() + theme_grey()

ggplot(iris, aes(Sepal.Length, fill = Species)) + geom_histogram() + theme_grey()

Presentation-ready figures

theme_black()

ggplot(iris, aes(Sepal.Length, Petal.Width, color = Species)) + geom_point() + theme_black()

ggplot(iris, aes(Sepal.Length, fill = Species)) + geom_histogram() + theme_black()

theme_blue()

ggplot(iris, aes(Sepal.Length, Petal.Width, color = Species)) + geom_point() + theme_blue()

ggplot(iris, aes(Sepal.Length, fill = Species)) + geom_histogram() + theme_blue()

theme_red()

ggplot(iris, aes(Sepal.Length, Petal.Width, color = Species)) + geom_point() + theme_red()

ggplot(iris, aes(Sepal.Length, fill = Species)) + geom_histogram() + theme_red()

FAQ

Can I submit color palettes or themes to be incorporated into ggpubfigs? Yes! Submissions are encouraged, please feel free to contact me via twitter or from my contact information.

Acknowledgements

I would like to thank the blooming R community for all the very helpful online forums, discussions, and open source books that have helped me learn R. I would also like to acknowledge that some of the example usage and color palette code was developed based on open source code from the wes anderson color palette package.

JLSteenwyk/ggpubfigs documentation built on Dec. 9, 2024, 10:29 a.m.