Scientific Journal and Sci-Fi Themed Color Palettes for ggplot2

Nan Xiao <http://nanx.me>
Miaozhu Li <http://miaozhu.li>

2016-11-20

1 Introduction

My eyes were finally opened and I understood nature.

I learned at the same time to love it.

— Claude Monet

ggsci offers a collection of high-quality color palettes inspired by colors used in scientific journals, data visualization libraries, and science fiction TV shows. The color palettes in ggsci are available as ggplot2 scales. For all the color palettes, the corresponding scales are named as:

We also provided aliases, such as scale_colour_palname() for scale_color_palname(). All available color palettes are summarized in the table below.

Name Scales Palette Types Palette Generator

NPG

scale_color_npg() scale_fill_npg()

"nrc"

pal_npg()

AAAS

scale_color_aaas() scale_fill_aaas()

"default"

pal_aaas()

Lancet

scale_color_lancet() scale_fill_lancet()

"lanonc"

pal_lancet()

JCO

scale_color_jco() scale_fill_jco()

"default"

pal_jco()

UCSCGB

scale_color_ucscgb() scale_fill_ucscgb()

"default"

pal_ucscgb()

D3

scale_color_d3()
scale_fill_d3()

"category10" "category20" "category20b" "category20c"

pal_d3()

UChicago

scale_color_uchicago() scale_fill_uchicago()

"default"
"light"
"dark"

pal_uchicago()

The Simpsons

scale_color_simpsons() scale_fill_simpsons()

"springfield"

pal_simpsons()

Futurama

scale_color_futurama() scale_fill_futurama()

"planetexpress"

pal_futurama()

Rick and Morty

scale_color_rickandmorty() scale_fill_rickandmorty()

"schwifty"

pal_rickandmorty()

GSEA

scale_color_gsea() scale_fill_gsea()

"default"

pal_gsea()

2 Discrete Color Palettes

We will use scatterplots with smooth curves, and bar plots to demonstrate the discrete color palettes in ggsci.

library("ggsci")
library("ggplot2")
library("gridExtra")

data("diamonds")

p1 = ggplot(subset(diamonds, carat >= 2.2),
       aes(x = table, y = price, colour = cut)) +
  geom_point(alpha = 0.7) +
  geom_smooth(method = "loess", alpha = 0.05, size = 1, span = 1) +
  theme_bw()

p2 = ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70), 
       aes(x = depth, fill = cut)) +
  geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
  theme_bw()

2.1 NPG

The NPG palette is inspired by the plots in journals published by Nature Publishing Group:

p1_npg = p1 + scale_color_npg()
p2_npg = p2 + scale_fill_npg()
grid.arrange(p1_npg, p2_npg, ncol = 2)

2.2 AAAS

The AAAS palette is inspired by the plots in journals published by American Association for the Advancement of Science:

p1_aaas = p1 + scale_color_aaas()
p2_aaas = p2 + scale_fill_aaas()
grid.arrange(p1_aaas, p2_aaas, ncol = 2)

2.3 Lancet

The Lancet palette is inspired by the plots in Lancet journals, such as Lancet Oncology:

p1_lancet = p1 + scale_color_lancet()
p2_lancet = p2 + scale_fill_lancet()
grid.arrange(p1_lancet, p2_lancet, ncol = 2)

2.4 JCO

The JCO palette is inspired by the the plots in Journal of Clinical Oncology:

p1_jco = p1 + scale_color_jco()
p2_jco = p2 + scale_fill_jco()
grid.arrange(p1_jco, p2_jco, ncol = 2)

2.5 UCSCGB

The UCSCGB palette is from the colors used by UCSC Genome Browser for representing chromosomes. This palette has been intensively used in visualizations produced by Circos.

p1_ucscgb = p1 + scale_color_ucscgb()
p2_ucscgb = p2 + scale_fill_ucscgb()
grid.arrange(p1_ucscgb, p2_ucscgb, ncol = 2)