knitr::knit_hooks$set(pngquant = knitr::hook_pngquant) knitr::opts_chunk$set( message = FALSE, collapse = TRUE, comment = "#>", dev = "ragg_png", dpi = 72, fig.retina = 2, fig.width = 10.6667, fig.height = 3.3334, fig.align = "center", out.width = "100%", pngquant = "--speed=1 --quality=50" )
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,
science fiction movies, and TV shows. The color palettes in ggsci
are available as ggplot2
scales. For all the color palettes,
the corresponding scales are named as:
scale_color_palname()
scale_fill_palname()
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()
| "nrc"
| pal_npg()
|
| | scale_fill_npg()
| | |
+-----------------+------------------------------+--------------------------------+----------------------+
| AAAS | scale_color_aaas()
| "default"
| pal_aaas()
|
| | scale_fill_aaas()
| | |
+-----------------+------------------------------+--------------------------------+----------------------+
| NEJM | scale_color_nejm()
| "default"
| pal_nejm()
|
| | scale_fill_nejm()
| | |
+-----------------+------------------------------+--------------------------------+----------------------+
| Lancet | scale_color_lancet()
| "lanonc"
| pal_lancet()
|
| | scale_fill_lancet()
| | |
+-----------------+------------------------------+--------------------------------+----------------------+
| JAMA | scale_color_jama()
| "default"
| pal_jama()
|
| | scale_fill_jama()
| | |
+-----------------+------------------------------+--------------------------------+----------------------+
| JCO | scale_color_jco()
| "default"
| pal_jco()
|
| | scale_fill_jco()
| | |
+-----------------+------------------------------+--------------------------------+----------------------+
| UCSCGB | scale_color_ucscgb()
| "default"
| pal_ucscgb()
|
| | scale_fill_ucscgb()
| | |
+-----------------+------------------------------+--------------------------------+----------------------+
| D3 | scale_color_d3()
| "category10"
| pal_d3()
|
| | scale_fill_d3()
| "category20"
| |
| | | "category20b"
| |
| | | "category20c"
| |
+-----------------+------------------------------+--------------------------------+----------------------+
| LocusZoom | scale_color_locuszoom()
| "default"
| pal_locuszoom()
|
| | scale_fill_locuszoom()
| | |
+-----------------+------------------------------+--------------------------------+----------------------+
| IGV | scale_color_igv()
| "default"
| pal_igv()
|
| | scale_fill_igv()
| "alternating"
| |
+-----------------+------------------------------+--------------------------------+----------------------+
| COSMIC | scale_color_cosmic()
| "hallmarks_light"
| pal_cosmic()
|
| | scale_fill_cosmic()
| "hallmarks_dark"
| |
| | | "signature_substitutions"
| |
+-----------------+------------------------------+--------------------------------+----------------------+
| UChicago | scale_color_uchicago()
| "default"
| pal_uchicago()
|
| | scale_fill_uchicago()
| "light"
| |
| | | "dark"
| |
+-----------------+------------------------------+--------------------------------+----------------------+
| Star Trek | scale_color_startrek()
| "uniform"
| pal_startrek()
|
| | scale_fill_startrek()
| | |
+-----------------+------------------------------+--------------------------------+----------------------+
| Tron Legacy | scale_color_tron()
| "legacy"
| pal_tron()
|
| | scale_fill_tron()
| | |
+-----------------+------------------------------+--------------------------------+----------------------+
| Futurama | scale_color_futurama()
| "planetexpress"
| pal_futurama()
|
| | scale_fill_futurama()
| | |
+-----------------+------------------------------+--------------------------------+----------------------+
| Rick and Morty | scale_color_rickandmorty()
| "schwifty"
| pal_rickandmorty()
|
| | scale_fill_rickandmorty()
| | |
+-----------------+------------------------------+--------------------------------+----------------------+
| The Simpsons | scale_color_simpsons()
| "springfield"
| pal_simpsons()
|
| | scale_fill_simpsons()
| | |
+-----------------+------------------------------+--------------------------------+----------------------+
| Flat UI | scale_color_flatui()
| "default"
| pal_flatui()
|
| | scale_fill_flatui()
| "flattastic"
| |
| | | "aussie"
| |
+-----------------+------------------------------+--------------------------------+----------------------+
| Frontiers | scale_color_frontiers()
| "default"
| pal_frontiers()
|
| | scale_fill_frontiers()
| | |
+-----------------+------------------------------+--------------------------------+----------------------+
| GSEA | scale_color_gsea()
| "default"
| pal_gsea()
|
| | scale_fill_gsea()
| | |
+-----------------+------------------------------+--------------------------------+----------------------+
| Material Design | scale_color_material()
| "red"
"pink"
| pal_material()
|
| | scale_fill_material()
| "purple"
"deep-purple"
| |
| | | "indigo"
"blue"
| |
| | | "light-blue"
"cyan"
| |
| | | "teal"
"green"
| |
| | | "light-green"
"lime"
| |
| | | "yellow"
"amber"
| |
| | | "orange"
"deep-orange"
| |
| | | "brown"
"grey"
| |
| | | "blue-grey"
| |
+-----------------+------------------------------+--------------------------------+----------------------+
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, linewidth = 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()
The NPG palette is inspired by the plots in the 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)
The AAAS palette is inspired by the plots in the 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)
The NEJM palette is inspired by the plots in the New England Journal of Medicine:
p1_nejm <- p1 + scale_color_nejm() p2_nejm <- p2 + scale_fill_nejm() grid.arrange(p1_nejm, p2_nejm, ncol = 2)
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)
The JAMA palette is inspired by the plots in the Journal of the American Medical Association:
p1_jama <- p1 + scale_color_jama() p2_jama <- p2 + scale_fill_jama() grid.arrange(p1_jama, p2_jama, ncol = 2)
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)
The UCSCGB palette is from the colors used by UCSC Genome Browser for representing chromosomes. This palette (interpolated, with alpha) is intensively used in visualizations generated by Circos.
p1_ucscgb <- p1 + scale_color_ucscgb() p2_ucscgb <- p2 + scale_fill_ucscgb() grid.arrange(p1_ucscgb, p2_ucscgb, ncol = 2)
The D3 palette is from the categorical colors used by
D3.js (version 3.x and before).
There are four palette types (category10
, category20
,
category20b
, category20c
) available.
p1_d3 <- p1 + scale_color_d3() p2_d3 <- p2 + scale_fill_d3() grid.arrange(p1_d3, p2_d3, ncol = 2)
The LocusZoom palette is based on the colors used by LocusZoom.
p1_locuszoom <- p1 + scale_color_locuszoom() p2_locuszoom <- p2 + scale_fill_locuszoom() grid.arrange(p1_locuszoom, p2_locuszoom, ncol = 2)
The IGV palette is from the colors used by
Integrative Genomics Viewer
for representing chromosomes. There are two palette types
(default
, alternating
) available.
p1_igv_default <- p1 + scale_color_igv() p2_igv_default <- p2 + scale_fill_igv() grid.arrange(p1_igv_default, p2_igv_default, ncol = 2)
Color palettes inspired by the colors used in projects from the Catalogue Of Somatic Mutations in Cancers (COSMIC).
p1_cosmic_hallmarks_light <- p1 + scale_color_cosmic("hallmarks_light") p2_cosmic_hallmarks_light <- p2 + scale_fill_cosmic("hallmarks_light") grid.arrange(p1_cosmic_hallmarks_light, p2_cosmic_hallmarks_light, ncol = 2)
p1_cosmic_hallmarks_dark <- p1 + scale_color_cosmic("hallmarks_dark") p2_cosmic_hallmarks_dark <- p2 + scale_fill_cosmic("hallmarks_dark") grid.arrange(p1_cosmic_hallmarks_dark, p2_cosmic_hallmarks_dark, ncol = 2)
p1_cosmic_signature <- p1 + scale_color_cosmic("signature_substitutions") p2_cosmic_signature <- p2 + scale_fill_cosmic("signature_substitutions") grid.arrange(p1_cosmic_signature, p2_cosmic_signature, ncol = 2)
The UChicago palette is based on
the colors
used by the University of Chicago.
There are three palette types (default
, light
, dark
) available.
p1_uchicago <- p1 + scale_color_uchicago() p2_uchicago <- p2 + scale_fill_uchicago() grid.arrange(p1_uchicago, p2_uchicago, ncol = 2)
This palette is inspired by the (uniform) colors in Star Trek:
p1_startrek <- p1 + scale_color_startrek() p2_startrek <- p2 + scale_fill_startrek() grid.arrange(p1_startrek, p2_startrek, ncol = 2)
This palette is inspired by the colors used in Tron Legacy. It is suitable for displaying data when using a dark theme:
p1_tron <- p1 + theme_dark() + theme( panel.background = element_rect(fill = "#2D2D2D"), legend.key = element_rect(fill = "#2D2D2D") ) + scale_color_tron() p2_tron <- p2 + theme_dark() + theme( panel.background = element_rect(fill = "#2D2D2D") ) + scale_fill_tron() grid.arrange(p1_tron, p2_tron, ncol = 2)
This palette is inspired by the colors used in the TV show Futurama:
p1_futurama <- p1 + scale_color_futurama() p2_futurama <- p2 + scale_fill_futurama() grid.arrange(p1_futurama, p2_futurama, ncol = 2)
This palette is inspired by the colors used in the TV show Rick and Morty:
p1_rickandmorty <- p1 + scale_color_rickandmorty() p2_rickandmorty <- p2 + scale_fill_rickandmorty() grid.arrange(p1_rickandmorty, p2_rickandmorty, ncol = 2)
This palette is inspired by the colors used in the TV show The Simpsons:
p1_simpsons <- p1 + scale_color_simpsons() p2_simpsons <- p2 + scale_fill_simpsons() grid.arrange(p1_simpsons, p2_simpsons, ncol = 2)
Three flat UI color palettes from Flat UI Colors 2:
p1_flatui <- p1 + scale_color_flatui() p2_flatui <- p2 + scale_fill_flatui() grid.arrange(p1_flatui, p2_flatui, ncol = 2)
This color palette inspired by Frontiers:
p1_frontiers <- p1 + scale_color_frontiers() p2_frontiers <- p2 + scale_fill_frontiers() grid.arrange(p1_frontiers, p2_frontiers, ncol = 2)
We will use a correlation matrix visualization (a special type of heatmap)
to demonstrate the continuous color palettes in ggsci
.
library("reshape2") data("mtcars") cor <- cor(unname(cbind(mtcars, mtcars, mtcars, mtcars))) cor_melt <- melt(cor) p3 <- ggplot( cor_melt, aes(x = Var1, y = Var2, fill = value) ) + geom_tile(colour = "black", linewidth = 0.3) + theme_void() + theme( axis.title.x = element_blank(), axis.title.y = element_blank() )
The GSEA palette (continuous) is inspired by the heatmaps generated by GSEA GenePattern.
p3_gsea <- p3 + scale_fill_gsea() p3_gsea_inv <- p3 + scale_fill_gsea(reverse = TRUE) grid.arrange(p3_gsea, p3_gsea_inv, ncol = 2)
The Material Design color palettes are from the Material Design color system.
We generate a random matrix first:
library("reshape2") set.seed(42) k <- 9 x <- diag(k) x[upper.tri(x)] <- runif(sum(1:(k - 1)), 0, 1) x_melt <- melt(x) p4 <- ggplot(x_melt, aes(x = Var1, y = Var2, fill = value)) + geom_tile(colour = "black", linewidth = 0.3) + scale_x_continuous(expand = c(0, 0)) + scale_y_continuous(expand = c(0, 0)) + theme_bw() + theme( legend.position = "none", plot.background = element_blank(), axis.line = element_blank(), axis.ticks = element_blank(), axis.text.x = element_blank(), axis.text.y = element_blank(), axis.title.x = element_blank(), axis.title.y = element_blank(), panel.background = element_blank(), panel.border = element_blank(), panel.grid.major = element_blank(), panel.grid.minor = element_blank() )
Plot the matrix with the 19 material design color palettes:
grid.arrange( p4 + scale_fill_material("red"), p4 + scale_fill_material("pink"), p4 + scale_fill_material("purple"), p4 + scale_fill_material("deep-purple"), p4 + scale_fill_material("indigo"), p4 + scale_fill_material("blue"), p4 + scale_fill_material("light-blue"), p4 + scale_fill_material("cyan"), p4 + scale_fill_material("teal"), p4 + scale_fill_material("green"), p4 + scale_fill_material("light-green"), p4 + scale_fill_material("lime"), p4 + scale_fill_material("yellow"), p4 + scale_fill_material("amber"), p4 + scale_fill_material("orange"), p4 + scale_fill_material("deep-orange"), p4 + scale_fill_material("brown"), p4 + scale_fill_material("grey"), p4 + scale_fill_material("blue-grey"), ncol = 6 )
From the figure above, we can see that even though an identical matrix was visualized by all plots, some palettes are more preferrable than the others because our eyes are more sensitive to the changes of their saturation levels.
To apply the color palettes in ggsci
to other graphics systems
(such as base graphics and lattice graphics), simply use the
palette generator functions in the table above. For example:
mypal <- pal_npg("nrc", alpha = 0.7)(9) mypal library("scales") show_col(mypal)
You will be able to use the generated hex color codes for such
graphics systems accordingly. The transparent level of the
entire palette is easily adjustable via the argument "alpha"
in every generator or scale function.
Please note some of the palettes might not be the best choice for certain purposes, such as color-blind safe, photocopy safe, or print friendly. If you do have such considerations, you might want to check out color palettes like ColorBrewer and viridis.
The color palettes in this package are solely created for research purposes. The authors are not responsible for the usage of such palettes.
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