Scientific Journal and Sci-Fi Themed ColorPalettes for ggplot2
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 bycolors used in scientific journals, data visualization libraries,science fiction movies, and TV shows. The color palettes in ggsci areavailable as ggplot2 scales. For all the color palettes, thecorresponding scales are named as:
scale_color_palname()scale_fill_palname()
We also provided aliases, such asscale_colour_palname()forscale_color_palname(). All available color palettes aresummarized 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() |
| NEJM | scale_color_nejm()scale_fill_nejm() | "default" | pal_nejm() |
| Lancet | scale_color_lancet()scale_fill_lancet() | "lanonc" | pal_lancet() |
| JAMA | scale_color_jama()scale_fill_jama() | "default" | pal_jama() |
| BMJ | scale_color_bmj()scale_fill_bmj() | "default" | pal_bmj() |
| 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() |
| Observable | scale_color_observable()scale_fill_observable() | "observable10" | pal_observable() |
| Primer | scale_color_primer()scale_fill_primer() | "mark17" | pal_primer() |
| Atlassian | scale_color_atlassian()scale_fill_atlassian() | "categorical8" | pal_atlassian() |
| iTerm | scale_color_iterm()scale_fill_iterm() | iterm_palettes() | pal_iterm() |
| LocusZoom | scale_color_locuszoom()scale_fill_locuszoom() | "default" | pal_locuszoom() |
| IGV | scale_color_igv()scale_fill_igv() | "default""alternating" | pal_igv() |
| COSMIC | scale_color_cosmic()scale_fill_cosmic() | "hallmarks_light""hallmarks_dark""signature_substitutions" | pal_cosmic() |
| UChicago | scale_color_uchicago()scale_fill_uchicago() | "default""light""dark" | pal_uchicago() |
| Star Trek | scale_color_startrek()scale_fill_startrek() | "uniform" | pal_startrek() |
| Tron Legacy | scale_color_tron()scale_fill_tron() | "legacy" | pal_tron() |
| Futurama | scale_color_futurama()scale_fill_futurama() | "planetexpress" | pal_futurama() |
| Rick and Morty | scale_color_rickandmorty()scale_fill_rickandmorty() | "schwifty" | pal_rickandmorty() |
| The Simpsons | scale_color_simpsons()scale_fill_simpsons() | "springfield" | pal_simpsons() |
| Flat UI | scale_color_flatui()scale_fill_flatui() | "default""flattastic""aussie" | pal_flatui() |
| Frontiers | scale_color_frontiers()scale_fill_frontiers() | "default" | pal_frontiers() |
| GSEA | scale_color_gsea()scale_fill_gsea() | "default" | pal_gsea() |
| Bootstrap 5 | scale_color_bs5()scale_fill_bs5() | "blue""indigo""purple""pink""red""orange""yellow""green""teal""cyan""gray" | pal_bs5() |
| Material Design | scale_color_material()scale_fill_material() | "red""pink""purple""deep-purple""indigo""blue""light-blue""cyan""teal""green""light-green""lime""yellow""amber""orange""deep-orange""brown""grey""blue-grey" | pal_material() |
| Tailwind CSS | scale_color_tw3()scale_fill_tw3() | "slate""gray""zinc""neutral""stone""red""orange""amber""yellow""lime""green""emerald""teal""cyan""sky""blue""indigo""violet""purple""fuchsia""pink""rose" | pal_tw3() |
Discrete color palettes
We will use scatterplots with smooth curves, and bar plots todemonstrate the discrete color palettes in ggsci.
library("ggsci")library("ggplot2")library("gridExtra")p1 <- example_scatterplot()p2 <- example_barplot()NPG
The NPG palette is inspired by the plots in the journals published byNature Publishing Group:
p1_npg <- p1 + scale_color_npg()p2_npg <- p2 + scale_fill_npg()grid.arrange(p1_npg, p2_npg, ncol = 2)AAAS
The AAAS palette is inspired by the plots in the journals publishedby 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)NEJM
The NEJM palette is inspired by the plots in theNew EnglandJournal of Medicine:
p1_nejm <- p1 + scale_color_nejm()p2_nejm <- p2 + scale_fill_nejm()grid.arrange(p1_nejm, p2_nejm, ncol = 2)Lancet
The Lancet palette is inspired by the plots inLancetjournals, such asLancet Oncology:
p1_lancet <- p1 + scale_color_lancet()p2_lancet <- p2 + scale_fill_lancet()grid.arrange(p1_lancet, p2_lancet, ncol = 2)JAMA
The JAMA palette is inspired by the plots in theJournal of theAmerican Medical Association:
p1_jama <- p1 + scale_color_jama()p2_jama <- p2 + scale_fill_jama()grid.arrange(p1_jama, p2_jama, ncol = 2)BMJ
The BMJ palette is from theBMJliving style guide:
p1_bmj <- p1 + scale_color_bmj()p2_bmj <- p2 + scale_fill_bmj()grid.arrange(p1_bmj, p2_bmj, ncol = 2)JCO
The JCO palette is inspired by the the plots inJournal ofClinical Oncology:
p1_jco <- p1 + scale_color_jco()p2_jco <- p2 + scale_fill_jco()grid.arrange(p1_jco, p2_jco, ncol = 2)UCSCGB
The UCSCGB palette is from the colors used byUCSC Genome Browser for representingchromosomes. This palette (interpolated, with alpha) is intensively usedin visualizations generated by Circos.
p1_ucscgb <- p1 + scale_color_ucscgb()p2_ucscgb <- p2 + scale_fill_ucscgb()grid.arrange(p1_ucscgb, p2_ucscgb, ncol = 2)D3
The D3 palette is from the categorical colors used byD3.js (version 3.x and before). There arefour 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)Observable
TheObservable 10palette is the default categorical colors scheme used byObservable.
p1_observable <- p1 + scale_color_observable()p2_observable <- p2 + scale_fill_observable()grid.arrange(p1_observable, p2_observable, ncol = 2)Primer
The Primer palette follows the data visualization colors fromGitHub’sPrimer design system.
p1_primer <- p1 + scale_color_primer()p2_primer <- p2 + scale_fill_primer()grid.arrange(p1_primer, p2_primer, ncol = 2)Atlassian
The palette follows the categorical chart colors fromAtlassianDesign System.
p1_atlassian <- p1 + scale_color_atlassian()p2_atlassian <- p2 + scale_fill_atlassian()grid.arrange(p1_atlassian, p2_atlassian, ncol = 2)iTerm
These palettes are sourced from the iterm2-color-schemes project,which includes 400+ color schemes (list them withiterm_palettes()). Each scheme provides six categoricalcolors with two possible variants:"normal" and"bright".
You can preview these color palettes in ggsci on a dedicatedmicrosite:https://nanx.me/ggsci-iterm/. It renders example plotsfor all palettes on a single page for fast visual comparison.
p1_iterm <- p1 + scale_color_iterm("Rose Pine")p2_iterm <- p2 + scale_fill_iterm("Rose Pine")grid.arrange(p1_iterm, p2_iterm, ncol = 2)LocusZoom
The LocusZoom palette is based on the colors used byLocusZoom.
p1_locuszoom <- p1 + scale_color_locuszoom()p2_locuszoom <- p2 + scale_fill_locuszoom()grid.arrange(p1_locuszoom, p2_locuszoom, ncol = 2)IGV
The IGV palette is from the colors used byIntegrative Genomics Viewer forrepresenting 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)COSMIC
Color palettes inspired by the colors used in projects from theCatalogue Of Somatic Mutationsin 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)UChicago
The UChicago palette is based onthecolors used by the University of Chicago. There are three palettetypes (default,light,dark)available.
p1_uchicago <- p1 + scale_color_uchicago()p2_uchicago <- p2 + scale_fill_uchicago()grid.arrange(p1_uchicago, p2_uchicago, ncol = 2)Star Trek
This palette is inspired by the (uniform) colors inStarTrek:
p1_startrek <- p1 + scale_color_startrek()p2_startrek <- p2 + scale_fill_startrek()grid.arrange(p1_startrek, p2_startrek, ncol = 2)Tron Legacy
This palette is inspired by the colors used inTron 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)Futurama
This palette is inspired by the colors used in the TV showFuturama:
p1_futurama <- p1 + scale_color_futurama()p2_futurama <- p2 + scale_fill_futurama()grid.arrange(p1_futurama, p2_futurama, ncol = 2)Rick and Morty
This palette is inspired by the colors used in the TV showRickand Morty:
p1_rickandmorty <- p1 + scale_color_rickandmorty()p2_rickandmorty <- p2 + scale_fill_rickandmorty()grid.arrange(p1_rickandmorty, p2_rickandmorty, ncol = 2)The Simpsons
This palette is inspired by the colors used in the TV showTheSimpsons:
p1_simpsons <- p1 + scale_color_simpsons()p2_simpsons <- p2 + scale_fill_simpsons()grid.arrange(p1_simpsons, p2_simpsons, ncol = 2)Flat UI
Three flat UI color palettes fromFlat UI Colors 2:
p1_flatui <- p1 + scale_color_flatui()p2_flatui <- p2 + scale_fill_flatui()grid.arrange(p1_flatui, p2_flatui, ncol = 2)Frontiers
This color palette inspired byFrontiers:
p1_frontiers <- p1 + scale_color_frontiers()p2_frontiers <- p2 + scale_fill_frontiers()grid.arrange(p1_frontiers, p2_frontiers, ncol = 2)Continuous color palettes
There are two types of continuous color palettes in ggsci: divergingand sequential. Diverging palettes have a central neutral color andcontrasting colors at the ends, making them suitable for visualizingdata with a natural midpoint. Sequential palettes use a gradient ofcolors that range from low to high intensity or lightness, making themideal for representing data with increasing or decreasing values.
We will use a correlation matrix visualization (a special type ofheatmap) to demonstrate the diverging color palettes.
data("mtcars")cor <- cor(unname(mtcars))cor_melt <- data.frame( Var1 = rep(seq_len(nrow(cor)), times = ncol(cor)), Var2 = rep(seq_len(ncol(cor)), each = nrow(cor)), value = as.vector(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() )To demonstrate sequential palettes, we use a random matrix:
set.seed(42)k <- 6x <- diag(k)x[upper.tri(x)] <- runif(sum(1:(k - 1)), 0, 1)x_melt <- data.frame( Var1 = rep(seq_len(nrow(x)), times = ncol(x)), Var2 = rep(seq_len(ncol(x)), each = nrow(x)), value = as.vector(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() )GSEA
The GSEA palette (continuous) is inspired by the heatmaps generatedbyGSEAGenePattern.
p3_gsea <- p3 + scale_fill_gsea()p3_gsea_inv <- p3 + scale_fill_gsea(reverse = TRUE)grid.arrange(p3_gsea, p3_gsea_inv, ncol = 2)Bootstrap 5
The Bootstrap 5 color palettes are from theBootstrap5 color system.
grid.arrange( p4 + scale_fill_bs5("blue"), p4 + scale_fill_bs5("indigo"), p4 + scale_fill_bs5("purple"), p4 + scale_fill_bs5("pink"), p4 + scale_fill_bs5("red"), p4 + scale_fill_bs5("orange"), p4 + scale_fill_bs5("yellow"), p4 + scale_fill_bs5("green"), p4 + scale_fill_bs5("teal"), p4 + scale_fill_bs5("cyan"), p4 + scale_fill_bs5("gray"), ncol = 8)Material Design
The Material Design color palettes are from theMaterialDesign color system.
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 = 8)Tailwind CSS
The Tailwind CSS color palettes are from theTailwind defaultcolors.
grid.arrange( p4 + scale_fill_tw3("slate"), p4 + scale_fill_tw3("gray"), p4 + scale_fill_tw3("zinc"), p4 + scale_fill_tw3("neutral"), p4 + scale_fill_tw3("stone"), p4 + scale_fill_tw3("red"), p4 + scale_fill_tw3("orange"), p4 + scale_fill_tw3("amber"), p4 + scale_fill_tw3("yellow"), p4 + scale_fill_tw3("lime"), p4 + scale_fill_tw3("green"), p4 + scale_fill_tw3("emerald"), p4 + scale_fill_tw3("teal"), p4 + scale_fill_tw3("cyan"), p4 + scale_fill_tw3("sky"), p4 + scale_fill_tw3("blue"), p4 + scale_fill_tw3("indigo"), p4 + scale_fill_tw3("violet"), p4 + scale_fill_tw3("purple"), p4 + scale_fill_tw3("fuchsia"), p4 + scale_fill_tw3("pink"), p4 + scale_fill_tw3("rose"), ncol = 8)From the figure above, we can see that even though an identicalmatrix was visualized by all plots, some palettes are more preferablethan the others because our eyes are more sensitive to the changes oftheir saturation levels.
Non-ggplot2 graphics
To apply the color palettes in ggsci to other graphics systems (suchas base graphics and lattice graphics), simply use the palette generatorfunctions in the table above. For example:
mypal <- pal_npg("nrc", alpha = 0.7)(9)mypal#> [1] "#E64B35B2" "#4DBBD5B2" "#00A087B2" "#3C5488B2" "#F39B7FB2" "#8491B4B2"#> [7] "#91D1C2B2" "#DC0000B2" "#7E6148B2"scales::show_col(mypal)You will be able to use the generated hex color codes for suchgraphics systems accordingly. The transparent level of the entirepalette is easily adjustable via the argument"alpha" inevery generator or scale function.
Discussion
Please note some of the palettes might not be the best choice forcertain purposes, such as color-blind safe, photocopy safe, or printfriendly. If you do have such considerations, you might want to checkout color palettes likeColorBrewer andviridis.
The color palettes in this package are solely created for researchpurposes. The authors are not responsible for the usage of suchpalettes.