Creating color palettes in R (2024)

There are several color palettes available in R such as rainbow(), heat.colors(), terrain.colors(), and topo.colors(). We can visualize these as 3D pie chartsusing theplotrix R package.

# Let's create a pie chart with n=7 colors using each palettelibrary(plotrix)sliceValues <- rep(10, 7) # each slice value=10 for proportionate slicespie3D(sliceValues,explode=0, theta=1.2, col=rainbow(n=7), main="rainbow()")# Let's create a figure with all 4 base color palettespar(mfrow=c(1, 4))pie3D(sliceValues,explode=0, theta=1.2, col=rainbow(n=7), main="rainbow()")pie3D(sliceValues,explode=0, theta=1.2, col=heat.colors(n=7), main="heat.colors()")pie3D(sliceValues,explode=0, theta=1.2, col=terrain.colors(n=7), main="terrain.colors()")pie3D(sliceValues,explode=0, theta=1.2, col=topo.colors(n=7), main="topo.colors()")

Other popular color palettes include the RColorBrewerpackage that has a variety of sequential, divergent andqualitative palettes and the wesandersonpackage that has color palettes derived from his films.

library(RColorBrewer)# To see all palettes available in this packagepar(mfrow=c(1, 1))display.brewer.all()# To create pie charts from a sequential, divergent and qualitative RColorBrewer palettepar(mfrow=c(1, 4))pie3D(sliceValues,explode=0, theta=1.2, col=brewer.pal(7, "RdPu"), main="Sequential RdPu")pie3D(sliceValues,explode=0, theta=1.2, col=brewer.pal(7, "RdGy"), main="Divergent RdGy")pie3D(sliceValues,explode=0, theta=1.2, col=brewer.pal(7, "Set1"), main="Qualitative Set1")# And add pie chart with a wes_anderson palette# we will only use 5 slices in the example since the Darjeeling palette only has 5 colorslibrary(wesanderson)pie3D(sliceValues[1:5],explode=0, theta=1.2, col=wes_palette("Darjeeling2"), main="Darjeeling2")

You can also create your own color palettes in Rwith your colors of choice with thecolors() function or creating a vector with the color names.A great review and cheat sheet for R colors can be found athttp://research.stowers-institute.org/efg/R/Color/Chart/.

# To get an idea of the colors availablehead(colors())length(colors()) # 657# To see all 657 colors as a color chart you can source the R script to generate a pdf version in your working directory

# We can create choose a palette based on the R chart as follow:mycols <- colors()[c(8, 5, 30, 53, 118, 72)] ## or you could enter the color names directly# mycols <- c("aquamarine", "antiquewhite2", "blue4", "chocolate1", "deeppink2", "cyan4")# You could also get and store all distinct colors in the cl object and use the sample function to select colors at randomcl <- colors(distinct = TRUE)set.seed(15887) # to set random generator seedmycols2 <- sample(cl, 7)

You can also create color palettes with hex color codes.A great example of this is to work with popular color palettes available on the http://www.colorcombos.comwebsite. This website has various palettes you can choose from and even derivecolor palettes from your favorite websites. For example, let’s grabthe color palette from the rjbioinformatics.com website athttp://www.colorcombos.com/grabcolors.html.

After entering the URL of ourwebsite, wewillreceive thehex codes for thecolorscheme used onthe website.

We can even export the colors as little pencils

You can also choose from hundred of color schemes based on yourcolor of choice. For example, we will also create a color palette based onthe color olive – ColorCombo382.

# For the rjbioinformatics.com color palettemycols3 <- c("#c6d4e1", "#2f2016", "#fcfaea", "#456789")# For ColorCombos382 palettemycols4 <- c("#C3D938", "#772877", "#7C821E", "#D8B98B", "#7A4012")# Now to get the pie charts for the last four palettespie3D(sliceValues,explode=0, theta=1.2, col=mycols, main="colors()")pie3D(sliceValues,explode=0, theta=1.2, col=mycols2, main="sample(colors(distinct=TRUE)")pie3D(sliceValues[1:4],explode=0, theta=1.2, col=mycols3, main="rjbioinformatics.com color grab")pie3D(sliceValues[1:5],explode=0, theta=1.2, col=mycols4, main="ColorCombos382 colorcombos.com")

We can also create a color palette with the colorRampPalette() to use for heatmaps and other plots.Forthis example, we will use the leukemia dataset available in the GSVAdata package, which corresponds to microarray data from 37 human acute leukemias where 20 of these cases are Acute lymphoblastic leukemia (ALL) and the other 17 are ALL’s with Mixed leukemia gene rearrangements. For more information on the study please seeArmstrong et al. Nat Genet 30:41-47, 2002.

library(GSVAdata)data(leukemia) # loads leukemia_eset# Create a matrix from the gene expression eset objectM1 <- exprs(leukemia_eset)# Get a matrix of the top 50 most variable probes accros the sampleslibrary(genefilter)topVarGenes <- head(order(-rowVars(M1)), 50)mat <- M1[ topVarGenes, ]mat <- mat - rowMeans(mat)# For sample annotation informationhead(pData(leukemia_eset))table(leukemia_eset$subtype)# Get sample group as a factor the ColSideColorsALLgroup <- as.factor(pData(leukemia_eset)[colnames(M1), 1])# Get the colors for the ALL subtypesidecols <- c("#4FD5D6", "#FF0000")# Here is a fancy color palette inspired by http://www.colbyimaging.com/wiki/statistics/color-barscool = rainbow(50, start=rgb2hsv(col2rgb('cyan'))[1], end=rgb2hsv(col2rgb('blue'))[1])warm = rainbow(50, start=rgb2hsv(col2rgb('red'))[1], end=rgb2hsv(col2rgb('yellow'))[1])cols = c(rev(cool), rev(warm))mypalette <- colorRampPalette(cols)(255)library("gplots") # for the heatmap.2 functionpar(mfrow=c(1,1))png(filename="Heatmap_Example.png", width=12, height=10, units = 'in', res = 300)heatmap.2(mat, trace="none", col=mypalette, ColSideColors=sidecols[ALLgroup],labRow=FALSE, labCol=FALSE, mar=c(6,12), scale="row", key.title="")legend("topright", legend=levels(ALLgroup), fill=sidecols, title="", cex=1.2)graphics.off()

Now you are all set to work with and create your own awesome color palettes! Happy R programing

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