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I'm trying to plots insect counts of 2 species in 18 experimental plots onto a single graph. Since the second species population peaks later, it is visually doable (see picture below). I would like the 18 population lines from species 1 to be green (using "Greens" from RColorBrewer) and the 18 of species 2 to be red (using "Reds"). I do realize this may be problematic for a colourblind audience, but that is irrelevant here.

I've read here that it is not possible with standard ggplot2 options: R ggplot two color palette on the same plot but this post is more than two years old.

There is a short of "cheat" for points: Using two scale colour gradients ggplot2 but since I prefer lines to show the population through time, I can't use it.

Are there any new "cheats" available for this? Or does anyone have another idea to visualize my data in a way that shows population trends through time in all plots and shows the difference in timing of the peak? I've included a picture at the bottom that shows my real data, all in the same colour scale though.

Sample code

# example data frame plot <- as.factor(rep(c("A","B","C"),each=5)) time <- as.numeric(rep(c(1:5),times=3)) S1 <- c(1,4,7,5,2, 2,8,9,3,1, 1,6,6,3,1) S2 <- c(0,0,2,3,2, 1,2,1,5,3, 0,1,1,6,7) df <- data.frame(time, plot, S1, S2) # example colour scales S1Colours <- colorRampPalette(brewer.pal(9,"Greens"))(3) S2Colours <- colorRampPalette(brewer.pal(9,"Reds"))(3) names(S1Colours) <- levels(df$plot) names(S2Colours) <- levels(df$plot) # example plot ggplot(data=df) + geom_line(aes(x=time, y=S1, colour=plot)) + geom_line(aes(x=time, y=S2, colour=plot)) + scale_colour_manual(name = "plot", values = S1Colours) + scale_colour_manual(name = "plot", values = S2Colours) # this gives the note "Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale."

Plot real data

enter image description here

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    Maybe you could use different line types for S1 and S2 of the same group? Commented Dec 18, 2019 at 11:53
  • That's indeed something I've tried before, but because I have 36 lines with quite some overlap, it is not very visible and that's why I prefer different colours. Commented Dec 18, 2019 at 11:55
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    Have you tried a manual colour scale? Creating your required theme by concatenating 18 values picked from a light green to dargkreen colour ramp and another 18 from a light red to darkred ramp? (I don't have at hand the instructions on how to create continuous colour palettes from two colours and then sampling n colours from them, but it's only a couple lines of code). Commented Dec 18, 2019 at 12:09
  • but then I would create a legend of 36 plots and will probably have to rename 18 of them to "plotS2" or someting. Though that might actually be a solution if I just cut the legend and assume the reader is not necessarily interested in which line is which exact plot... I'll certainly give this a try! Commented Dec 18, 2019 at 13:25

2 Answers 2

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You can do this easily with the ggnewscale package (disclaimer: I'm the author).

This is how you would do it:

library(RColorBrewer) library(ggplot2) library(ggnewscale) plot <- as.factor(rep(c("A","B","C"),each=5)) time <- as.numeric(rep(c(1:5),times=3)) S1 <- c(1,4,7,5,2, 2,8,9,3,1, 1,6,6,3,1) S2 <- c(0,0,2,3,2, 1,2,1,5,3, 0,1,1,6,7) df <- data.frame(time, plot, S1, S2) # example colour scales S1Colours <- colorRampPalette(brewer.pal(9,"Greens"))(3) S2Colours <- colorRampPalette(brewer.pal(9,"Reds"))(3) names(S1Colours) <- levels(df$plot) names(S2Colours) <- levels(df$plot) ggplot(data=df) + geom_line(aes(x=time, y=S1, colour=plot)) + scale_colour_manual(name = "plot 1", values = S1Colours) + new_scale_color() + geom_line(aes(x=time, y=S2, colour=plot)) + scale_colour_manual(name = "plot 2", values = S2Colours)

Created on 2019-12-19 by the reprex package (v0.3.0)

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your package is super nice, congrats!
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I also would go by creating a manual color scale for all the combinations.

library(tidyverse) library(RColorBrewer) df_long=pivot_longer(df,cols=c(S1,S2),names_to = "Species",values_to = "counts") %>% # create long format and mutate(plot_Species=paste(plot,Species,sep="_")) # make identifiers for combined plot and Species #make color palette mycolors=c(colorRampPalette(brewer.pal(9,"Greens"))(sum(grepl("S1",unique(df_long$plot_Species)))), colorRampPalette(brewer.pal(9,"Reds"))(sum(grepl("S2",unique(df_long$plot_Species))))) names(mycolors)=c(grep("S1",unique(df_long$plot_Species),value = T), grep("S2",unique(df_long$plot_Species),value = T)) # example plot ggplot(data=df_long) + geom_line(aes(x=time, y=counts, colour=plot_Species)) + scale_colour_manual(name = "Species by plot", values = mycolors)

enter image description here

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3 Comments

You should use library instead of require.
Thanks! I learned something :-) and edited my answer accordingly
@Tingolfin If you want to have the legend ordered by species, just switch the order of variables in the plot_Species=paste() statement

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