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I would like superimpose two scatter plots in R so that each set of points has its own (different) y-axis (i.e., in positions 2 and 4 on the figure) but the points appear superimposed on the same figure.

Is it possible to do this with plot?

Edit Example code showing the problem

# example code for SO question y1 <- rnorm(10, 100, 20) y2 <- rnorm(10, 1, 1) x <- 1:10 # in this plot y2 is plotted on what is clearly an inappropriate scale plot(y1 ~ x, ylim = c(-1, 150)) points(y2 ~ x, pch = 2)
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  • Please provide sample data. This is generally a bad idea from an aesthetic perspective. Commented May 26, 2011 at 17:55
  • 3
    answers and discussion in the specific case of ggplot2: stackoverflow.com/questions/3099219/… (searching SO for [r] two y-axes or [r] twoord.plot) -- there are a few other related answers, although (to my surprise since it's an R FAQ) nothing identical Commented May 26, 2011 at 18:17
  • @chase - I added a working example of the problem. Thanks for the warning on the aesthetic issues. Commented May 26, 2011 at 18:44

6 Answers 6

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update: Copied material that was on the R wiki at http://rwiki.sciviews.org/doku.php?id=tips:graphics-base:2yaxes, link now broken: also available from the wayback machine

Two different y axes on the same plot

(some material originally by Daniel Rajdl 2006/03/31 15:26)

Please note that there are very few situations where it is appropriate to use two different scales on the same plot. It is very easy to mislead the viewer of the graphic. Check the following two examples and comments on this issue (example1, example2 from Junk Charts), as well as this article by Stephen Few (which concludes “I certainly cannot conclude, once and for all, that graphs with dual-scaled axes are never useful; only that I cannot think of a situation that warrants them in light of other, better solutions.”) Also see point #4 in this cartoon ...

If you are determined, the basic recipe is to create your first plot, set par(new=TRUE) to prevent R from clearing the graphics device, creating the second plot with axes=FALSE (and setting xlab and ylab to be blank – ann=FALSE should also work) and then using axis(side=4) to add a new axis on the right-hand side, and mtext(...,side=4) to add an axis label on the right-hand side. Here is an example using a little bit of made-up data:

set.seed(101) x <- 1:10 y <- rnorm(10) ## second data set on a very different scale z <- runif(10, min=1000, max=10000) par(mar = c(5, 4, 4, 4) + 0.3) # Leave space for z axis plot(x, y) # first plot par(new = TRUE) plot(x, z, type = "l", axes = FALSE, bty = "n", xlab = "", ylab = "") axis(side=4, at = pretty(range(z))) mtext("z", side=4, line=3)

twoord.plot() in the plotrix package automates this process, as does doubleYScale() in the latticeExtra package.

Another example (adapted from an R mailing list post by Robert W. Baer):

## set up some fake test data time <- seq(0,72,12) betagal.abs <- c(0.05,0.18,0.25,0.31,0.32,0.34,0.35) cell.density <- c(0,1000,2000,3000,4000,5000,6000) ## add extra space to right margin of plot within frame par(mar=c(5, 4, 4, 6) + 0.1) ## Plot first set of data and draw its axis plot(time, betagal.abs, pch=16, axes=FALSE, ylim=c(0,1), xlab="", ylab="", type="b",col="black", main="Mike's test data") axis(2, ylim=c(0,1),col="black",las=1) ## las=1 makes horizontal labels mtext("Beta Gal Absorbance",side=2,line=2.5) box() ## Allow a second plot on the same graph par(new=TRUE) ## Plot the second plot and put axis scale on right plot(time, cell.density, pch=15, xlab="", ylab="", ylim=c(0,7000), axes=FALSE, type="b", col="red") ## a little farther out (line=4) to make room for labels mtext("Cell Density",side=4,col="red",line=4) axis(4, ylim=c(0,7000), col="red",col.axis="red",las=1) ## Draw the time axis axis(1,pretty(range(time),10)) mtext("Time (Hours)",side=1,col="black",line=2.5) ## Add Legend legend("topleft",legend=c("Beta Gal","Cell Density"), text.col=c("black","red"),pch=c(16,15),col=c("black","red"))

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Similar recipes can be used to superimpose plots of different types – bar plots, histograms, etc..

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3 Comments

this is why link-only answers are a bad idea ... wiki.r-project.org appears defunct, I'm asking on [email protected].
@BenBolker your solution is genius! however i have one question. If it's more than one line on the both sides, I am still able to use this method but only with symbols. When I try to use line=plot, it tries to plot them continuously. Would you happen to suggest a trick to fix this?
@BenBolker What if Time is date format of type: "2019-01-01". How will you change the axis(1,pretty(range(time),10)) line?
39

As its name suggests, twoord.plot() in the plotrix package plots with two ordinate axes.

library(plotrix) example(twoord.plot)

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slick. thanks for the truck load of examples. I'd love to see one of those line and bar examples with negative values as well. Also stacking would be nice.
7

If you can give up the scales/axis labels, you can rescale the data to (0, 1) interval. This works for example for different 'wiggle' trakcs on chromosomes, when you're generally interested in local correlations between the tracks and they have different scales (coverage in thousands, Fst 0-1).

# rescale numeric vector into (0, 1) interval # clip everything outside the range rescale <- function(vec, lims=range(vec), clip=c(0, 1)) { # find the coeficients of transforming linear equation # that maps the lims range to (0, 1) slope <- (1 - 0) / (lims[2] - lims[1]) intercept <- - slope * lims[1] xformed <- slope * vec + intercept # do the clipping xformed[xformed < 0] <- clip[1] xformed[xformed > 1] <- clip[2] xformed }

Then, having a data frame with chrom, position, coverage and fst columns, you can do something like:

ggplot(d, aes(position)) + geom_line(aes(y = rescale(fst))) + geom_line(aes(y = rescale(coverage))) + facet_wrap(~chrom)

The advantage of this is that you're not limited to two trakcs.

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7

Another alternative which is similar to the accepted answer by @BenBolker is redefining the coordinates of the existing plot when adding a second set of points.

Here is a minimal example.

Data:

x <- 1:10 y1 <- rnorm(10, 100, 20) y2 <- rnorm(10, 1, 1)

Plot:

par(mar=c(5,5,5,5)+0.1, las=1) plot.new() plot.window(xlim=range(x), ylim=range(y1)) points(x, y1, col="red", pch=19) axis(1) axis(2, col.axis="red") box() plot.window(xlim=range(x), ylim=range(y2)) points(x, y2, col="limegreen", pch=19) axis(4, col.axis="limegreen") title("my plot", adj=0) mtext("2nd y axis", side = 4, las=3, line=3, col="limegreen") mtext("1st y axis", side = 2, las=3, line=3, col="red")

example

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5

One option is to make two plots side by side. ggplot2 provides a nice option for this with facet_wrap():

dat <- data.frame(x = c(rnorm(100), rnorm(100, 10, 2)) , y = c(rnorm(100), rlnorm(100, 9, 2)) , index = rep(1:2, each = 100) ) require(ggplot2) ggplot(dat, aes(x,y)) + geom_point() + facet_wrap(~ index, scales = "free_y")
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5

I too suggests, twoord.stackplot() in the plotrix package plots with more of two ordinate axes.

data<-read.table(text= "e0AL fxAL e0CO fxCO e0BR fxBR anos 51.8 5.9 50.6 6.8 51.0 6.2 1955 54.7 5.9 55.2 6.8 53.5 6.2 1960 57.1 6.0 57.9 6.8 55.9 6.2 1965 59.1 5.6 60.1 6.2 57.9 5.4 1970 61.2 5.1 61.8 5.0 59.8 4.7 1975 63.4 4.5 64.0 4.3 61.8 4.3 1980 65.4 3.9 66.9 3.7 63.5 3.8 1985 67.3 3.4 68.0 3.2 65.5 3.1 1990 69.1 3.0 68.7 3.0 67.5 2.6 1995 70.9 2.8 70.3 2.8 69.5 2.5 2000 72.4 2.5 71.7 2.6 71.1 2.3 2005 73.3 2.3 72.9 2.5 72.1 1.9 2010 74.3 2.2 73.8 2.4 73.2 1.8 2015 75.2 2.0 74.6 2.3 74.2 1.7 2020 76.0 2.0 75.4 2.2 75.2 1.6 2025 76.8 1.9 76.2 2.1 76.1 1.6 2030 77.6 1.9 76.9 2.1 77.1 1.6 2035 78.4 1.9 77.6 2.0 77.9 1.7 2040 79.1 1.8 78.3 1.9 78.7 1.7 2045 79.8 1.8 79.0 1.9 79.5 1.7 2050 80.5 1.8 79.7 1.9 80.3 1.7 2055 81.1 1.8 80.3 1.8 80.9 1.8 2060 81.7 1.8 80.9 1.8 81.6 1.8 2065 82.3 1.8 81.4 1.8 82.2 1.8 2070 82.8 1.8 82.0 1.7 82.8 1.8 2075 83.3 1.8 82.5 1.7 83.4 1.9 2080 83.8 1.8 83.0 1.7 83.9 1.9 2085 84.3 1.9 83.5 1.8 84.4 1.9 2090 84.7 1.9 83.9 1.8 84.9 1.9 2095 85.1 1.9 84.3 1.8 85.4 1.9 2100", header=T) require(plotrix) twoord.stackplot(lx=data$anos, rx=data$anos, ldata=cbind(data$e0AL, data$e0BR, data$e0CO), rdata=cbind(data$fxAL, data$fxBR, data$fxCO), lcol=c("black","red", "blue"), rcol=c("black","red", "blue"), ltype=c("l","o","b"), rtype=c("l","o","b"), lylab="Años de Vida", rylab="Hijos x Mujer", xlab="Tiempo", main="Mortalidad/Fecundidad:1950–2100", border="grey80") legend("bottomright", c(paste("Proy:", c("A. Latina", "Brasil", "Colombia"))), cex=1, col=c("black","red", "blue"), lwd=2, bty="n", lty=c(1,1,2), pch=c(NA,1,1) )
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