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How can scatter plots with alpha transparent, scale-less histograms can be made in R, like this figure?

looks like it's not made in ggplot2.enter image description here

does anyone know what command is used?

  • This thread gets you close, but maybe not quite to where you want to be: http://stackoverflow.com/questions/8545035/scatterplot-with-marginal-histograms-in-ggplot2 – Drew Steen Jun 28 '13 at 17:37
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    See also http://blog.mckuhn.de/2009/09/learning-ggplot2-2d-plot-with.html – Drew Steen Jun 28 '13 at 17:52

2 Answers2

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library(ggplot2)
library(gridExtra)

set.seed(42)
DF <- data.frame(x=rnorm(100,mean=c(1,5)),y=rlnorm(100,meanlog=c(8,6)),group=1:2)

p1 <- ggplot(DF,aes(x=x,y=y,colour=factor(group))) + geom_point() +
  scale_x_continuous(expand=c(0.02,0)) +
  scale_y_continuous(expand=c(0.02,0)) +
  theme_bw() +
  theme(legend.position="none",plot.margin=unit(c(0,0,0,0),"points"))

theme0 <- function(...) theme( legend.position = "none",
                               panel.background = element_blank(),
                               panel.grid.major = element_blank(),
                               panel.grid.minor = element_blank(),
                               panel.margin = unit(0,"null"),
                               axis.ticks = element_blank(),
                               axis.text.x = element_blank(),
                               axis.text.y = element_blank(),
                               axis.title.x = element_blank(),
                               axis.title.y = element_blank(),
                               axis.ticks.length = unit(0,"null"),
                               axis.ticks.margin = unit(0,"null"),
                               panel.border=element_rect(color=NA),...)

p2 <- ggplot(DF,aes(x=x,colour=factor(group),fill=factor(group))) + 
  geom_density(alpha=0.5) + 
  scale_x_continuous(breaks=NULL,expand=c(0.02,0)) +
  scale_y_continuous(breaks=NULL,expand=c(0.02,0)) +
  theme_bw() +
  theme0(plot.margin = unit(c(1,0,0,2.2),"lines")) 
  
p3 <- ggplot(DF,aes(x=y,colour=factor(group),fill=factor(group))) + 
  geom_density(alpha=0.5) + 
  coord_flip()  + 
  scale_x_continuous(labels = NULL,breaks=NULL,expand=c(0.02,0)) +
  scale_y_continuous(labels = NULL,breaks=NULL,expand=c(0.02,0)) +
  theme_bw() +
  theme0(plot.margin = unit(c(0,1,1.2,0),"lines"))

grid.arrange(arrangeGrob(p2,ncol=2,widths=c(3,1)),
             arrangeGrob(p1,p3,ncol=2,widths=c(3,1)),
             heights=c(1,3))

enter image description here

Edit:

I couldn't find out what causes the space below the densities geoms. You can fiddle with the plot margins to avoid it, but I don't really like that.

p2 <- ggplot(DF,aes(x=x,colour=factor(group),fill=factor(group))) + 
  geom_density(alpha=0.5) + 
  scale_x_continuous(breaks=NULL,expand=c(0.02,0)) +
  scale_y_continuous(breaks=NULL,expand=c(0.00,0)) +
  theme_bw() +
  theme0(plot.margin = unit(c(1,0,-0.48,2.2),"lines")) 

p3 <- ggplot(DF,aes(x=y,colour=factor(group),fill=factor(group))) + 
  geom_density(alpha=0.5) + 
  coord_flip()  + 
  scale_x_continuous(labels = NULL,breaks=NULL,expand=c(0.02,0)) +
  scale_y_continuous(labels = NULL,breaks=NULL,expand=c(0.00,0)) +
  theme_bw() +
  theme0(plot.margin = unit(c(0,1,1.2,-0.48),"lines"))

enter image description here

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Roland
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  • very nice! how can you make the density plots closer to the axis though, so that they are touching the bounding box of the plots like in original figure? –  Jun 30 '13 at 15:12
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I have no idea whether there is a package that does that directly, but I'm sure this can be done in R. Transparency is easy: you add another two digits to the RGB specification of a color for a given transparency:

#FF0000 # red
#FF0000FF # full opacity
#FF000000 # full transparency

Combining different plots is also easy using the layout function. As for the vertical density plot, it is just the same as the horizontal plot with x and y switched. The example given here can easily be expanded to include colors, smaller margins etc. I can try to come up with a more elaborate example if this description is not sufficient.

January
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