Scatterplot with marginal histograms in ggplot2

Question

Is there a way of creating scatterplots with marginal histograms just like in the sample below in ggplot2? In Matlab it is the scatterhist() function and there exist equivalents for R as well. However, I haven't seen it for ggplot2.

I started an attempt by creating the single graphs but don't know how to arrange them properly.

 require(ggplot2)
 x<-rnorm(300)
 y<-rt(300,df=2)
 xy<-data.frame(x,y)
     xhist <- qplot(x, geom="histogram") + scale_x_continuous(limits=c(min(x),max(x))) + opts(axis.text.x = theme_blank(), axis.title.x=theme_blank(), axis.ticks = theme_blank(), aspect.ratio = 5/16, axis.text.y = theme_blank(), axis.title.y=theme_blank(), background.colour="white")
     yhist <- qplot(y, geom="histogram") + coord_flip() + opts(background.fill = "white", background.color ="black")

     yhist <- yhist + scale_x_continuous(limits=c(min(x),max(x))) + opts(axis.text.x = theme_blank(), axis.title.x=theme_blank(), axis.ticks = theme_blank(), aspect.ratio = 16/5, axis.text.y = theme_blank(), axis.title.y=theme_blank() )


     scatter <- qplot(x,y, data=xy)  + scale_x_continuous(limits=c(min(x),max(x))) + scale_y_continuous(limits=c(min(y),max(y)))
none <- qplot(x,y, data=xy) + geom_blank()

and arranging them with the function posted here. But to make long story short: Is there a way of creating these graphs?

Answer 1

This is not a completely responsive answer but it is very simple. It illustrates an alternate method to display marginal densities and also how to use alpha levels for graphical output that supports transparency:

scatter <- qplot(x,y, data=xy)  + 
         scale_x_continuous(limits=c(min(x),max(x))) + 
         scale_y_continuous(limits=c(min(y),max(y))) + 
         geom_rug(col=rgb(.5,0,0,alpha=.2))
scatter

Answer 2

This might be a bit late, but I decided to make a package (ggExtra) for this since it involved a bit of code and can be tedious to write. The package also tries to address some common issue such as ensuring that even if there is a title or the text is enlarged, the plots will still be inline with one another.

The basic idea is similar to what the answers here gave, but it goes a bit beyond that. Here is an example of how to add marginal histograms to a random set of 1000 points. Hopefully this makes it easier to add histograms/density plots in the future.

Link to ggExtra package

library(ggplot2)
df <- data.frame(x = rnorm(1000, 50, 10), y = rnorm(1000, 50, 10))
p <- ggplot(df, aes(x, y)) + geom_point() + theme_classic()
ggExtra::ggMarginal(p, type = "histogram")

Answer 3

The gridExtra package should work here. Start by making each of the ggplot objects:

hist_top <- ggplot()+geom_histogram(aes(rnorm(100)))
empty <- ggplot()+geom_point(aes(1,1), colour="white")+
         theme(axis.ticks=element_blank(), 
               panel.background=element_blank(), 
               axis.text.x=element_blank(), axis.text.y=element_blank(),           
               axis.title.x=element_blank(), axis.title.y=element_blank())

scatter <- ggplot()+geom_point(aes(rnorm(100), rnorm(100)))
hist_right <- ggplot()+geom_histogram(aes(rnorm(100)))+coord_flip()

Then use the grid.arrange function:

grid.arrange(hist_top, empty, scatter, hist_right, ncol=2, nrow=2, widths=c(4, 1), heights=c(1, 4))

Answer 4

One addition, just to save some searching time for people doing this after us.

Legends, axis labels, axis texts, ticks make the plots drifted away from each other, so your plot will look ugly and inconsistent.

You can correct this by using some of these theme settings,

+theme(legend.position = "none",          
       axis.title.x = element_blank(),
       axis.title.y = element_blank(),
       axis.text.x = element_blank(),
       axis.text.y = element_blank(), 
       plot.margin = unit(c(3,-5.5,4,3), "mm"))

and align scales,

+scale_x_continuous(breaks = 0:6,
                    limits = c(0,6),
                    expand = c(.05,.05))

so the results will look OK:

Answer 5

Just a very minor variation on BondedDust's answer, in the general spirit of marginal indicators of distribution.

Edward Tufte has called this use of rug plots a 'dot-dash plot', and has an example in VDQI of using the axis lines to indicate the range of each variable. In my example the axis labels and grid lines also indicate the distribution of the data. The labels are located at the values of Tukey's five number summary (minimum, lower-hinge, median, upper-hinge, maximum), giving a quick impression of the spread of each variable.

These five numbers are thus a numerical representation of a boxplot. It's a bit tricky because the unevenly spaced grid-lines suggest that the axes have a non-linear scale (in this example they are linear). Perhaps it would be best to omit grid lines or force them to be in regular locations, and just let the labels show the five number summary.

x<-rnorm(300)
y<-rt(300,df=10)
xy<-data.frame(x,y)

require(ggplot2); require(grid)
# make the basic plot object
ggplot(xy, aes(x, y)) +        
  # set the locations of the x-axis labels as Tukey's five numbers   
  scale_x_continuous(limit=c(min(x), max(x)), 
                     breaks=round(fivenum(x),1)) +     
  # ditto for y-axis labels 
  scale_y_continuous(limit=c(min(y), max(y)),
                     breaks=round(fivenum(y),1)) +     
  # specify points
  geom_point() +
  # specify that we want the rug plot
  geom_rug(size=0.1) +   
  # improve the data/ink ratio
  theme_set(theme_minimal(base_size = 18))

Answer 6

I tried those options, but wasn't satisfied by the results or the messy code one would need to use to get there. Lucky me, Thomas Lin Pedersen just developed a package called patchwork, which gets the job done in a pretty elegant manner.

If you want to create a scatterplot with marginal histograms, first you'd have to create those three plots seperately.

library(ggplot2)

x <- rnorm(300)
y <- rt(300, df = 2)
xy <- data.frame(x, y)

plot1 <- ggplot(xy, aes(x = x, y = y)) + 
  geom_point() 

dens1 <- ggplot(xy, aes(x = x)) + 
  geom_histogram(color = "black", fill = "white") + 
  theme_void()

dens2 <- ggplot(xy, aes(x = y)) + 
  geom_histogram(color = "black", fill = "white") + 
  theme_void() + 
  coord_flip()

The only thing left to do, is to add those plots with a simple + and specify the layout with the function plot_layout().

library(patchwork)

dens1 + plot_spacer() + plot1 + dens2 + 
  plot_layout(
    ncol = 2, 
    nrow = 2, 
    widths = c(4, 1),
    heights = c(1, 4)
  ) 

The function plot_spacer() adds an empty plot to the top right corner. All the other arguments should be self-explanatory.

Since histograms heavily depend on the chosen binwidth, one might argue to prefer density plots. With some small modifications one would get e.g. for eye tracking data a beautiful plot.

library(ggpubr)

plot1 <- ggplot(df, aes(x = Density, y = Face_sum, color = Group)) + 
  geom_point(aes(color = Group), size = 3) + 
  geom_point(shape = 1, color = "black", size = 3) + 
  stat_smooth(method = "lm", fullrange = TRUE) +
  geom_rug() + 
  scale_y_continuous(name = "Number of fixated faces", 
                     limits = c(0, 205), expand = c(0, 0)) + 
  scale_x_continuous(name = "Population density (lg10)", 
                     limits = c(1, 4), expand = c(0, 0)) + 
  theme_pubr() +
  theme(legend.position = c(0.15, 0.9)) 

dens1 <- ggplot(df, aes(x = Density, fill = Group)) + 
  geom_density(alpha = 0.4) + 
  theme_void() + 
  theme(legend.position = "none")

dens2 <- ggplot(df, aes(x = Face_sum, fill = Group)) + 
  geom_density(alpha = 0.4) + 
  theme_void() + 
  theme(legend.position = "none") + 
  coord_flip()

dens1 + plot_spacer() + plot1 + dens2 + 
  plot_layout(ncol = 2, nrow = 2, widths = c(4, 1), heights = c(1, 4))

Though the data is not provided at this point, the underlying principles should be clear.

Answer 7

As there was no satisfying solution for this kind of plot when comparing different groups, I wrote a function to do this.

It works for both grouped and ungrouped data and accepts additional graphical parameters:

marginal_plot(x = iris$Sepal.Width, y = iris$Sepal.Length)

marginal_plot(x = Sepal.Width, y = Sepal.Length, group = Species, data = iris, bw = "nrd", lm_formula = NULL, xlab = "Sepal width", ylab = "Sepal length", pch = 15, cex = 0.5)

Answer 8

I've found the package (ggpubr) that seems to work very well for this problem and it considers several possibilities to display the data.

The link to the package is here, and in this link you will find a nice tutorial to use it. For completeness, I attach one of the examples I reproduced.

I first installed the package (it requires devtools)

if(!require(devtools)) install.packages("devtools")
devtools::install_github("kassambara/ggpubr")

For the particular example of displaying different histograms for different groups, it mentions in relation with ggExtra: "One limitation of ggExtra is that it can’t cope with multiple groups in the scatter plot and the marginal plots. In the R code below, we provide a solution using the cowplot package." In my case, I had to install the latter package:

install.packages("cowplot")

And I followed this piece of code:

# Scatter plot colored by groups ("Species")
sp <- ggscatter(iris, x = "Sepal.Length", y = "Sepal.Width",
            color = "Species", palette = "jco",
            size = 3, alpha = 0.6)+
border()                                         
# Marginal density plot of x (top panel) and y (right panel)
xplot <- ggdensity(iris, "Sepal.Length", fill = "Species",
               palette = "jco")
yplot <- ggdensity(iris, "Sepal.Width", fill = "Species", 
               palette = "jco")+
rotate()
# Cleaning the plots
sp <- sp + rremove("legend")
yplot <- yplot + clean_theme() + rremove("legend") 
xplot <- xplot + clean_theme() + rremove("legend")
# Arranging the plot using cowplot
library(cowplot)
plot_grid(xplot, NULL, sp, yplot, ncol = 2, align = "hv", 
      rel_widths = c(2, 1), rel_heights = c(1, 2))

Which worked fine for me:

Iris set marginal histograms scatterplot

Answer 9

You can easily create attractive scatterplots with marginal histograms using ggstatsplot (it will also fit and describe a model):

data(iris)

library(ggstatsplot)

ggscatterstats(
  data = iris,                                          
  x = Sepal.Length,                                                  
  y = Sepal.Width,
  xlab = "Sepal Length",
  ylab = "Sepal Width",
  marginal = TRUE,
  marginal.type = "histogram",
  centrality.para = "mean",
  margins = "both",
  title = "Relationship between Sepal Length and Sepal Width",
  messages = FALSE
)

Or slightly more appealing (by default) ggpubr:

devtools::install_github("kassambara/ggpubr")
library(ggpubr)

ggscatterhist(
  iris, x = "Sepal.Length", y = "Sepal.Width",
  color = "Species", # comment out this and last line to remove the split by species
  margin.plot = "histogram", # I'd suggest removing this line to get density plots
  margin.params = list(fill = "Species", color = "black", size = 0.2)
)

UPDATE:

As suggested by @aickley I used the developmental version to create the plot.

Answer 10

To build on the answer by @alf-pascu, setting up each plot manually and arranging them with cowplot grants a lot of flexibility with respect to both the main and the marginal plots (compared to some of the other solutions). Distributions by groups is one example. Changing the main plot to a 2D-density plot is another.

The following creates a scatterplot with (properly aligned) marginal histograms.

library("ggplot2")
library("cowplot")

# Set up scatterplot
scatterplot <- ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, color = Species)) +
  geom_point(size = 3, alpha = 0.6) +
  guides(color = FALSE) +
  theme(plot.margin = margin())


# Define marginal histogram
marginal_distribution <- function(x, var, group) {
  ggplot(x, aes_string(x = var, fill = group)) +
    geom_histogram(bins = 30, alpha = 0.4, position = "identity") +
    # geom_density(alpha = 0.4, size = 0.1) +
    guides(fill = FALSE) +
    theme_void() +
    theme(plot.margin = margin())
}

# Set up marginal histograms
x_hist <- marginal_distribution(iris, "Sepal.Length", "Species")
y_hist <- marginal_distribution(iris, "Sepal.Width", "Species") +
  coord_flip()

# Align histograms with scatterplot
aligned_x_hist <- align_plots(x_hist, scatterplot, align = "v")[[1]]
aligned_y_hist <- align_plots(y_hist, scatterplot, align = "h")[[1]]

# Arrange plots
plot_grid(
  aligned_x_hist
  , NULL
  , scatterplot
  , aligned_y_hist
  , ncol = 2
  , nrow = 2
  , rel_heights = c(0.2, 1)
  , rel_widths = c(1, 0.2)
)

To plot a 2D-density plot instead, just change the main plot.

# Set up 2D-density plot
contour_plot <- ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, color = Species)) +
  stat_density_2d(aes(alpha = ..piece..)) +
  guides(color = FALSE, alpha = FALSE) +
  theme(plot.margin = margin())

# Arrange plots
plot_grid(
  aligned_x_hist
  , NULL
  , contour_plot
  , aligned_y_hist
  , ncol = 2
  , nrow = 2
  , rel_heights = c(0.2, 1)
  , rel_widths = c(1, 0.2)
)

Answer 11

This is an old question, but I thought it would be useful to post an update here since I've come across this same problem recently (thanks to Stefanie Mueller for the help!).

The most upvoted answer using gridExtra works, but aligning axes is difficult/hacky, as has been pointed out in the comments. This can now be solved using the command ggMarginal from the ggExtra package, as such:

#load packages
library(tidyverse) #for creating dummy dataset only
library(ggExtra)

#create dummy data
a = round(rnorm(1000,mean=10,sd=6),digits=0)
b = runif(1000,min=1.0,max=1.6)*a
b = b+runif(1000,min=9,max=15)

DummyData <- data.frame(var1 = b, var2 = a) %>% 
  filter(var1 > 0 & var2 > 0)

#plot
p = ggplot(DummyData, aes(var1, var2)) + geom_point(alpha=0.3)
ggMarginal(p, type = "histogram")

Answer 12

Another solution using ggpubr and cowplot, but here we create plots using cowplot::axis_canvas and add them to original plot with cowplot::insert_xaxis_grob:

library(cowplot) 
library(ggpubr)

# Create main plot
plot_main <- ggplot(faithful, aes(eruptions, waiting)) +
  geom_point()

# Create marginal plots
# Use geom_density/histogram for whatever you plotted on x/y axis 
plot_x <- axis_canvas(plot_main, axis = "x") +
  geom_density(aes(eruptions), faithful)
plot_y <- axis_canvas(plot_main, axis = "y", coord_flip = TRUE) +
  geom_density(aes(waiting), faithful) +
  coord_flip()

# Combine all plots into one
plot_final <- insert_xaxis_grob(plot_main, plot_x, position = "top")
plot_final <- insert_yaxis_grob(plot_final, plot_y, position = "right")
ggdraw(plot_final)

Answer 13

Nowadays, there is at least one CRAN package that makes the scatterplot with its marginal histograms.

library(psych)
scatterHist(rnorm(1000), runif(1000))

Answer 14

You can use the interactive form of ggExtra::ggMarginalGadget(yourplot) and choose between boxplots, violin plots, density plots and histograms whit easy.

like that