Specifying the Scale for the Density in Ggplot2's Stat_Density2D

Specifying the scale for the density in ggplot2's stat_density2d

So to have both plots show contours with the same levels, use the breaks=... argument in stat_densit2d(...). To have both plots with the same mapping of alpha to level, use scale_alpha_continuous(limits=...).

Here is the full code to demonstrate:

library(ggplot2)
set.seed(4)
g = list(NA,NA)
for (i in 1:2) {
  sdev = runif(1)
  X = rnorm(1000, mean = 512, sd= 300*sdev)
  Y = rnorm(1000, mean = 384, sd= 200*sdev)
  this_df = as.data.frame( cbind(X = X,Y = Y, condition = 1:2) )

  g[[i]] = ggplot(data= this_df, aes(x=X, y=Y) ) + 
    geom_point(aes(color= as.factor(condition)), alpha= .25) +
    coord_cartesian(ylim= c(0, 768), xlim= c(0,1024)) + scale_y_reverse() +
    stat_density2d(mapping= aes(alpha = ..level.., color= as.factor(condition)), 
                   breaks=1e-6*seq(0,10,by=2),geom="contour", bins=4, size= 2)+
    scale_alpha_continuous(limits=c(0,1e-5))+
    scale_color_discrete("Condition")
}
library(gridExtra)
do.call(grid.arrange,c(g,ncol=2))

And the result...

Manually setting scale_alpha for stat_density2d plot

Add the same limits argument to scale_fill_gradient in both plots. For example, scale_fill_gradient(low = "green", high = "red", limits=c(0,70000)) (or whatever range you wish). Then the same colors will be mapped to the same values in each plot.

Here's what the plots look like with the limits I added:

(Note: The title of your question mentions scale_alpha, but the body of your question asks how to get the same fill legend. I've assumed you want the same fill legend in each plot, but please let me know if you wanted something different.)

How can I make a density scatterplot with log scale in R?

You can log10-transform the density; here's a minimal & reproducible example

library(MASS)
library(tidyverse)

set.seed(2020)
mvrnorm(100, mu = c(0, 0), Sigma = matrix(c(1, 0.5, 0.5, 1), 2, 2)) %>%
    as_tibble() %>%
    ggplot(aes(V1, V2)) + 
    stat_density2d(
        aes(fill = log10(..density..)), geom = "tile", contour = FALSE, n = 100) + 
    scale_fill_distiller(palette = 'YlOrRd', direction = 1) + 
    theme_bw()

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Update

It's not clear to me what you mean by ""I'd like to make the density scatterplot in the point distributed area, not the whole area of the plot."" If you're asking how to increase the height of the gradient colour bar, you can do the following

set.seed(2020)
mvrnorm(100, mu = c(0, 0), Sigma = matrix(c(1, 0.5, 0.5, 1), 2, 2)) %>%
    as_tibble() %>%
    ggplot(aes(V1, V2)) + 
    stat_density2d(
        aes(fill = log10(..density..)), geom = "tile", contour = FALSE, n = 100) + 
    scale_fill_distiller(palette = 'YlOrRd', direction = 1) + 
    theme_bw() + 
    guides(fill = guide_colorbar(barheight = unit(3.5, "in"), title.position = "right"))    

what does ..level.. mean in ggplot::stat_density2d

Expanding on the answer provided by @hrbrmstr -- first, the call to geom_density2d() is redundant. That is, you can achieve the same results with:

library(ggplot2)
library(MASS)

gg <- ggplot(geyser, aes(x = duration, y = waiting)) + 
    geom_point() + 
    stat_density2d(aes(fill = ..level..), geom = "polygon")

Let's consider some other ways to visualize this density estimate that may help clarify what is going on:

base_plot <- ggplot(geyser, aes(x = duration, y = waiting)) + 
  geom_point()

base_plot + 
  stat_density2d(aes(color = ..level..))

base_plot + 
  stat_density2d(aes(fill = ..density..), geom = "raster", contour = FALSE)

base_plot +
  stat_density2d(aes(alpha = ..density..), geom = "tile", contour = FALSE)

Notice, however, we can no longer see the points generated from geom_point().

Finally, note that you can control the bandwidth of the density estimate. To do this, we pass x and y bandwidth arguments to h (see ?kde2d):

base_plot +
  stat_density2d(aes(fill = ..density..), geom = "raster", contour = FALSE,
                 h = c(2, 5))

Again, the points from geom_point() are hidden as they are behind the call to stat_density2d().

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