[R] scatter plot with point colors from kernel density

From: James Kellner <jkellner_at_plantbio.uga.edu>
Date: Tue, 05 Feb 2008 14:05:04 -0500


I am using R 2.6.1 on a 64 bit PC running Windows XP Pro.

My main problem is that I want to produce a scatter plot with density estimation, where the colors of points correspond to a kernel density estimate at the location of the points. I have not found a package that will do this.

If there is no package, one option would to estimate the bivariate density first, and then use it to define a color table for the points.

If I obtain a bivariate kernel density for X and Y coordinates as follows:

 require(MASS)

 x.coord <- rnorm(1000)
 y.coord <- rnorm(1000)

 kernel <- kde2d(x.coord, y.coord, n = 100)

par(mfrow=c(2, 1))

 image(kernel)

 points(x.coord, y.coord)

 plot(x.coord, y.coord, main="I want to color these points using the kernel density")

how can I extract the kernel density estimates at the x.coord and y.coord locations for each point? What I would like is a matrix with three columns for "X", "Y" and "DENSITY", like this:

> matrix

      X      Y      DENSITY
1    1.56  -0.03     0.05  

 ...

Is there an easier way to do this?

Thanks in advance,

Jim   

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