[R] Adding 95% contours around scatterplot points with ggplot2

[Ista Zahn]

Hi Nathan,

This only fits some of your criteria, but have you looked at ?stat_density2d?

Best,
Ista

On Mon, Jan 28, 2013 at 12:53 PM, Nathan Miller <natemiller77 at gmail.com> wrote:
> Hi all,
>
> I have been looking for means of add a contour around some points in a
> scatterplot as a means of representing the center of density for of the
> data. I'm imagining something like a 95% confidence estimate drawn around
> the data.
>
> So far I have found some code for drawing polygons around the data. These
> look nice, but in some cases the polygons are strongly influenced by
> outlying points. Does anyone have a thought on how to draw a contour which
> is more along the lines of a 95% confidence space?
>
> I have provided a working example below to illustrate the drawing of the
> polygons. As I said I would rather have three "ovals"/95% contours drawn
> around the points by "level" to capture the different density distributions
> without the visualization being heavily influenced by outliers.
>
> I have looked into the code provided here from Hadley
> https://groups.google.com/forum/?fromgroups=#!topic/ggplot2/85q4SQ9q3V8
> using the mvtnorm package and the dmvnorm function, but haven't been able
> to get it work for my data example. The calculated densities are always
> zero (at this step of Hadley's code: dgrid$dens <-
> dmvnorm(as.matrix(dgrid), ex_mu, ex_sigma)   )
>
> I appreciate any assistance.
>
> Thanks,
> Nate
>
> x<-c(seq(0.15,0.4,length.out=30),seq(0.2,0.6,length.out=30),
> seq(0.4,0.6,length.out=30))
> y<-c(0.55,x[1:29]+0.2*rnorm(29,0.4,0.3),x[31:60]*rnorm(30,0.3,0.1),x[61:90]*rnorm(30,0.4,0.25))
> data<-data.frame(level=c(rep(1, 30),rep(2,30), rep(3,30)), x=x,y=y)
>
>
> find_hull <- function(data) data[chull(data$x, data$y), ]
> hulls <- ddply(data, .(level), find_hull)
>
> fig1 <- ggplot(data=data, aes(x, y, colour=(factor(level)),
> fill=level))+geom_point()
> fig1 <- fig1 + geom_polygon(data=hulls, alpha=.2)
> fig1
>
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