geom_bkde2d: Contours from a 2d density estimate.

Description

Contours from a 2d density estimate.

Perform a 2D kernel density estimation using bkde2D and display the results with contours. This can be useful for dealing with overplotting

Usage

geom_bkde2d(mapping = NULL, data = NULL, stat = "bkde2d", position = "identity", bandwidth = NULL, range.x = NULL, lineend = "butt", contour = TRUE, linejoin = "round", linemitre = 1, na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, ...)
stat_bkde2d(mapping = NULL, data = NULL, geom = "density2d", position = "identity", contour = TRUE, bandwidth = NULL, grid_size = c(51, 51), range.x = NULL, truncate = TRUE, na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, ...)

Arguments

mapping

Set of aesthetic mappings created by aes or aes_. If specified and inherit.aes = TRUE (the default), is combined with the default mapping at the top level of the plot. You only need to supply mapping if there isn't a mapping defined for the plot.

data

A data frame. If specified, overrides the default data frame defined at the top level of the plot.

stat

The statistical transformation to use on the data for this layer, as a string.

position

Position adjustment, either as a string, or the result of a call to a position adjustment function.

bandwidth

the kernel bandwidth smoothing parameter. see bkde2D for details. If NULL, it will be computed for you but will most likely not yield optimal results. see bkde2D for details

range.x

a list containing two vectors, where each vector contains the minimum and maximum values of x at which to compute the estimate for each direction. see bkde2D for details

lineend

Line end style (round, butt, square)

contour

If TRUE, contour the results of the 2d density estimation

linejoin

Line join style (round, mitre, bevel)

linemitre

Line mitre limit (number greater than 1)

na.rm

If FALSE (the default), removes missing values with a warning. If TRUE silently removes missing values.

show.legend

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes.

inherit.aes

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders.

...

other arguments passed on to layer. There are three types of arguments you can use here:

Aesthetics: to set an aesthetic to a fixed value, like color = "red" or size = 3.
Other arguments to the layer, for example you override the default stat associated with the layer.
Other arguments passed on to the stat.

geom

default geom to use with this stat

grid_size

vector containing the number of equally spaced points in each direction over which the density is to be estimated. see bkde2D for details

truncate

logical flag: if TRUE, data with x values outside the range specified by range.x are ignored. see bkde2D for details

Computed variables

Same as stat_contour

Details

A sample of the output from geom_bkde2d():

geom_bkde2d_01.pngoptions: width="100%" alt="Figure: geom_bkde2d_01.png"

Examples

Run this code

m <- ggplot(faithful, aes(x = eruptions, y = waiting)) +
       geom_point() +
       xlim(0.5, 6) +
       ylim(40, 110)

m + geom_bkde2d(bandwidth=c(0.5, 4))

m + stat_bkde2d(bandwidth=c(0.5, 4), aes(fill = ..level..), geom = "polygon")

# If you map an aesthetic to a categorical variable, you will get a
# set of contours for each value of that variable
set.seed(4393)
dsmall <- diamonds[sample(nrow(diamonds), 1000), ]
d <- ggplot(dsmall, aes(x, y)) +
       geom_bkde2d(bandwidth=c(0.5, 0.5), aes(colour = cut))
d

# If we turn contouring off, we can use use geoms like tiles:
d + stat_bkde2d(bandwidth=c(0.5, 0.5), geom = "raster",
                aes(fill = ..density..), contour = FALSE)

# Or points:
d + stat_bkde2d(bandwidth=c(0.5, 0.5), geom = "point",
                aes(size = ..density..),  contour = FALSE)