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KDE contours for ggplot2

geom_kde.Rd

Kernel density estimate contours for ggplot2

Usage

geom_kde(
  mapping = NULL,
  data = NULL,
  position = "identity",
  ...,
  coverage = 0.95,
  n = 100,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

mapping

Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

data

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

position

A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following:

  • The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position.

  • A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter".

  • For more information and other ways to specify the position, see the layer position documentation.

...

Additional parameters passed to underlying ggplot2::geom_polygon() or to ggplot2::layer().

coverage

What fraction of the points should be enclosed by the contour

n

Number of grid points in each direction (passed to kde2d)

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. It can also be a named logical vector to finely select the aesthetics to display. To include legend keys for all levels, even when no data exists, use TRUE. If NA, all levels are shown in legend, but unobserved levels are omitted.

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. annotation_borders().

Details

This function uses the kde2d function to estimate density along a grid, and then plots a contour for a selected coverage.

See also

geom_hull() for simple convex contours and geom_hotelling() for Hotelling T² ellipses.

Examples

library(ggplot2)

# following shows a comparison
# between a convex hull and KDE contour
df <- data.frame(x=rnorm(500) + 5)
df$y <- df$x^5 + rnorm(500)*500
ggplot(df, aes(x=x, y=y)) +
  geom_point()+
  geom_hull(color = "grey") +
  geom_kde(color="red", linewidth=1)

  
# we can also achieve similar effects to geom_contour
pca <- prcomp(iris[, 1:4], scale.=TRUE)
df <- cbind(iris, pca$x)
  
# following is similar to geom_contour
pca <- prcomp(iris[, 1:4], scale.=TRUE)
df <- cbind(iris, pca$x)
p <- ggplot(df, aes(x = PC1, y = PC2, color=Species))
for(i in seq(.05, .95, length.out = 10)) {
  p <- p + geom_kde(aes(fill = Species), alpha =.05, coverage = i, n = 100)
}
p + geom_point()