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Hotelling ellipses for ggplot2

geom_hotelling.Rd

Hotelling ellipses for ggplot2

Usage

geom_hotelling(
  mapping = NULL,
  data = NULL,
  position = "identity",
  ...,
  level = 0.95,
  type = "t2data",
  robust = FALSE,
  npoints = 100,
  na.rm = FALSE,
  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().

level

Either coverage probability (for type = "t2data" or "c2data") or confidence level (for type = "t2mean").

type

t2data - Hotelling T2 data ellipse; t2mean - Hotelling confidence interval for the mean; c2data - normal data ellipse (using chi squared distribution).

robust

If TRUE, then robust estimates of mean and covariance are used

npoints

Number of points to estimate

na.rm

Logical. Should missing values be removed? Default is FALSE.

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 geom adds data or confidence ellipses to the plot. See hotelling_ellipse() documentation for more information.

Examples

pca <- prcomp(iris[, 1:4], scale.=TRUE)
df <- cbind(iris, pca$x)
library(ggplot2)
  
  ggplot(df, aes(PC1, PC2)) +
    geom_hotelling(level=.99) +
    geom_point()

  
  ggplot(df, aes(PC1, PC2, color=Species)) +
    geom_hotelling() +
    geom_point()

  
  ggplot(df, aes(PC1, PC2, color=Species)) +
    geom_hotelling(alpha=0.1, aes(fill = Species)) +
    geom_point()

  
# compare the robust and regular approaches:
  ggplot(df, aes(PC1, PC2, color=Species)) +
    geom_hotelling() +
    geom_hotelling(robust = TRUE, linetype = "dashed") +
    geom_point()