ggtern (version 3.5.0)

geom_density_tern: Density Estimate (ggtern version)

Description

Perform a 2D kernel density estimatation using kde2d and display the results with contours. This can be useful for dealing with overplotting. Additional weight aesthetic (see aesthetic section below) permits better weighting if desired

Usage

geom_density_tern(
  mapping = NULL,
  data = NULL,
  stat = "DensityTern",
  position = "identity",
  ...,
  lineend = "butt",
  linejoin = "round",
  linemitre = 1,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)
stat_density_tern(
  mapping = NULL,
  data = NULL,
  geom = "density_tern",
  position = "identity",
  ...,
  contour = TRUE,
  n = 100,
  h = NULL,
  bdl = 0,
  bdl.val = NA,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  weight = 1,
  base = "ilr",
  expand = c(0.5, 0.5)
)

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)).

stat

The statistical transformation to use on the data for this layer, either as a ggproto Geom subclass or as a string naming the stat stripped of the stat_ prefix (e.g. "count" rather than "stat_count")

position

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

...

Other arguments passed on to layer(). These are often aesthetics, used to set an aesthetic to a fixed value, like colour = "red" or size = 3. They may also be parameters to the paired geom/stat.

lineend

Line end style (round, butt, square).

linejoin

Line join style (round, mitre, bevel).

linemitre

Line mitre limit (number greater than 1).

na.rm

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

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.

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().

geom

Use to override the default connection between geom_density_tern() and stat_density_tern()

contour

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

n

Number of grid points in each direction.

h

Bandwidth (vector of length two) as a multiple of the best estimate, estimated using bandwidth.nrd.

bdl

the threshold for detection limit. This is applied against the output of acomp function, so it is expected as a fraction in the range [0,1]

bdl.val

compositions which have components that are below the detection limit, will have these components replaced by this val. If it is NA then these items will be discarded. If the value is something other than 'NA', then all values less than bdl will be replaced and therefore included in the final density estimate.

weight

weighting for weighted kde2d esimate, default's to 1, which is non-weighted and equivalent to the usual kde2d calculation

base

the base transformation of the data, options include 'identity' (ie direct on the cartesian space), or 'ilr' which means to use the isometric log ratio transformation.

expand

Calculate on a mesh which extends beyond the grid of the plot region by this amount If NULL, estimated using bandwidth.nrd.

Aesthetics

ggtern:::rd_aesthetics("geom", "density_tern")

Author

Nicholas Hamilton

Examples

#Plot Density Estimate, on isometric log ratio transformation of original data
data('Feldspar')
ggtern(Feldspar,aes(Ab,An,Or)) + 
 geom_density_tern(aes(color=..level..),bins=5) +
 geom_point()

#Plot Density Estimate w/ Polygon Geometry
data('Feldspar')
ggtern(data=Feldspar,aes(Ab,An,Or)) + 
    stat_density_tern(
        geom='polygon',
        aes(fill=..level..),
        bins=5,
        color='grey') +
    geom_point()