R: Density Estimate (ggtern version)

geom_density_tern {ggtern}

R Documentation

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

geom_density_ternunderstands the following aesthetics (required aesthetics are in bold):

x
y
alpha
colour
linetype
size
weight

Author(s)

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()

[Package ggtern version 3.5.0 Index]