geom_range: Ranges

In teunbrand/ggnomics: ggnomics

Description

Alternative parameterisation of rectangles which can take a Ranges-class, such as IRanges or GRanges as x or y argument.

Usage

geom_range(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  linejoin = "mitre",
  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), 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, as a string.
position	Position adjustment, either as a string, or the result of a call to a position adjustment function.
...	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.
linejoin	Line join style (round, mitre, bevel).
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().

Details

If the x position aesthetic is given while y is not, and vice versa, the default behaviour is to center the aesthetic that is not provided around zero with a height/width of 0.8. If the position aesthetic is numeric, it is expected that also the (x|y)end aesthetic is provided.

Value

A Layer ggproto object.

Aesthetics

geom_range understands the following aesthetics (required aesthetics are in bold, optional in italic).

• x

• y

• xend (if data is numeric)

• yend (if data is numeric)

• alpha

• colour

• fill

• group

• linetype

• size

Examples

require(IRanges)
df <- DataFrame(x = IRanges(c(1, 2), c(3, 4)))

ggplot(df) +
  geom_range(aes(x))

teunbrand/ggnomics documentation built on Aug. 2, 2020, 7:34 p.m.