geom_phylomorpho: Plot a 2-D phylomorphospace in ggplot2

In deeptime: Plotting Tools for Anyone Working in Deep Time

Plot a 2-D phylomorphospace in ggplot2

Description

This behaves similar to phytools::phylomorphospace(), but is for plotting a 2-D phylomorphospace with ggplot2::ggplot(). This function works like any other ggplot2 geom; it can be combined with other geoms (see the example below), and the output can be modified using scales, themes, etc.

Usage

geom_phylomorpho(
  tree,
  mapping = NULL,
  data = NULL,
  position = "identity",
  ...,
  seg_args = list(),
  point_args = list(),
  arrow = NULL,
  arrow.fill = NULL,
  lineend = "butt",
  linejoin = "round",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

tree	An object of class "phylo".
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".
...	Other arguments passed on to both ggplot2::geom_segment() and ggplot2::geom_point().
seg_args	A list of arguments passed only to ggplot2::geom_segment().
point_args	A list of arguments passed only to ggplot2::geom_point().
arrow	specification for arrow heads, as created by grid::arrow().
arrow.fill	fill colour to use for the arrow head (if closed). NULL means use colour aesthetic.
lineend	Line end style (round, butt, square).
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

The ancestral states are estimated using phytools::fastAnc(). Note that phytools is not necessarily installed with deeptime, but it is required to use this function. Following the estimation of the ancestral states, the nodes are connected using ggplot2::geom_segment(), while the tips are indicated using ggplot2::geom_point().

The default expectation is that the order of the data is the same order as the tip labels of the tree (tree$tip.label). However, if this is not the case, you can map the optional label aesthetic to a column in the data that contains the tip names (see example below).

Examples

library(ggplot2)

library(ape)
tr <- rtree(10)
dat <- data.frame(
  x = runif(10), y = runif(10), label = tr$tip.label,
  row.names = tr$tip.label
)
ggplot(dat, aes(x = x, y = y, label = label)) +
  geom_phylomorpho(tr) +
  geom_label(size = 5)

deeptime documentation built on Oct. 30, 2024, 9:08 a.m.