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.
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
)An object of class "phylo".
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.
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)).
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().
A list of arguments passed only to ggplot2::geom_segment().
A list of arguments passed only to ggplot2::geom_point().
specification for arrow heads, as created by grid::arrow().
fill colour to use for the arrow head (if closed). NULL
means use colour aesthetic.
Line end style (round, butt, square).
Line join style (round, mitre, bevel).
If FALSE, the default, missing values are removed with
a warning. If TRUE, missing values are silently removed.
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.
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().
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$tip.label). However, if this is not the
case, you can map the optional label aesthetic to a column in the data that
contains the tip names (see example below).
library(ggplot2)
if (FALSE) { # require(ape)
library(ape)
tr <- rtree(10)
dat <- data.frame(
x = runif(10), y = runif(10), label = tr$tip.label,
row.names = tr$tip.label
)
ggplot(dat, aes(x = x, y = y, label = label)) +
geom_phylomorpho(tr) +
geom_label(size = 5)
}
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