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.
Arguments
- tree
An object of class "phylo".
- mapping
Set of aesthetic mappings created by
aes()
. If specified andinherit.aes = TRUE
(the default), it is combined with the default mapping at the top level of the plot. You must supplymapping
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 toggplot()
.A
data.frame
, or other object, will override the plot data. All objects will be fortified to produce a data frame. Seefortify()
for which variables will be created.A
function
will be called with a single argument, the plot data. The return value must be adata.frame
, and will be used as the layer data. Afunction
can be created from aformula
(e.g.~ head(.x, 10)
).- position
Position adjustment, either as a string naming the adjustment (e.g.
"jitter"
to useposition_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 both
ggplot2::geom_segment()
andggplot2::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 usecolour
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. IfTRUE
, 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, andTRUE
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()
.
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).