This geom adds labels to all or a subset of the nodes of a phylogenetic tree
that has been plotted using ggtree::ggtree(). It is therefore very similar
to ggtree::geom_tiplab(), ggtree::geom_tiplab2(),
ggtree::geom_nodelab(), and ggtree::geom_nodelab2(). However, unlike
those geoms, this geom is intended to work with all coordinate systems,
including coord_geo() and coord_geo_radial().
geom_text_phylo(
mapping = NULL,
data = NULL,
stat = "identity",
position = "identity",
...,
parse = FALSE,
nudge_x = 0,
nudge_y = 0,
node_type = "tip",
auto_adjust = TRUE,
check_overlap = FALSE,
size.unit = "mm",
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE
)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)).
The statistical transformation to use on the data for this layer.
When using a geom_*() function to construct a layer, the stat
argument can be used the override the default coupling between geoms and
stats. The stat argument accepts the following:
A Stat ggproto subclass, for example StatCount.
A string naming the stat. To give the stat as a string, strip the
function name of the stat_ prefix. For example, to use stat_count(),
give the stat as "count".
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 layer()'s params argument. These
arguments broadly fall into one of 4 categories below. Notably, further
arguments to the position argument, or aesthetics that are required
can not be passed through .... Unknown arguments that are not part
of the 4 categories below are ignored.
Static aesthetics that are not mapped to a scale, but are at a fixed
value and apply to the layer as a whole. For example, colour = "red"
or linewidth = 3. The geom's documentation has an Aesthetics
section that lists the available options. The 'required' aesthetics
cannot be passed on to the params. Please note that while passing
unmapped aesthetics as vectors is technically possible, the order and
required length is not guaranteed to be parallel to the input data.
When constructing a layer using
a stat_*() function, the ... argument can be used to pass on
parameters to the geom part of the layer. An example of this is
stat_density(geom = "area", outline.type = "both"). The geom's
documentation lists which parameters it can accept.
Inversely, when constructing a layer using a
geom_*() function, the ... argument can be used to pass on parameters
to the stat part of the layer. An example of this is
geom_area(stat = "density", adjust = 0.5). The stat's documentation
lists which parameters it can accept.
The key_glyph argument of layer() may also be passed on through
.... This can be one of the functions described as
key glyphs, to change the display of the layer in the legend.
If TRUE, the labels will be parsed into expressions and
displayed as described in ?plotmath.
Horizontal and vertical adjustment to nudge labels by.
Useful for offsetting text from points, particularly on discrete scales.
Cannot be jointly specified with position.
Determines the subset of nodes to label. Valid options are "tip" for tip nodes, "internal" for non-tip nodes, and "all" for all nodes.
Should upside-down text labels automatically be rotated 180° to improve readability?
If TRUE, text that overlaps previous text in the
same layer will not be plotted. check_overlap happens at draw time and in
the order of the data. Therefore data should be arranged by the label
column before calling geom_text(). Note that this argument is not
supported by geom_label().
How the size aesthetic is interpreted: as millimetres
("mm", default), points ("pt"), centimetres ("cm"), inches ("in"),
or picas ("pc").
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().
geom_text_phylo() understands the following
aesthetics (required aesthetics are in bold):
x (pulled from the phylogeny by default)
y (pulled from the phylogeny by default)
label (pulled from the phylogeny by default)
alpha
angle
color/colour
family
fontface
group
hjust
lineheight
size
vjust
You can modify text alignment with the vjust and hjust
aesthetics. These can either be a number between 0 (left/bottom) and
1 (right/top) or a character ("left", "middle", "right", "bottom",
"center", "top"). There are two special alignments: "inward" and
"outward". Inward always aligns text towards the center, and outward
aligns it away from the center.
Each label will be plotted with the same angle as the branch/edge leading to
its node by default. The angle, hjust, and vjust aesthetics can be used
to adjust this. If custom angle values are specified, these will be
added to the default angle as calculated as described above.
As with ggplot2::geom_text(), the limits of axes will not be
expanded to accommodate the new labels, so you may need to extend them
manually using the limits or expand arguments within scale_ or coord_
functions. Note that coord_geo() by default sets expand = FALSE.
library(ggplot2)
if (FALSE) { # require(ggtree)
library(ape)
library(ggtree)
tr <- rtree(10)
revts(ggtree(tr)) +
geom_text_phylo() +
coord_geo_radial("epochs")
}
Run the code above in your browser using DataLab