Label clades on a phylogenetic tree plotted with ggtree

This geom adds labels and corresponding vertical bars to specified clades of a phylogenetic tree that has been plotted using ggtree::ggtree(). It is therefore very similar to ggtree::geom_cladelab(). However, unlike ggtree::geom_cladelab(), this geom is intended to work with all coordinate systems, including coord_geo() and coord_geo_radial().

Usage

geom_text_clade(
  mapping = NULL,
  data = NULL,
  text_geom = "text",
  stat = "identity",
  position = "identity",
  ...,
  parse = FALSE,
  auto_adjust = TRUE,
  extend = c(0, 0),
  check_overlap = FALSE,
  lineend = "butt",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

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)).

text_geom

Which geom to use for the text labels. Valid options are "text" for ggplot2::geom_text() and "label" for ggplot2::geom_label().

stat

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 to 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".
For more information and other ways to specify the stat, see the layer stat documentation.

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_nudge(). 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_nudge(), give the position as "nudge".

...

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.

parse

If TRUE, the labels will be parsed into expressions and displayed as described in ?plotmath.

auto_adjust

Should upside-down text labels automatically be rotated 180° to improve readability?

extend

A numeric vector of length 2 indicating how much to extend the vertical bar beyond the minimum and maximum y-values of the clade. The first value extends the bar above the maximum y-value, and the second value extends the bar below the minimum y-value.

check_overlap

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().

lineend

Line end style (round, butt, square).

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. 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.

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. annotation_borders().

Details

The clades to be labeled are specified using the node aesthetic which identifies the most recent common ancestor of the clade. The label aesthetic specifies the text label for each clade. The ggfun::%<+%() operator should be used to combine custom clade labels with the tree (see Examples). If no nodes are specified, a label will be added to every tip by default (like geom_text_phylo()).

The vertical bar for each clade extends from the minimum to the maximum y-values of all descendant nodes of the specified node, with optional extensions above and below these values controlled by the extend parameter. Each label will be plotted center aligned and perpendicular to its corresponding bar 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.

Aesthetics

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)
parent (pulled from the phylogeny by default)
node (pulled from the phylogeny by default)
label (pulled from the phylogeny by default)
alpha
angle
color/colour
family
fontface
group
hjust
lineheight
size
vjust

Alignment

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. Note that numeric values outside of [0, 1] will also work and will move the text beyond the normal alignment positions (e.g., the default hjust value is -0.02).

Examples

library(ggplot2)
library(ggtree)
library(phytools)
data(primate.tree)
# single annotation
revts(ggtree(primate.tree)) +
  geom_text_clade(label = "Hominoidea", node = 114, extend = c(0.1, 0.1)) +
  coord_geo_radial()
#> Warning: Unknown or uninitialised column: `subgroup`.
#> Warning: Unknown or uninitialised column: `subgroup`.
#> Warning: Unknown or uninitialised column: `subgroup`.
#> Warning: Unknown or uninitialised column: `subgroup`.


# data frame of clade labels
clades.df <- data.frame(
  clade = c("Lorisoidea", "Lemuroidea", "Tarsioidea", "Ceboidea",
            "Cercopithecoidea", "Hominoidea"),
  node = c(166, 146, 144, 120, 95, 114)
)
revts(ggtree(primate.tree)) %<+% clades.df +
  geom_text_clade(aes(label = clade), extend = c(0.1, 0.1)) +
  coord_geo_radial()
#> Warning: Removed 173 rows containing missing values or values outside the scale range.
#> Warning: Unknown or uninitialised column: `subgroup`.
#> Warning: Unknown or uninitialised column: `subgroup`.
#> Warning: Unknown or uninitialised column: `subgroup`.
#> Warning: Unknown or uninitialised column: `subgroup`.


# display with other tip data
data(primate.data)
activity <- subset(primate.data, select = "Activity_pattern")
revts(gheatmap(ggtree(primate.tree), activity, offset = -70,
               colnames = FALSE, width = 0.03, color = NA)) %<+% clades.df +
  geom_text_clade(aes(label = clade), extend = c(0.1, 0.1),
                  position = position_nudge(x = 10)) +
  coord_geo_radial()
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.
#> Warning: Removed 173 rows containing missing values or values outside the scale range.
#> Warning: Unknown or uninitialised column: `subgroup`.
#> Warning: Unknown or uninitialised column: `subgroup`.
#> Warning: Unknown or uninitialised column: `subgroup`.
#> Warning: Unknown or uninitialised column: `subgroup`.