Annotate areas with ellipses

Source: R/mark_ellipse.R

This geom lets you annotate sets of points via ellipses. The enclosing ellipses are estimated using the Khachiyan algorithm which guarantees an optimal solution within the given tolerance level. As this geom is often expanded it is of lesser concern that some points are slightly outside the ellipsis. The Khachiyan algorithm has polynomial complexity and can thus suffer from scaling issues. Still, it is only calculated on the convex hull of the groups, so performance issues should be rare (it can easily handle a hull consisting of 1000 points).

geom_mark_ellipse(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  expand = unit(5, "mm"),
  radius = expand,
  n = 100,
  tol = 0.01,
  label.margin = margin(2, 2, 2, 2, "mm"),
  label.width = NULL,
  label.minwidth = unit(50, "mm"),
  label.hjust = 0,
  label.fontsize = 12,
  label.family = "",
  label.lineheight = 1,
  label.fontface = c("bold", "plain"),
  label.fill = "white",
  label.colour = "black",
  label.buffer = unit(10, "mm"),
  con.colour = "black",
  con.size = 0.5,
  con.type = "elbow",
  con.linetype = 1,
  con.border = "one",
  con.cap = unit(3, "mm"),
  con.arrow = NULL,
  ...,
  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)).

stat

The statistical transformation to use on the data for this layer, either as a ggproto Geom subclass or as a string naming the stat stripped of the stat_ prefix (e.g. "count" rather than "stat_count")

position

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_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.

expand

A numeric or unit vector of length one, specifying the expansion amount. Negative values will result in contraction instead. If the value is given as a numeric it will be understood as a proportion of the plot area width.

radius

As expand but specifying the corner radius.

n

The number of points used to draw each ellipse. Defaults to 100.

tol

The tolerance cutoff. Lower values will result in ellipses closer to the optimal solution. Defaults to 0.01.

label.margin

The margin around the annotation boxes, given by a call to ggplot2::margin().

label.width

A fixed width for the label. Set to NULL to let the text or label.minwidth decide.

label.minwidth

The minimum width to provide for the description. If the size of the label exceeds this, the description is allowed to fill as much as the label.

label.hjust

The horizontal justification for the annotation. If it contains two elements the first will be used for the label and the second for the description.

label.fontsize

The size of the text for the annotation. If it contains two elements the first will be used for the label and the second for the description.

label.family

The font family used for the annotation. If it contains two elements the first will be used for the label and the second for the description.

label.lineheight

The height of a line as a multipler of the fontsize. If it contains two elements the first will be used for the label and the second for the description.

label.fontface

The font face used for the annotation. If it contains two elements the first will be used for the label and the second for the description.

label.fill

The fill colour for the annotation box. Use "inherit" to use the fill from the enclosure or "inherit_col" to use the border colour of the enclosure.

label.colour

The text colour for the annotation. If it contains two elements the first will be used for the label and the second for the description. Use "inherit" to use the border colour of the enclosure or "inherit_fill" to use the fill colour from the enclosure.

label.buffer

The size of the region around the mark where labels cannot be placed.

con.colour

The colour for the line connecting the annotation to the mark. Use "inherit" to use the border colour of the enclosure or "inherit_fill" to use the fill colour from the enclosure.

con.size

The width of the connector. Use "inherit" to use the border width of the enclosure.

con.type

The type of the connector. Either "elbow", "straight", or "none".

con.linetype

The linetype of the connector. Use "inherit" to use the border linetype of the enclosure.

con.border

The bordertype of the connector. Either "one" (to draw a line on the horizontal side closest to the mark), "all" (to draw a border on all sides), or "none" (not going to explain that one).

con.cap

The distance before the mark that the line should stop at.

con.arrow

An arrow specification for the connection using grid::arrow() for the end pointing towards the mark.

...

Other arguments passed on to layer(). These are often aesthetics, used to set an aesthetic to a fixed value, like colour = "red" or size = 3. They may also be parameters to the paired geom/stat.

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().

Aesthetics

geom_mark_ellipse understands the following aesthetics (required aesthetics are in bold):

  • x

  • y

  • x0 (used to anchor the label)

  • y0 (used to anchor the label)

  • filter

  • label

  • description

  • color

  • fill

  • group

  • size

  • linetype

  • alpha

Annotation

All geom_mark_* allow you to put descriptive textboxes connected to the mark on the plot, using the label and description aesthetics. The textboxes are automatically placed close to the mark, but without obscuring any of the datapoints in the layer. The placement is dynamic so if you resize the plot you'll see that the annotation might move around as areas become big enough or too small to fit the annotation. If there's not enough space for the annotation without overlapping data it will not get drawn. In these cases try resizing the plot, change the size of the annotation, or decrease the buffer region around the marks.

Filtering

Often marks are used to draw attention to, or annotate specific features of the plot and it is thus not desirable to have marks around everything. While it is possible to simply pre-filter the data used for the mark layer, the geom_mark_* geoms also comes with a dedicated filter aesthetic that, if set, will remove all rows where it evalutates to FALSE. There are multiple benefits of using this instead of prefiltering. First, you don't have to change your data source, making your code more adaptable for exploration. Second, the data removed by the filter aesthetic is remembered by the geom, and any annotation will take care not to overlap with the removed data.

See also

Other mark geoms: geom_mark_circle(), geom_mark_hull(), geom_mark_rect()

Examples

ggplot(iris, aes(Petal.Length, Petal.Width)) +
  geom_mark_ellipse(aes(fill = Species, filter = Species != 'versicolor')) +
  geom_point()


# Add annotation
ggplot(iris, aes(Petal.Length, Petal.Width)) +
  geom_mark_ellipse(aes(fill = Species, label = Species)) +
  geom_point()


# Long descriptions are automatically wrapped to fit into the width
iris$desc <- c(
  'A super Iris - and it knows it',
  'Pretty mediocre Iris, but give it a couple of years and it might surprise you',
  "You'll never guess what this Iris does every Sunday"
)[iris$Species]

ggplot(iris, aes(Petal.Length, Petal.Width)) +
  geom_mark_ellipse(aes(fill = Species, label = Species, description = desc,
                        filter = Species == 'setosa')) +
  geom_point()


# Change the buffer size to move labels farther away (or closer) from the
# marks
ggplot(iris, aes(Petal.Length, Petal.Width)) +
  geom_mark_ellipse(aes(fill = Species, label = Species),
                    label.buffer = unit(40, 'mm')) +
  geom_point()


# The connector is capped a bit before it reaches the mark, but this can be
# controlled
ggplot(iris, aes(Petal.Length, Petal.Width)) +
  geom_mark_ellipse(aes(fill = Species, label = Species),
                    con.cap = 0) +
  geom_point()


# If you want to use the scaled colours for the labels or connectors you can
# use the "inherit" keyword instead
ggplot(iris, aes(Petal.Length, Petal.Width)) +
  geom_mark_ellipse(aes(fill = Species, label = Species),
                    label.fill = "inherit") +
  geom_point()