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Add markers to swimmer plots

Source: R/geom_swim_marker.R
geom_swim_marker.Rd

Markers are specific symbols or indicators placed on the lanes of a swimmer plot to denote particular events, milestones, or statuses. They provide additional contextual information about significant occurrences during the timeline, such as treatment responses or adverse events.

Usage

geom_swim_marker(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  check_overlap = FALSE,
  size.unit = "mm",
  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. 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_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".

  • For more information and other ways to specify the position, see the layer position documentation.

...

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.

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().

size.unit

How the size aesthetic is interpreted: as millimetres ("mm", default), points ("pt"), centimetres ("cm"), inches ("in"), or picas ("pc").

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

Map the event category to marker; the category selects a glyph and colour through scale_marker_discrete(). The marker scale controls both the plot glyph and its legend key. It sets the marker colour after ggplot2 applies aesthetic scales, so colour mappings, fixed colour settings, and after_scale() colour transformations do not override marker colours. Set marker colours with the scale's colours argument instead.

If using icon glyphs from fontawesome or bootstrap, first call load_fonts() to register the matching fonts. The supported family values are:

  • "Bootstrap"

  • "FontAwesome-Brands"

  • "FontAwesome-Regular"

  • "FontAwesome-Solid"

Aesthetics

Required aesthetics are x, y, and marker. marker should identify the event category; use scale_marker_discrete() to assign glyphs, colours, and legend labels. Other text aesthetics are inherited from ggplot2::geom_text().

Marker alignment

Markers are rendered as text glyphs. Even when a marker and lane share the same y-coordinate, the visible symbol can appear slightly above or below the lane because glyphs occupy different positions within the text reference box. This placement can vary with the font and graphics device, including when emoji or fallback fonts are used. You can adjust vjust for a particular plot, though one value may not suit every glyph or font; inspect the exported figure. ggswim retains ggplot2's text-rendering behavior because a correction based on one glyph or font may misalign others.

Examples

events <- data.frame(
  time = c(2, 4),
  id = c("A", "B"),
  event = c("Response", "Relapse")
)
ggplot2::ggplot(events, ggplot2::aes(x = time, y = id, marker = event)) +
  geom_swim_marker(size = 5) +
  scale_marker_discrete(
    glyphs = c("+", "x"),
    colours = c("steelblue", "firebrick"),
    limits = c("Response", "Relapse")
  )


if (FALSE) { # \dontrun{
# The first call downloads fonts into the user cache and needs internet.
load_fonts()
icon_events <- data.frame(time = 2, id = "A", event = "Review")
ggplot2::ggplot() +
  geom_swim_marker(
    data = icon_events,
    mapping = ggplot2::aes(x = time, y = id, marker = event),
    family = "FontAwesome-Solid", size = 5
  ) +
  scale_marker_discrete(
    glyphs = fontawesome("fa-check"), limits = "Review"
  )
} # }