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Tone discs

Source: R/geom-halftone.R
geom_spot.Rd

Each point becomes a disc of radius r mm (or aes(size = ), in mm) filled with a halftone whose tone is the point's value. Use it for a dot plot in which a second quantity is shown by ink density instead of a colour ramp. Each disc has its own centred hex lattice, clipped to the disc, and a ring in the disc's colour.

Usage

geom_spot(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  r = 3,
  pitch = 0.35,
  levels = NULL,
  bayer_n = 4,
  dot_max = 0.9,
  range = NULL,
  ring = TRUE,
  ring_lwd = 0.3,
  min_feature = 0.09,
  angle = NULL,
  shape = "circle",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

# S3 method for class 'spot'
makeContent(x)

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 to ggplot2::layer(), such as fixed aesthetics (colour = "black").

r

Disc radius in mm when size is not mapped.

pitch

Lattice spacing inside the discs, in mm.

levels

NULL for continuous tone (dot area follows tone exactly). An integer quantises tone to that many steps and dithers the remainder with algorithm; levels = 1 is a binary stipple.

bayer_n

Size of the Bayer matrix when algorithm = "bayer".

dot_max

Diameter of a full-tone dot as a fraction of pitch (0.9). Above 1 dots merge; it is the ink weight of the screen at 100% tone. For line screens it is the full-tone strip width, as a fraction of pitch.

range

Value range mapped to tone 0..1 when z is used; NULL uses the data range. A wider range lightens the screen.

ring

Draw the disc outline.

ring_lwd

Line width of the ring.

min_feature

Smallest printable feature in mm (0.09, i.e. 0.25 pt, the minimum line weight in journal artwork guidelines; see References). A cell whose dot would be smaller prints at the floor with probability tone/floor, so coverage is preserved and light tone becomes sparse minimum dots or broken hairlines. Hatch strips are never thinner. Set to 0 to disable.

angle

Rotation of the rosette in degrees; NULL means 15 for dots and 45 for hatching. Added to a mapped screen spec's angle only when given.

shape

"circle", "square", "diamond" or "line" (hatched discs, for one-ink dot plots). aes(screen = ) with scale_screen_discrete() varies angle and shape per group.

na.rm

Remove missing values silently.

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().

x

A spot grob (internal; makeContent method).

Value

A ggplot2 layer.

Details

Tone comes from aes(tone = ) through scale_tone_continuous(), which gives it a legend of discs at the breaks, or from aes(z = ) normalised inside the geom.

Examples

d <- expand.grid(gene = c("A", "B", "C"), cluster = 1:4); d$expr <- runif(12); d$pct <- runif(12)
ggplot2::ggplot(d, ggplot2::aes(cluster, gene, tone = expr, size = pct)) + geom_spot() +
    scale_tone_continuous() + ggplot2::scale_radius(range = c(1, 2.2)) +
  ggplot2::theme_minimal() + theme_halftone()