Skip to contents

Scale for resection

Source: R/scale_arrow.R
scale_resect.Rd

Arrow geoms have a resect aesthetic that controls how much an arrow should be shortened. These scales can help to rescale the output range of resection.

Usage

scale_resect_continuous(
  ...,
  range = NULL,
  aesthetics = c("resect_head", "resect_fins"),
  guide = "none"
)

scale_resect_discrete(
  ...,
  values = NULL,
  aesthetics = c("resect_head", "resect_fins"),
  range = NULL,
  guide = "none"
)

Arguments

...

Arguments passed on to ggplot2::continuous_scale, ggplot2::discrete_scale

name

The name of the scale. Used as the axis or legend title. If waiver(), the default, the name of the scale is taken from the first mapping used for that aesthetic. If NULL, the legend title will be omitted.

breaks

One of:

  • NULL for no breaks

  • waiver() for the default breaks computed by the transformation object

  • A numeric vector of positions

  • A function that takes the limits as input and returns breaks as output (e.g., a function returned by scales::extended_breaks()). Note that for position scales, limits are provided after scale expansion. Also accepts rlang lambda function notation.

minor_breaks

One of:

  • NULL for no minor breaks

  • waiver() for the default breaks (none for discrete, one minor break between each major break for continuous)

  • A numeric vector of positions

  • A function that given the limits returns a vector of minor breaks. Also accepts rlang lambda function notation. When the function has two arguments, it will be given the limits and major break positions.

n.breaks

An integer guiding the number of major breaks. The algorithm may choose a slightly different number to ensure nice break labels. Will only have an effect if breaks = waiver(). Use NULL to use the default number of breaks given by the transformation.

labels

One of the options below. Please note that when labels is a vector, it is highly recommended to also set the breaks argument as a vector to protect against unintended mismatches.

  • NULL for no labels

  • waiver() for the default labels computed by the transformation object

  • A character vector giving labels (must be same length as breaks)

  • An expression vector (must be the same length as breaks). See ?plotmath for details.

  • A function that takes the breaks as input and returns labels as output. Also accepts rlang lambda function notation.

limits

One of:

  • NULL to use the default scale range

  • A numeric vector of length two providing limits of the scale. Use NA to refer to the existing minimum or maximum

  • A function that accepts the existing (automatic) limits and returns new limits. Also accepts rlang lambda function notation. Note that setting limits on positional scales will remove data outside of the limits. If the purpose is to zoom, use the limit argument in the coordinate system (see coord_cartesian()).

rescaler

A function used to scale the input values to the range [0, 1]. This is always scales::rescale(), except for diverging and n colour gradients (i.e., scale_colour_gradient2(), scale_colour_gradientn()). The rescaler is ignored by position scales, which always use scales::rescale(). Also accepts rlang lambda function notation.

oob

One of:

  • Function that handles limits outside of the scale limits (out of bounds). Also accepts rlang lambda function notation.

  • The default (scales::censor()) replaces out of bounds values with NA.

  • scales::squish() for squishing out of bounds values into range.

  • scales::squish_infinite() for squishing infinite values into range.

expand

For position scales, a vector of range expansion constants used to add some padding around the data to ensure that they are placed some distance away from the axes. Use the convenience function expansion() to generate the values for the expand argument. The defaults are to expand the scale by 5% on each side for continuous variables, and by 0.6 units on each side for discrete variables.

na.value

Missing values will be replaced with this value.

transform

For continuous scales, the name of a transformation object or the object itself. Built-in transformations include "asn", "atanh", "boxcox", "date", "exp", "hms", "identity", "log", "log10", "log1p", "log2", "logit", "modulus", "probability", "probit", "pseudo_log", "reciprocal", "reverse", "sqrt" and "time".

A transformation object bundles together a transform, its inverse, and methods for generating breaks and labels. Transformation objects are defined in the scales package, and are called transform_<name>. If transformations require arguments, you can call them from the scales package, e.g. scales::transform_boxcox(p = 2). You can create your own transformation with scales::new_transform().

trans

[Deprecated] Deprecated in favour of transform.

position

For position scales, The position of the axis. left or right for y axes, top or bottom for x axes.

call

The call used to construct the scale for reporting messages.

na.translate

Unlike continuous scales, discrete scales can easily show missing values, and do so by default. If you want to remove missing values from a discrete scale, specify na.translate = FALSE.

drop

Should unused factor levels be omitted from the scale? The default, TRUE, uses the levels that appear in the data; FALSE includes the levels in the factor. Please note that to display every level in a legend, the layer should use show.legend = TRUE.

range

A numeric vector of length 2 indicating the minimum and maximum size of the resection after transformation in millimetres. range is mutually exclusive with the values argument in discrete scales.

aesthetics

The names of the aesthetics that this scale works with.

guide

A function used to create a guide or its name. See guides() for more information.

values

(Discrete scale only) A numeric vector to map data values to. The values will be matched in order with the limits of the scale, or with breaks if provided. If this is a named vector, the values will be matched based on the names instead. Data values that don't match will be given na.value. values is mutually exclusive with the range

Value

A <Scale> that can be added to a plot.

Details

Conceptually, these scales depart slightly from ggplot2 conventions. The scale_resect_continuous() function returns an identity scale when range = NULL (default) and a typical continuous scale when the range argument is set. The scale_resect_discrete() acts as a manual scale when values is set and as an ordinal scale when range is set.

Examples

# A plot with points indicating path ends
p <- ggplot(whirlpool(5), aes(x, y, colour = group)) +
  geom_point(data = ~ subset(.x, arc == ave(arc, group, FUN = max)))

# Resect scale as an identity scale
p + geom_arrow(aes(resect_head = as.integer(group))) +
  scale_resect_continuous()


# Resect scale as typical continuous scale
p + geom_arrow(aes(resect_head = as.integer(group))) +
  scale_resect_continuous(range = c(0, 10))


# Resect scale as manual scale
p + geom_arrow(aes(resect_head = group)) +
  scale_resect_discrete(values = c(10, 5, 0, 5, 10))


# Resect scale as ordinal scale
p + geom_arrow(aes(resect_head = group)) +
  scale_resect_discrete(range = c(0, 10))