geom_slabinterval: Slab + point + interval meta-geom
In ggdist: Visualizations of Distributions and Uncertainty

geom_slabinterval

R Documentation

Slab + point + interval meta-geom

Description

This meta-geom supports drawing combinations of functions (as slabs, aka ridge plots or joy plots), points, and intervals. It acts as a meta-geom for many other ggdist geoms that are wrappers around this geom, including eye plots, half-eye plots, CCDF barplots, and point+multiple interval plots, and supports both horizontal and vertical orientations, dodging (via the position argument), and relative justification of slabs with their corresponding intervals.

Usage

geom_slabinterval(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  orientation = NA,
  normalize = "all",
  fill_type = "segments",
  interval_size_domain = c(1, 6),
  interval_size_range = c(0.6, 1.4),
  fatten_point = 1.8,
  arrow = NULL,
  show_slab = TRUE,
  show_point = TRUE,
  show_interval = TRUE,
  subguide = "none",
  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, or the result of a call to a position adjustment function. Setting this equal to `"dodge"` (`position_dodge()`) or `"dodgejust"` (`position_dodgejust()`) can be useful if you have overlapping geometries.
`...`	Other arguments passed to `layer()`. These are often aesthetics, used to set an aesthetic to a fixed value, like `colour = "red"` or `linewidth = 3` (see Aesthetics, below). They may also be parameters to the paired geom/stat.
`orientation`	Whether this geom is drawn horizontally or vertically. One of: `NA` (default): automatically detect the orientation based on how the aesthetics are assigned. Automatic detection works most of the time. `"horizontal"` (or `"y"`): draw horizontally, using the `y` aesthetic to identify different groups. For each group, uses the `x`, `xmin`, `xmax`, and `thickness` aesthetics to draw points, intervals, and slabs. `"vertical"` (or `"x"`): draw vertically, using the `x` aesthetic to identify different groups. For each group, uses the `y`, `ymin`, `ymax`, and `thickness` aesthetics to draw points, intervals, and slabs. For compatibility with the base ggplot naming scheme for `orientation`, `"x"` can be used as an alias for `"vertical"` and `"y"` as an alias for `"horizontal"` (ggdist had an `orientation` parameter before base ggplot did, hence the discrepancy).
`normalize`	How to normalize heights of functions input to the `thickness` aesthetic. One of: `"all"`: normalize so that the maximum height across all data is `1`. `"panels"`: normalize within panels so that the maximum height in each panel is `1`. `"xy"`: normalize within the x/y axis opposite the `orientation` of this geom so that the maximum height at each value of the opposite axis is `1`. `"groups"`: normalize within values of the opposite axis and within each group so that the maximum height in each group is `1`. `"none"`: values are taken as is with no normalization (this should probably only be used with functions whose values are in [0,1], such as CDFs). For a comprehensive discussion and examples of slab scaling and normalization, see the `thickness` scale article.
`fill_type`	What type of fill to use when the fill color or alpha varies within a slab. One of: `"segments"`: breaks up the slab geometry into segments for each unique combination of fill color and alpha value. This approach is supported by all graphics devices and works well for sharp cutoff values, but can give ugly results if a large number of unique fill colors are being used (as in gradients, like in `stat_gradientinterval()`). `"gradient"`: a `grid::linearGradient()` is used to create a smooth gradient fill. This works well for large numbers of unique fill colors, but requires R >= 4.1 and is not yet supported on all graphics devices. As of this writing, the `png()` graphics device with `type = "cairo"`, the `svg()` device, the `pdf()` device, and the `ragg::agg_png()` devices are known to support this option. On R < 4.1, this option will fall back to `fill_type = "segments"` with a message. `"auto"`: attempts to use `fill_type = "gradient"` if support for it can be auto-detected. On R >= 4.2, support for gradients can be auto-detected on some graphics devices; if support is not detected, this option will fall back to `fill_type = "segments"` (in case of a false negative, `fill_type = "gradient"` can be set explicitly). On R < 4.2, support for gradients cannot be auto-detected, so this will always fall back to `fill_type = "segments"`, in which case you can set `fill_type = "gradient"` explicitly if you are using a graphics device that support gradients.
`interval_size_domain`	A length-2 numeric vector giving the minimum and maximum of the values of the `size` and `linewidth` aesthetics that will be translated into actual sizes for intervals drawn according to `interval_size_range` (see the documentation for that argument.)
`interval_size_range`	A length-2 numeric vector. This geom scales the raw size aesthetic values when drawing interval and point sizes, as they tend to be too thick when using the default settings of `scale_size_continuous()`, which give sizes with a range of `c(1, 6)`. The `interval_size_domain` value indicates the input domain of raw size values (typically this should be equal to the value of the `range` argument of the `scale_size_continuous()` function), and `interval_size_range` indicates the desired output range of the size values (the min and max of the actual sizes used to draw intervals). Most of the time it is not recommended to change the value of this argument, as it may result in strange scaling of legends; this argument is a holdover from earlier versions that did not have size aesthetics targeting the point and interval separately. If you want to adjust the size of the interval or points separately, you can also use the `linewidth` or `point_size` aesthetics; see sub-geometry-scales.
`fatten_point`	A multiplicative factor used to adjust the size of the point relative to the size of the thickest interval line. If you wish to specify point sizes directly, you can also use the `point_size` aesthetic and `scale_point_size_continuous()` or `scale_point_size_discrete()`; sizes specified with that aesthetic will not be adjusted using `fatten_point`.
`arrow`	`grid::arrow()` giving the arrow heads to use on the interval, or `NULL` for no arrows.
`show_slab`	Should the slab portion of the geom be drawn?
`show_point`	Should the point portion of the geom be drawn?
`show_interval`	Should the interval portion of the geom be drawn?
`subguide`	Sub-guide used to annotate the `thickness` scale. One of: A function that takes a `scale` argument giving a ggplot2::Scale object and an `orientation` argument giving the orientation of the geometry and then returns a grid::grob that will draw the axis annotation, such as `subguide_axis()` (to draw a traditional axis) or `subguide_none()` (to draw no annotation). See `subguide_axis()` for a list of possibilities and examples. A string giving the name of such a function when prefixed with `"subguide"`; e.g. `"axis"` or `"none"`.
`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()`.

Details

geom_slabinterval() is a flexible meta-geom that you can use directly or through a variety of "shortcut" geoms that represent useful combinations of the various parameters of this geom. In many cases you will want to use the shortcut geoms instead as they create more useful mnemonic primitives, such as eye plots, half-eye plots, point+interval plots, or CCDF barplots.

The slab portion of the geom is much like a ridge or "joy" plot: it represents the value of a function scaled to fit between values on the x or y axis (depending on the value of orientation). Values of the functions are specified using the thickness aesthetic and are scaled to fit into scale times the distance between points on the relevant axis. E.g., if orientation is "horizontal", scale is 0.9, and y is a discrete variable, then the thickness aesthetic specifies the value of some function of x that is drawn for every y value and scaled to fit into 0.9 times the distance between points on the y axis.

For the interval portion of the geom, x and y aesthetics specify the location of the point, and ymin/ymax or xmin/xmax (depending on the value of orientation) specify the endpoints of the interval. A scaling factor for interval line width and point size is applied through the interval_size_domain, interval_size_range, and fatten_point parameters. These scaling factors are designed to give multiple uncertainty intervals reasonable scaling at the default settings for scale_size_continuous().

As a combination geom, this geom expects a datatype aesthetic specifying which part of the geom a given row in the input data corresponds to: "slab" or "interval". However, specifying this aesthetic manually is typically only necessary if you use this geom directly; the numerous wrapper geoms will usually set this aesthetic for you as needed, and their use is recommended unless you have a very custom use case.

Wrapper geoms include:

geom_pointinterval()
geom_interval()
geom_slab()

In addition, the stat_slabinterval() family of stats uses geoms from the geom_slabinterval() family, and is often easier to use than using these geoms directly. Typically, the ⁠geom_*⁠ versions are meant for use with already-summarized data (such as intervals) and the ⁠stat_*⁠ versions are summarize the data themselves (usually draws from a distribution) to produce the geom.

Value

A ggplot2::Geom representing a slab or combined slab+interval geometry which can be added to a ggplot() object.

Aesthetics

The slab+interval stats and geoms have a wide variety of aesthetics that control the appearance of their three sub-geometries: the slab, the point, and the interval.

Positional aesthetics

x: x position of the geometry
y: y position of the geometry

Slab-specific aesthetics

thickness: The thickness of the slab at each x value (if orientation = "horizontal") or y value (if orientation = "vertical") of the slab.
side: Which side to place the slab on. "topright", "top", and "right" are synonyms which cause the slab to be drawn on the top or the right depending on if orientation is "horizontal" or "vertical". "bottomleft", "bottom", and "left" are synonyms which cause the slab to be drawn on the bottom or the left depending on if orientation is "horizontal" or "vertical". "topleft" causes the slab to be drawn on the top or the left, and "bottomright" causes the slab to be drawn on the bottom or the right. "both" draws the slab mirrored on both sides (as in a violin plot).
scale: What proportion of the region allocated to this geom to use to draw the slab. If scale = 1, slabs that use the maximum range will just touch each other. Default is 0.9 to leave some space between adjacent slabs. For a comprehensive discussion and examples of slab scaling and normalization, see the thickness scale article.
justification: Justification of the interval relative to the slab, where 0 indicates bottom/left justification and 1 indicates top/right justification (depending on orientation). If justification is NULL (the default), then it is set automatically based on the value of side: when side is "top"/"right" justification is set to 0, when side is "bottom"/"left" justification is set to 1, and when side is "both" justification is set to 0.5.
datatype: When using composite geoms directly without a stat (e.g. geom_slabinterval()), datatype is used to indicate which part of the geom a row in the data targets: rows with datatype = "slab" target the slab portion of the geometry and rows with datatype = "interval" target the interval portion of the geometry. This is set automatically when using ggdist stats.

Interval-specific aesthetics

xmin: Left end of the interval sub-geometry (if orientation = "horizontal").
xmax: Right end of the interval sub-geometry (if orientation = "horizontal").
ymin: Lower end of the interval sub-geometry (if orientation = "vertical").
ymax: Upper end of the interval sub-geometry (if orientation = "vertical").

Point-specific aesthetics

shape: Shape type used to draw the point sub-geometry.

Color aesthetics

colour: (or color) The color of the interval and point sub-geometries. Use the slab_color, interval_color, or point_color aesthetics (below) to set sub-geometry colors separately.
fill: The fill color of the slab and point sub-geometries. Use the slab_fill or point_fill aesthetics (below) to set sub-geometry colors separately.
alpha: The opacity of the slab, interval, and point sub-geometries. Use the slab_alpha, interval_alpha, or point_alpha aesthetics (below) to set sub-geometry colors separately.
colour_ramp: (or color_ramp) A secondary scale that modifies the color scale to "ramp" to another color. See scale_colour_ramp() for examples.
fill_ramp: A secondary scale that modifies the fill scale to "ramp" to another color. See scale_fill_ramp() for examples.

Line aesthetics

linewidth: Width of the line used to draw the interval (except with geom_slab(): then it is the width of the slab). With composite geometries including an interval and slab, use slab_linewidth to set the line width of the slab (see below). For interval, raw linewidth values are transformed according to the interval_size_domain and interval_size_range parameters of the geom (see above).
size: Determines the size of the point. If linewidth is not provided, size will also determines the width of the line used to draw the interval (this allows line width and point size to be modified together by setting only size and not linewidth). Raw size values are transformed according to the interval_size_domain, interval_size_range, and fatten_point parameters of the geom (see above). Use the point_size aesthetic (below) to set sub-geometry size directly without applying the effects of interval_size_domain, interval_size_range, and fatten_point.
stroke: Width of the outline around the point sub-geometry.
linetype: Type of line (e.g., "solid", "dashed", etc) used to draw the interval and the outline of the slab (if it is visible). Use the slab_linetype or interval_linetype aesthetics (below) to set sub-geometry line types separately.

Slab-specific color and line override aesthetics

slab_fill: Override for fill: the fill color of the slab.
slab_colour: (or slab_color) Override for colour/color: the outline color of the slab.
slab_alpha: Override for alpha: the opacity of the slab.
slab_linewidth: Override for linwidth: the width of the outline of the slab.
slab_linetype: Override for linetype: the line type of the outline of the slab.

Interval-specific color and line override aesthetics

interval_colour: (or interval_color) Override for colour/color: the color of the interval.
interval_alpha: Override for alpha: the opacity of the interval.
interval_linetype: Override for linetype: the line type of the interval.

Point-specific color and line override aesthetics

point_fill: Override for fill: the fill color of the point.
point_colour: (or point_color) Override for colour/color: the outline color of the point.
point_alpha: Override for alpha: the opacity of the point.
point_size: Override for size: the size of the point.

Deprecated aesthetics

slab_size: Use slab_linewidth.
interval_size: Use interval_linewidth.

Other aesthetics (these work as in standard geoms)

width
height
group

See examples of some of these aesthetics in action in vignette("slabinterval"). Learn more about the sub-geom override aesthetics (like interval_color) in the scales documentation. Learn more about basic ggplot aesthetics in vignette("ggplot2-specs").

Author(s)

Matthew Kay

Examples


# geom_slabinterval() is typically not that useful on its own.
# See vignette("slabinterval") for a variety of examples of the use of its
# shortcut geoms and stats, which are more useful than using
# geom_slabinterval() directly.

ggdist documentation built on July 4, 2024, 9:08 a.m.