geom_pointinterval: Point + multiple uncertainty interval plots (ggplot geom)

Description

Combined point + multiple interval geoms with default aesthetics designed for use with output from point_interval(). Wrapper around geom_slabinterval().

Usage

geom_pointinterval(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  orientation = NA,
  show_slab = FALSE,
  show.legend = c(size = FALSE)
)

Arguments

mapping

Set of aesthetic mappings created by aes() or 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, as a string.

position

The position adjustment to use for overlapping points on this layer. Setting this equal to "dodge" can be useful if you have overlapping intervals.

...

Arguments passed on to geom_slabinterval

normalize: How to normalize heights of functions input to the thickness aesthetic. If "all" (the default), normalize so that the maximum height across all data is 1; if "panels", normalize within panels so that the maximum height in each panel is 1; if "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; if "groups", normalize within values of the opposite axis and within groups so that the maximum height in each group is 1; if "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).
fill_type: What type of fill to use when the fill color or alpha varies within a slab. The default, "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 result in ugly results if a large number of unique fill colors are being used (as in gradients, like in stat_gradientinterval()). When fill_type == "gradient", a 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.
interval_size_domain: The minimum and maximum of the values of the size aesthetic that will be translated into actual sizes for intervals drawn according to interval_size_range (see the documentation for that argument.)
interval_size_range: (Deprecated). 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 instead use the interval_size or point_size aesthetics; see 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.
show_point: Should the point portion of the geom be drawn? Default TRUE.
show_interval: Should the interval portion of the geom be drawn? Default TRUE.
na.rm: If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.
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().

orientation

Whether this geom is drawn horizontally ("horizontal") or vertically ("vertical"). The default, NA, automatically detects the orientation based on how the aesthetics are assigned, and should generally do an okay job at this. When horizontal (resp. vertical), the geom uses the y (resp. x) aesthetic to identify different groups, then for each group uses the x (resp. y) aesthetic and the thickness aesthetic to draw a function as an slab, and draws points and intervals horizontally (resp. vertically) using the xmin, x, and xmax (resp. ymin, y, and ymax) aesthetics. 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" (tidybayes had an orientation parameter before ggplot did, and I think the tidybayes naming scheme is more intuitive: "x" and "y" are not orientations and their mapping to orientations is, in my opinion, backwards; but the base ggplot naming scheme is allowed for compatibility).

show_slab

Should the slab portion of the geom be drawn? Default TRUE.

show.legend

Should this layer be included in the legends? Default is c(size = FALSE), unlike most geoms, to match its common use cases. FALSE hides all legends, TRUE shows all legends, and NA shows only those that are mapped (the default for most geoms).

Value

A ggplot2::Geom representing a point+multiple uncertainty 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.
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: (or fill_ramp) A secondary scale that modifies the fill scale to "ramp" to another color. See scale_fill_ramp() for examples.

Line aesthetics

size: Width of the outline around the slab (if visible). Also determines the width of the line used to draw the interval and the size of the point, but 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 slab_size, interval_size, or point_size aesthetics (below) to set sub-geometry line widths separately (note that when size is set directly using the override aesthetics, interval and point sizes are not affected by 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/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_size: Override for size: 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/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_size: Override for size: the line width of the interval.
interval_linetype: Override for linetype: the line type of the interval.

Point-specific color/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.

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").

Details

These geoms are wrappers around geom_slabinterval() with defaults designed to produce points+interval plots. These geoms set some default aesthetics equal to the .lower, .upper, and .width columns generated by the point_interval family of functions, making them often more convenient than vanilla geom_pointrange() when used with functions like median_qi(), mean_qi(), mode_hdi(), etc.

Specifically, geom_pointinterval acts as if its default aesthetics are aes(size = -.width).

Examples

Run this code

# NOT RUN {
library(dplyr)
library(ggplot2)

data(RankCorr_u_tau, package = "ggdist")

# orientation is detected automatically based on
# use of xmin/xmax or ymin/ymax

RankCorr_u_tau %>%
  group_by(i) %>%
  median_qi(.width = c(.8, .95)) %>%
  ggplot(aes(y = i, x = u_tau, xmin = .lower, xmax = .upper)) +
  geom_pointinterval()

RankCorr_u_tau %>%
  group_by(i) %>%
  median_qi(.width = c(.8, .95)) %>%
  ggplot(aes(x = i, y = u_tau, ymin = .lower, ymax = .upper)) +
  geom_pointinterval()

# }

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