Skip to contents

Uncertain Smooth

Source: R/geom-smooth-sample.R, R/stat-smooth-sample.R
geom_smooth_sample.Rd

Identical to geom_smooth, except that it will accept a distribution in place of any of the usual aesthetics.

Usage

geom_smooth_sample(
  mapping = NULL,
  data = NULL,
  times = 10,
  seed = NULL,
  stat = "smooth_sample",
  position = "identity",
  ...,
  method = NULL,
  formula = NULL,
  se = TRUE,
  na.rm = FALSE,
  orientation = NA,
  show.legend = NA,
  inherit.aes = TRUE
)

stat_smooth_sample(
  mapping = NULL,
  data = NULL,
  geom = "smooth",
  position = "identity",
  ...,
  times = 10,
  seed = NULL,
  method = NULL,
  formula = NULL,
  se = TRUE,
  n = 80,
  span = 0.75,
  fullrange = FALSE,
  xseq = NULL,
  level = 0.95,
  method.args = list(),
  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)).

times

A parameter used to control the number of values sampled from each distribution.

seed

Set the seed for the layers random draw, allows you to plot the same draw across multiple layers.

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.

method

Smoothing method (function) to use, accepts either NULL or a character vector, e.g. "lm", "glm", "gam", "loess" or a function, e.g. MASS::rlm or mgcv::gam, stats::lm, or stats::loess. "auto" is also accepted for backwards compatibility. It is equivalent to NULL.

For method = NULL the smoothing method is chosen based on the size of the largest group (across all panels). stats::loess() is used for less than 1,000 observations; otherwise mgcv::gam() is used with formula = y ~ s(x, bs = "cs") with method = "REML". Somewhat anecdotally, loess gives a better appearance, but is \(O(N^{2})\) in memory, so does not work for larger datasets.

If you have fewer than 1,000 observations but want to use the same gam() model that method = NULL would use, then set method = "gam", formula = y ~ s(x, bs = "cs").

formula

Formula to use in smoothing function, eg. y ~ x, y ~ poly(x, 2), y ~ log(x). NULL by default, in which case method = NULL implies formula = y ~ x when there are fewer than 1,000 observations and formula = y ~ s(x, bs = "cs") otherwise.

se

Display confidence band around smooth? (TRUE by default, see level to control.)

na.rm

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

orientation

The orientation of the layer. The default (NA) automatically determines the orientation from the aesthetic mapping. In the rare event that this fails it can be given explicitly by setting orientation to either "x" or "y". See the Orientation section for more detail.

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().

geom, stat

Use to override the default connection between geom_smooth() and stat_smooth(). For more information about overriding these connections, see how the stat and geom arguments work.

n

Number of points at which to evaluate smoother.

span

Controls the amount of smoothing for the default loess smoother. Smaller numbers produce wigglier lines, larger numbers produce smoother lines. Only used with loess, i.e. when method = "loess", or when method = NULL (the default) and there are fewer than 1,000 observations.

fullrange

If TRUE, the smoothing line gets expanded to the range of the plot, potentially beyond the data. This does not extend the line into any additional padding created by expansion.

xseq

A numeric vector of values at which the smoother is evaluated. When NULL (default), xseq is internally evaluated as a sequence of n equally spaced points for continuous data.

level

Level of confidence band to use (0.95 by default).

method.args

List of additional arguments passed on to the modelling function defined by method.

Value

A ggplot2 layer

Examples

library(ggplot2)
# ggplot
ggplot(mpg, aes(displ, hwy)) +
  geom_point() +
  geom_smooth()
#> `geom_smooth()` using method = 'loess' and formula = 'y ~ x'


# ggdibbbler
ggplot(uncertain_mpg, aes(displ, hwy)) +
  geom_point_sample(alpha=0.5, size=0.2, seed = 22) + 
  geom_smooth_sample(linewidth=0.2, alpha=0.1, seed = 22) 
#> `geom_smooth()` using method = 'loess' and formula = 'y ~ x'


# Smooths are automatically fit to each group (defined by categorical
# aesthetics or the group aesthetic) and for each facet.
# ggplot
ggplot(mpg, aes(displ, hwy, colour = class)) +
  geom_point() +
  geom_smooth(se = FALSE, method = lm)
#> `geom_smooth()` using formula = 'y ~ x'

# ggdibbler
ggplot(uncertain_mpg, aes(displ, hwy, colour = class)) +
  geom_point_sample(alpha=0.5, size=0.2, seed = 22) +
  geom_smooth_sample(linewidth=0.2, alpha=0.1, 
    se = FALSE, method = lm, seed = 22)
#> `geom_smooth()` using formula = 'y ~ x'