stat_bagplot: Bagplots
In corybrunson/ordr: A Tidyverse Extension for Ordinations and Biplots

stat_bagplot

R Documentation

Bagplots

Description

Construct medians, bags, fences, and outlier specifications for bagplots.

Usage

stat_bagplot(
  mapping = NULL,
  data = NULL,
  geom = "bagplot",
  position = "identity",
  fraction = 0.5,
  coef = 3,
  median = TRUE,
  fence = TRUE,
  outliers = TRUE,
  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)`).
`geom`	The geometric object to use to display the data for this layer. When using a `⁠stat_*()⁠` function to construct a layer, the `geom` argument can be used to override the default coupling between stats and geoms. The `geom` argument accepts the following: A `Geom` ggproto subclass, for example `GeomPoint`. A string naming the geom. To give the geom as a string, strip the function name of the `geom_` prefix. For example, to use `geom_point()`, give the geom as `"point"`. For more information and other ways to specify the geom, see the layer geom 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.
`fraction`	Fraction of the data to include in the bag.
`coef`	Scale factor of the fence relative to the bag.
`median`, `fence`, `outliers`	Logical indicators whether to include median, fence, and outliers in the composite output.
`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()`.
`...`	Arguments passed on to `stat_depth` `notion` Character; the name of the depth function (passed to `ddalpha::depth.()`). `notion_params` List of additional parameters passed via `...` to `ddalpha::depth.()`.

Details

A bagplot comprises a single, often filled, depth contour (the "bag") overlaid with the hull of its union with the data points contained in its scaled expansion from the depth median (the "fence") and a scatterplot of outliers beyond the fence (the "loop"). Rousseeuw &al (1999) suggest the term "bag-and-bolster plot" evocative of the "box-and-whisker plot".

While the depth median can be obtained using stat_center(), the data depth values used to compute it are also used to demarcate the bag, so it is implemented separately in StatBagplot$compute_group() for efficiency.

stat_bagplot() is designed to pair with geom_bagplot(), analogously to the pairing of ggplot2::stat_boxplot() with ggplot2::geom_boxplot(). In particular, GeomBagplot is the only ggproto that recognizes the computed variable component, used by StatBagplot to separate data for the four bagplot elements.

Biplot layers

ggbiplot() uses ggplot2::fortify() internally to produce a single data frame with a .matrix column distinguishing the subjects ("rows") and variables ("cols"). The stat layers stat_rows() and stat_cols() simply filter the data frame to one of these two.

The geom layers ⁠geom_rows_*()⁠ and ⁠geom_cols_*()⁠ call the corresponding stat in order to render plot elements for the corresponding factor matrix. ⁠geom_dims_*()⁠ selects a default matrix based on common practice, e.g. points for rows and arrows for columns.

Ordination aesthetics

This statistical transformation is compatible with the convenience function ord_aes().

Some transformations (e.g. stat_center()) commute with projection to the lower (1 or 2)-dimensional biplot space. If they detect aesthetics of the form ⁠..coord[0-9]+⁠, then ..coord1 and ..coord2 are converted to x and y while any remaining are ignored.

Other transformations (e.g. stat_spantree()) yield different results in a lower-dimensional biplot when they are computed before versus after projection. If the stat layer detects these aesthetics, then the transformation is performed before projection, and the results in the first two dimensions are returned as x and y.

A small number of transformations (stat_rule()) are incompatible with ordination aesthetics but will accept ord_aes() without warning.

Computed variables

These are calculated during the statistical transformation and can be accessed with delayed evaluation.

component: the component of the composite plot; used internally

References

Rousseeuw PJ, Ruts I, & Tukey JW (1999) "The Bagplot: A Bivariate Boxplot". The American Statistician, 53(4): 382–387. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1080/00031305.1999.10474494")}

Examples

# petroleum rock base plot
p <- ggplot(rock, aes(area, shape, size = peri)) + theme_bw()
# scatterplot
p + geom_point()
# NB: Non-standard aesthetics are handled as in version > 3.5.1; see:
# https://github.com/tidyverse/ggplot2/issues/6191
# custom bag fraction, coefficient, and aesthetics
p + stat_bagplot(fraction = .4, coef = 1.5,
                 outlier_gp = list(shape = "asterisk"))
# invisible fence
p + stat_bagplot(fence = FALSE)

corybrunson/ordr documentation built on Feb. 24, 2025, 6:34 a.m.