stat_dens1d_filter: Filter observations by local 1D density
In ggpp: Grammar Extensions to 'ggplot2'

stat_dens1d_filter

R Documentation

Filter observations by local 1D density

Description

stat_dens1d_filter Filters-out/filters-in observations in regions of a plot panel with high density of observations, based on the values mapped to one of x and y aesthetics. stat_dens1d_filter_g does the same filtering by group instead of by panel. This second stat is useful for highlighting observations, while the first one tends to be most useful when the aim is to prevent clashes among text labels. By default the data are handled all together, but it is also possible to control labeling separately in each tail.

Usage

stat_dens1d_filter(
  mapping = NULL,
  data = NULL,
  geom = "point",
  position = "identity",
  ...,
  keep.fraction = 0.1,
  keep.number = Inf,
  keep.sparse = TRUE,
  keep.these = FALSE,
  exclude.these = FALSE,
  these.target = "label",
  pool.along = c("x", "none"),
  xintercept = 0,
  invert.selection = FALSE,
  bw = "SJ",
  kernel = "gaussian",
  adjust = 1,
  n = 512,
  return.density = FALSE,
  orientation = c("x", "y"),
  na.rm = TRUE,
  show.legend = FALSE,
  inherit.aes = TRUE
)

stat_dens1d_filter_g(
  mapping = NULL,
  data = NULL,
  geom = "point",
  position = "identity",
  keep.fraction = 0.1,
  keep.number = Inf,
  keep.sparse = TRUE,
  keep.these = FALSE,
  exclude.these = FALSE,
  these.target = "label",
  pool.along = c("x", "none"),
  xintercept = 0,
  invert.selection = FALSE,
  na.rm = TRUE,
  show.legend = FALSE,
  inherit.aes = TRUE,
  bw = "SJ",
  adjust = 1,
  kernel = "gaussian",
  n = 512,
  return.density = FALSE,
  orientation = c("x", "y"),
  ...
)

Arguments

`mapping`	The aesthetic mapping, usually constructed with `aes` or `aes_`. Only needs to be set at the layer level if you are overriding the plot defaults.
`data`	A layer specific dataset - only needed if you want to override the plot defaults.
`geom`	The geometric object to use display the data.
`position`	The position adjustment to use for overlapping points on this layer
`...`	other arguments passed on to `layer`. This can include aesthetics whose values you want to set, not map. See `layer` for more details.
`keep.fraction`	numeric vector of length 1 or 2 [0..1]. The fraction of the observations (or rows) in `data` to be retained.
`keep.number`	integer vector of length 1 or 2. Set the maximum number of observations to retain, effective only if obeying `keep.fraction` would result in a larger number.
`keep.sparse`	logical If `TRUE`, the default, observations from the more sparse regions are retained, if `FALSE` those from the densest regions.
`keep.these, exclude.these`	character vector, integer vector, logical vector or function that takes one or more variables in data selected by `these.target`. Negative integers behave as in R's extraction methods. The rows from `data` indicated by `keep.these` and `exclude.these` are kept or excluded irrespective of the local density.
`these.target`	character, numeric or logical selecting one or more column(s) of `data`. If `TRUE` the whole `data` object is passed.
`pool.along`	character, one of `"none"` or `"x"`, indicating if selection should be done pooling the observations along the x aesthetic, or separately on either side of `xintercept`.
`xintercept`	numeric The split point for the data filtering. If `NA` the data are not split.
`invert.selection`	logical If `TRUE`, the complement of the selected rows are returned.
`bw`	numeric or character The smoothing bandwidth to be used. If numeric, the standard deviation of the smoothing kernel. If character, a rule to choose the bandwidth, as listed in `bw.nrd`.
`kernel`	character See `density` for details.
`adjust`	numeric A multiplicative bandwidth adjustment. This makes it possible to adjust the bandwidth while still using the a bandwidth estimator through an argument passed to `bw`. The larger the value passed to `adjust` the stronger the smoothing, hence decreasing sensitivity to local changes in density.
`n`	numeric Number of equally spaced points at which the density is to be estimated for applying the cut point. See `density` for details.
`return.density`	logical vector of lenght 1. If `TRUE` add columns `"density"` and `"keep.obs"` to the returned data frame.
`orientation`	character The aesthetic along which density is computed. Given explicitly by setting orientation to either `"x"` or `"y"`.
`na.rm`	a logical value indicating whether `NA` values should be stripped before the computation proceeds.
`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.
`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

The 1D density of observations of x or y is computed with function density and used to select observations, passing to the geom a subset of the rows in its data input. The default is to select observations in sparse regions of the plot, but the selection can be inverted so that only observations in the densest regions are returned. Specific observations can be protected from being deselected and "kept" by passing a suitable argument to keep.these. Logical and integer vectors work as indexes to rows in data, while a values in a character vector are compared to the character values mapped to the label aesthetic. A function passed as argument to keep.these will receive as argument the values in the variable mapped to label and should return a character, logical or numeric vector as described above. If no variable has been mapped to label, row names are used in its place.

How many rows are retained in addition to those in keep.these is controlled with arguments passed to keep.number and keep.fraction. keep.number sets the maximum number of observations selected, whenever keep.fraction results in fewer observations selected, it is obeyed. If 'xintercept' is a finite value within the x range of the data and pool.along is passed "none" the data as are split into two groups and keep.number and keep.fraction are applied separately to each tail with density still computed jointly from all observations. If the length of keep.number and keep.fraction is one, this value is used for both tails, if their length is two, the first value is use for the left tail and the second value for the right tail.

Computation of density and of the default bandwidth require at least two observations with different values. If data do not fulfill this condition, they are kept only if keep.fraction = 1. This is correct behavior for a single observation, but can be surprising in the case of multiple observations.

Parameters keep.these and exclude.these make it possible to force inclusion or exclusion of observations after the density is computed. In case of conflict, exclude.these overrides keep.these.

Value

A plot layer instance. Using as output data a subset of the rows in input data retained based on a 1D filtering criterion.

Note

Which points are kept and which not depends on how dense and flexible is the density curve estimate. This depends on the values passed as arguments to parameters n, bw and kernel. It is also important to be aware that both geom_text() and geom_text_repel() can avoid over plotting by discarding labels at the plot rendering stage, i.e., what is plotted may differ from what is returned by this statistic.

Examples


random_string <-
  function(len = 6) {
    paste(sample(letters, len, replace = TRUE), collapse = "")
  }

# Make random data.
set.seed(1001)
d <- tibble::tibble(
  x = rnorm(100),
  y = rnorm(100),
  group = rep(c("A", "B"), c(50, 50)),
  lab = replicate(100, { random_string() })
)
d$xg <- d$x
d$xg[51:100] <- d$xg[51:100] + 1

# highlight the 1/10 of observations in sparsest regions of the plot
ggplot(data = d, aes(x, y)) +
  geom_point() +
  geom_rug(sides = "b") +
  stat_dens1d_filter(colour = "red") +
  stat_dens1d_filter(geom = "rug", colour = "red", sides = "b")

# highlight the 1/4 of observations in densest regions of the plot
ggplot(data = d, aes(x, y)) +
  geom_point() +
  geom_rug(sides = "b") +
  stat_dens1d_filter(colour = "blue",
                     keep.fraction = 1/4, keep.sparse = FALSE) +
  stat_dens1d_filter(geom = "rug", colour = "blue",
                     keep.fraction = 1/4, keep.sparse = FALSE,
                     sides = "b")

# switching axes
ggplot(data = d, aes(x, y)) +
  geom_point() +
  geom_rug(sides = "l") +
  stat_dens1d_filter(colour = "red", orientation = "y") +
  stat_dens1d_filter(geom = "rug", colour = "red", orientation = "y",
                     sides = "l")

# highlight 1/10 plus 1/10 observations in high and low density regions
ggplot(data = d, aes(x, y)) +
  geom_point() +
  geom_rug(sides = "b") +
  stat_dens1d_filter(colour = "red") +
  stat_dens1d_filter(geom = "rug", colour = "red", sides = "b") +
  stat_dens1d_filter(colour = "blue", keep.sparse = FALSE) +
  stat_dens1d_filter(geom = "rug",
                     colour = "blue", keep.sparse = FALSE, sides = "b")

# selecting the 1/10 observations in sparsest regions and their complement
ggplot(data = d, aes(x, y)) +
  stat_dens1d_filter(colour = "red") +
  stat_dens1d_filter(geom = "rug", colour = "red", sides = "b") +
  stat_dens1d_filter(colour = "blue", invert.selection = TRUE) +
  stat_dens1d_filter(geom = "rug",
                     colour = "blue", invert.selection = TRUE, sides = "b")

# density filtering done jointly across groups
ggplot(data = d, aes(xg, y, colour = group)) +
  geom_point() +
  geom_rug(sides = "b", colour = "black") +
  stat_dens1d_filter(shape = 1, size = 3, keep.fraction = 1/4, adjust = 2)

# density filtering done independently for each group
ggplot(data = d, aes(xg, y, colour = group)) +
  geom_point() +
  geom_rug(sides = "b") +
  stat_dens1d_filter_g(shape = 1, size = 3, keep.fraction = 1/4, adjust = 2)

# density filtering done jointly across groups by overriding grouping
ggplot(data = d, aes(xg, y, colour = group)) +
  geom_point() +
  geom_rug(sides = "b") +
  stat_dens1d_filter_g(colour = "black",
                       shape = 1, size = 3, keep.fraction = 1/4, adjust = 2)

# label observations
ggplot(data = d, aes(x, y, label = lab, colour = group)) +
  geom_point() +
  stat_dens1d_filter(geom = "text", hjust = "outward")

# looking under the hood with gginnards::geom_debug()
gginnards.installed <- requireNamespace("ggrepel", quietly = TRUE)
if (gginnards.installed) {
  library(gginnards)

  ggplot(data = d, aes(x, y, label = lab, colour = group)) +
    stat_dens1d_filter(geom = "debug")

  ggplot(data = d, aes(x, y, label = lab, colour = group)) +
    stat_dens1d_filter(geom = "debug", return.density = TRUE)

}

ggpp documentation built on Nov. 8, 2023, 1:10 a.m.