ggalluvial: stat_stratum – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

stat_stratum

Stratum positions

Description

Given a dataset with alluvial structure, stat_stratum calculates the centroids (x and y) and heights (ymin and ymax) of the strata at each axis.

Usage

stat_stratum(
  mapping = NULL,
  data = NULL,
  geom = "stratum",
  position = "identity",
  decreasing = NULL,
  reverse = NULL,
  absolute = NULL,
  discern = FALSE,
  distill = first,
  negate.strata = NULL,
  infer.label = FALSE,
  label.strata = NULL,
  min.y = NULL,
  max.y = NULL,
  min.height = NULL,
  max.height = NULL,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  ...
)

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)`).
`geom`	The geometric object to use display the data; override the default.
`position`	Position adjustment, either as a string, or the result of a call to a position adjustment function.
`decreasing`	Logical; whether to arrange the strata at each axis in the order of the variable values (`NA`, the default), in ascending order of totals (largest on top, `FALSE`), or in descending order of totals (largest on bottom, `TRUE`).
`reverse`	Logical; if `decreasing` is `NA`, whether to arrange the strata at each axis in the reverse order of the variable values, so that they match the order of the values in the legend. Ignored if `decreasing` is not `NA`. Defaults to `TRUE`.
`absolute`	Logical; if some cases or strata are negative, whether to arrange them (respecting `decreasing` and `reverse`) using negative or absolute values of `y`.
`discern`	Passed to `to_lodes_form()` if `data` is in alluvia format.
`distill`	A function (or its name) to be used to distill alluvium values to a single lode label, accessible via `ggplot2::after_stat()` (similar to its behavior in `to_alluvia_form()`). In addition to existing functions, accepts the character values `"first"` (the default), `"last"`, and `"most"` (which returns the first modal value).
`negate.strata`	A vector of values of the `stratum` aesthetic to be treated as negative (will ignore missing values with a warning).
`infer.label`	Logical; whether to assign the `stratum` or `alluvium` variable to the `label` aesthetic. Defaults to `FALSE`, and requires that no `label` aesthetic is assigned. This parameter is intended for use only with data in alluva form, which are converted to lode form before the statistical transformation. Deprecated; use `ggplot2::after_stat()` instead.
`label.strata`	Defunct; alias for `infer.label`.
`min.y, max.y`	Numeric; bounds on the heights of the strata to be rendered. Use these bounds to exclude strata outside a certain range, for example when labeling strata using `ggplot2::geom_text()`.
`min.height, max.height`	Deprecated aliases for `min.y` and `max.y`.
`na.rm`	Logical: if `FALSE`, the default, `NA` lodes are not included; if `TRUE`, `NA` lodes constitute a separate category, plotted in grey (regardless of the color scheme).
`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()`.
`...`	Additional arguments passed to `ggplot2::layer()`.

Aesthetics

stat_alluvium, stat_flow, and stat_stratum require one of two sets of aesthetics:

x and at least one of alluvium and stratum
any number of axis[0-9]* (axis1, axis2, etc.)

Use x, alluvium, and/or stratum for data in lodes format and axis[0-9]* for data in alluvia format (see alluvial-data). Arguments to parameters inconsistent with the format will be ignored. Additionally, each stat_*() accepts the following optional aesthetics:

y
weight
order
group
label

y controls the heights of the alluvia, and may be aggregated across equivalent observations. weight applies to the computed variables (see that section below) but does not affect the positional aesthetics. order, recognized by stat_alluvium() and stat_flow(), is used to arrange the lodes within each stratum. It tolerates duplicates and takes precedence over the differentiation aesthetics (when aes.bind is not "none") and lode guidance with respect to the remaining axes. (It replaces the deprecated parameter lode.ordering.) group is used internally; arguments are ignored. label is used to label the strata or lodes and must take a unique value across the observations within each stratum or lode.

These and any other aesthetics are aggregated as follows: Numeric aesthetics, including y, are summed. Character and factor aesthetics, including label, are assigned to strata or lodes provided they take unique values across the observations within each (and are otherwise assigned NA).

Computed variables

These can be used with ggplot2::after_stat() to control aesthetic evaluation.

n: number of cases in lode
count: cumulative weight of lode
prop: weighted proportion of lode
stratum: value of variable used to define strata
deposit: order in which (signed) strata are deposited
lode: lode label distilled from alluvia (stat_alluvium() and stat_flow() only)
flow: direction of flow "to" or "from" from its axis (stat_flow() only)

The numerical variables n, count, and prop are calculated after the data are grouped by x and weighted by weight (in addition to y). The integer variable deposit is used internally to sort the data before calculating heights. The character variable lode is obtained from alluvium according to distill.

Package options

stat_stratum, stat_alluvium, and stat_flow order strata and lodes according to the values of several parameters, which must be held fixed across every layer in an alluvial plot. These package-specific options set global values for these parameters that will be defaulted to when not manually set:

ggalluvial.decreasing (each stat_*): defaults to NA.
ggalluvial.reverse (each stat_*): defaults to TRUE.
ggalluvial.absolute (each stat_*): defaults to TRUE.
ggalluvial.cement.alluvia (stat_alluvium): defaults to FALSE.
ggalluvial.lode.guidance (stat_alluvium): defaults to "zigzag".
ggalluvial.aes.bind (stat_alluvium and stat_flow): defaults to "none".

See base::options() for how to use options.

Defunct parameters

The previously defunct parameters weight and aggregate.wts have been discontinued. Use y and cement.alluvia instead.

Examples

data(vaccinations)
# only `stratum` assignment is necessary to generate strata
ggplot(vaccinations,
       aes(y = freq,
           x = survey, stratum = response,
           fill = response)) +
  stat_stratum(width = .5)

# lode data, positioning with y labels
ggplot(vaccinations,
       aes(y = freq,
           x = survey, stratum = response, alluvium = subject,
           label = after_stat(count))) +
  stat_stratum(geom = "errorbar") +
  geom_text(stat = "stratum")
# alluvium data, positioning with stratum labels
ggplot(as.data.frame(Titanic),
       aes(y = Freq,
           axis1 = Class, axis2 = Sex, axis3 = Age, axis4 = Survived)) +
  geom_text(stat = "stratum", aes(label = after_stat(stratum))) +
  stat_stratum(geom = "errorbar") +
  scale_x_discrete(limits = c("Class", "Sex", "Age", "Survived"))

# omit labels for strata outside a y range
ggplot(vaccinations,
       aes(y = freq,
           x = survey, stratum = response,
           fill = response, label = response)) +
  stat_stratum(width = .5) +
  geom_text(stat = "stratum", min.y = 100)

# date-valued axis variables
ggplot(vaccinations,
       aes(x = end_date, y = freq, stratum = response, alluvium = subject,
           fill = response)) +
  stat_alluvium(geom = "flow", lode.guidance = "forward",
                width = 30) +
  stat_stratum(width = 30) +
  labs(x = "Survey date", y = "Number of respondents")

admissions <- as.data.frame(UCBAdmissions)
admissions <- transform(admissions, Count = Freq * (-1) ^ (Admit == "Rejected"))
# use negative y values to encode rejection versus acceptance
ggplot(admissions,
       aes(y = Count, axis1 = Dept, axis2 = Gender)) +
  geom_alluvium(aes(fill = Dept), width = 1/12) +
  geom_stratum(width = 1/12, fill = "black", color = "grey") +
  geom_label(stat = "stratum", aes(label = after_stat(stratum)), min.y = 200) +
  scale_x_discrete(limits = c("Department", "Gender"), expand = c(.05, .05))
# computed variable 'deposit' indicates order of each signed stratum
ggplot(admissions,
       aes(y = Count, axis1 = Dept, axis2 = Gender)) +
  geom_alluvium(aes(fill = Dept), width = 1/12) +
  geom_stratum(width = 1/12, fill = "black", color = "grey") +
  geom_text(stat = "stratum", aes(label = after_stat(deposit)),
            color = "white") +
  scale_x_discrete(limits = c("Department", "Gender"), expand = c(.05, .05))
# fixed-width strata with acceptance and rejection totals
ggplot(admissions,
       aes(y = sign(Count), weight = Count, axis1 = Dept, axis2 = Gender)) +
  geom_alluvium(aes(fill = Dept), width = 1/8) +
  geom_stratum(width = 1/8, fill = "black", color = "grey") +
  geom_text(stat = "stratum",
            aes(label = paste0(stratum,
                               ifelse(nchar(as.character(stratum)) == 1L,
                                      ": ", "\n"),
                               after_stat(n))),
            color = "white", size = 3) +
  scale_x_discrete(limits = c("Department", "Gender"), expand = c(.05, .05))

ggalluvial

Alluvial Plots in 'ggplot2'

v0.12.3

GPL-3

Authors

Jason Cory Brunson [aut, cre], Quentin D. Read [aut]

Initial release

2020-12-04