Package 'ggalluvial' reference manual

Title:	Alluvial Plots in 'ggplot2'
Description:	Alluvial plots use variable-width ribbons and stacked bar plots to represent multi-dimensional or repeated-measures data with categorical or ordinal variables; see Riehmann, Hanfler, and Froehlich (2005) <doi:10.1109/INFVIS.2005.1532152> and Rosvall and Bergstrom (2010) <doi:10.1371/journal.pone.0008694>. Alluvial plots are statistical graphics in the sense of Wilkinson (2006) <doi:10.1007/0-387-28695-0>; they share elements with Sankey diagrams and parallel sets plots but are uniquely determined from the data and a small set of parameters. This package extends Wickham's (2010) <doi:10.1198/jcgs.2009.07098> layered grammar of graphics to generate alluvial plots from tidy data.
Authors:	Jason Cory Brunson [aut, cre], Quentin D. Read [aut]
Maintainer:	Jason Cory Brunson <[email protected]>
License:	GPL-3
Version:	0.12.5
Built:	2024-11-08 04:59:21 UTC
Source:	https://github.com/corybrunson/ggalluvial

Check for alluvial structure and convert between alluvial formats

Description

Alluvial plots consist of multiple horizontally-distributed columns (axes) representing factor variables, vertical divisions (strata) of these axes representing these variables' values; and splines (alluvial flows) connecting vertical subdivisions (lodes) within strata of adjacent axes representing subsets or amounts of observations that take the corresponding values of the corresponding variables. This function checks a data frame for either of two types of alluvial structure:

Usage

is_lodes_form(
  data,
  key,
  value,
  id,
  weight = NULL,
  site = NULL,
  logical = TRUE,
  silent = FALSE
)

is_alluvia_form(
  data,
  ...,
  axes = NULL,
  weight = NULL,
  logical = TRUE,
  silent = FALSE
)

to_lodes_form(
  data,
  ...,
  axes = NULL,
  key = "x",
  value = "stratum",
  id = "alluvium",
  diffuse = FALSE,
  discern = FALSE
)

to_alluvia_form(data, key, value, id, distill = FALSE)
is_lodes_form(
  data,
  key,
  value,
  id,
  weight = NULL,
  site = NULL,
  logical = TRUE,
  silent = FALSE
)

is_alluvia_form(
  data,
  ...,
  axes = NULL,
  weight = NULL,
  logical = TRUE,
  silent = FALSE
)

to_lodes_form(
  data,
  ...,
  axes = NULL,
  key = "x",
  value = "stratum",
  id = "alluvium",
  diffuse = FALSE,
  discern = FALSE
)

to_alluvia_form(data, key, value, id, distill = FALSE)

Arguments

`data`	A data frame.
`key`, `value`, `id`	In `to_lodes_form`, handled as in `tidyr::gather()` and used to name the new axis (key), stratum (value), and alluvium (identifying) variables. In `to_alluvia_form`, handled as in `tidyr::spread()` and used to identify the fields of `data` to be used as the axis (key), stratum (value), and alluvium (identifying) variables.
`weight`	Optional field of `data`, handled using `rlang::enquo()`, to be used as heights or depths of the alluvia or lodes.
`site`	Optional vector of fields of `data`, handled using `rlang::enquos()`, to be used to group rows before testing for duplicate and missing id-axis pairings. Variables intended for faceting should be passed to `site`.
`logical`	Defunct. Whether to return a logical value or a character string indicating the type of alluvial structure ("none", "lodes", or "alluvia").
`silent`	Whether to print messages.
`...`	Used in `is_alluvia_form` and `to_lodes_form` as in `dplyr::select()` to determine axis variables, as an alternative to `axes`. Ignored when `axes` is provided.
`axes`	In `⁠*_alluvia_form⁠`, handled as in `dplyr::select()` and used to identify the field(s) of `data` to be used as axes.
`diffuse`	Fields of `data`, handled using `tidyselect::vars_select()`, to merge into the reshapen data by `id`. They must be a subset of the axis variables. Alternatively, a logical value indicating whether to merge all (`TRUE`) or none (`FALSE`) of the axis variables.
`discern`	Logical value indicating whether to suffix values of the variables used as axes that appear at more than one variable in order to distinguish their factor levels. This forces the levels of the combined factor variable `value` to be in the order of the axes.
`distill`	A logical value indicating whether to include variables, other than those passed to `key` and `value`, that vary within values of `id`. Alternatively, a function (or its name) to be used to distill each such variable to a single value. In addition to existing functions, `distill` accepts the character values `"first"` (used if `distill` is `TRUE`), `"last"`, and `"most"` (which returns the first modal value).

Details

One row per lode, wherein each row encodes a subset or amount of observations having a specific profile of axis values, a key field encodes the axis, a value field encodes the value within each axis, and a id column identifies multiple lodes corresponding to the same subset or amount of observations. is_lodes_form tests for this structure.
One row per alluvium, wherein each row encodes a subset or amount of observations having a specific profile of axis values and a set axes of fields encodes its values at each axis variable. is_alluvia_form tests for this structure.

to_lodes_form takes a data frame with several designated variables to be used as axes in an alluvial plot, and reshapes the data frame so that the axis variable names constitute a new factor variable and their values comprise another. Other variables' values will be repeated, and a row-grouping variable can be introduced. This function invokes tidyr::gather().

to_alluvia_form takes a data frame with axis and axis value variables to be used in an alluvial plot, and reshape the data frame so that the axes constitute separate variables whose values are given by the value variable. This function invokes tidyr::spread().

Examples

# Titanic data in alluvia format
titanic_alluvia <- as.data.frame(Titanic)
head(titanic_alluvia)
is_alluvia_form(titanic_alluvia,
                weight = "Freq")
# Titanic data in lodes format
titanic_lodes <- to_lodes_form(titanic_alluvia,
                               key = "x", value = "stratum", id = "alluvium",
                               axes = 1:4)
head(titanic_lodes)
is_lodes_form(titanic_lodes,
              key = "x", value = "stratum", id = "alluvium",
              weight = "Freq")
# again in lodes format, this time diffusing the `Class` variable
titanic_lodes2 <- to_lodes_form(titanic_alluvia,
                                key = variable, value = value,
                                id = cohort,
                                1:3, diffuse = Class)
head(titanic_lodes2)
is_lodes_form(titanic_lodes2,
              key = variable, value = value, id = cohort,
              weight = Freq)
# use `site` to separate data before lode testing
is_lodes_form(titanic_lodes2,
              key = variable, value = value, id = Class,
              weight = Freq)
is_lodes_form(titanic_lodes2,
              key = variable, value = value, id = Class,
              weight = Freq, site = cohort)

# curriculum data in lodes format
data(majors)
head(majors)
is_lodes_form(majors,
              key = "semester", value = "curriculum", id = "student")
# curriculum data in alluvia format
majors_alluvia <- to_alluvia_form(majors,
                                  key = "semester", value = "curriculum",
                                  id = "student")
head(majors_alluvia)
is_alluvia_form(majors_alluvia, tidyselect::starts_with("CURR"))

# distill variables that vary within `id` values
set.seed(1)
majors$hypo_grade <- LETTERS[sample(5, size = nrow(majors), replace = TRUE)]
majors_alluvia2 <- to_alluvia_form(majors,
                                   key = "semester", value = "curriculum",
                                   id = "student",
                                   distill = "most")
head(majors_alluvia2)

# options to distinguish strata at different axes
gg <- ggplot(majors_alluvia,
             aes(axis1 = CURR1, axis2 = CURR7, axis3 = CURR13))
gg +
  geom_alluvium(aes(fill = as.factor(student)), width = 2/5, discern = TRUE) +
  geom_stratum(width = 2/5, discern = TRUE) +
  geom_text(stat = "stratum", discern = TRUE, aes(label = after_stat(stratum)))
gg +
  geom_alluvium(aes(fill = as.factor(student)), width = 2/5, discern = FALSE) +
  geom_stratum(width = 2/5, discern = FALSE) +
  geom_text(stat = "stratum", discern = FALSE, aes(label = after_stat(stratum)))
# warning when inappropriate
ggplot(majors[majors$semester %in% paste0("CURR", c(1, 7, 13)), ],
       aes(x = semester, stratum = curriculum, alluvium = student,
           label = curriculum)) +
  geom_alluvium(aes(fill = as.factor(student)), width = 2/5, discern = TRUE) +
  geom_stratum(width = 2/5, discern = TRUE) +
  geom_text(stat = "stratum", discern = TRUE)
# Titanic data in alluvia format
titanic_alluvia <- as.data.frame(Titanic)
head(titanic_alluvia)
is_alluvia_form(titanic_alluvia,
                weight = "Freq")
# Titanic data in lodes format
titanic_lodes <- to_lodes_form(titanic_alluvia,
                               key = "x", value = "stratum", id = "alluvium",
                               axes = 1:4)
head(titanic_lodes)
is_lodes_form(titanic_lodes,
              key = "x", value = "stratum", id = "alluvium",
              weight = "Freq")
# again in lodes format, this time diffusing the `Class` variable
titanic_lodes2 <- to_lodes_form(titanic_alluvia,
                                key = variable, value = value,
                                id = cohort,
                                1:3, diffuse = Class)
head(titanic_lodes2)
is_lodes_form(titanic_lodes2,
              key = variable, value = value, id = cohort,
              weight = Freq)
# use `site` to separate data before lode testing
is_lodes_form(titanic_lodes2,
              key = variable, value = value, id = Class,
              weight = Freq)
is_lodes_form(titanic_lodes2,
              key = variable, value = value, id = Class,
              weight = Freq, site = cohort)

# curriculum data in lodes format
data(majors)
head(majors)
is_lodes_form(majors,
              key = "semester", value = "curriculum", id = "student")
# curriculum data in alluvia format
majors_alluvia <- to_alluvia_form(majors,
                                  key = "semester", value = "curriculum",
                                  id = "student")
head(majors_alluvia)
is_alluvia_form(majors_alluvia, tidyselect::starts_with("CURR"))

# distill variables that vary within `id` values
set.seed(1)
majors$hypo_grade <- LETTERS[sample(5, size = nrow(majors), replace = TRUE)]
majors_alluvia2 <- to_alluvia_form(majors,
                                   key = "semester", value = "curriculum",
                                   id = "student",
                                   distill = "most")
head(majors_alluvia2)

# options to distinguish strata at different axes
gg <- ggplot(majors_alluvia,
             aes(axis1 = CURR1, axis2 = CURR7, axis3 = CURR13))
gg +
  geom_alluvium(aes(fill = as.factor(student)), width = 2/5, discern = TRUE) +
  geom_stratum(width = 2/5, discern = TRUE) +
  geom_text(stat = "stratum", discern = TRUE, aes(label = after_stat(stratum)))
gg +
  geom_alluvium(aes(fill = as.factor(student)), width = 2/5, discern = FALSE) +
  geom_stratum(width = 2/5, discern = FALSE) +
  geom_text(stat = "stratum", discern = FALSE, aes(label = after_stat(stratum)))
# warning when inappropriate
ggplot(majors[majors$semester %in% paste0("CURR", c(1, 7, 13)), ],
       aes(x = semester, stratum = curriculum, alluvium = student,
           label = curriculum)) +
  geom_alluvium(aes(fill = as.factor(student)), width = 2/5, discern = TRUE) +
  geom_stratum(width = 2/5, discern = TRUE) +
  geom_text(stat = "stratum", discern = TRUE)

Alluvia across strata

Description

geom_alluvium receives a dataset of the horizontal (x) and vertical (y, ymin, ymax) positions of the lodes of an alluvial plot, the intersections of the alluvia with the strata. It plots both the lodes themselves, using geom_lode(), and the flows between them, using geom_flow().

Usage

geom_alluvium(
  mapping = NULL,
  data = NULL,
  stat = "alluvium",
  position = "identity",
  width = 1/3,
  knot.pos = 1/4,
  knot.prop = TRUE,
  curve_type = NULL,
  curve_range = NULL,
  segments = NULL,
  outline.type = "both",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  ...
)

data_to_alluvium(
  data,
  knot.prop = TRUE,
  curve_type = "spline",
  curve_range = NULL,
  segments = NULL
)
geom_alluvium(
  mapping = NULL,
  data = NULL,
  stat = "alluvium",
  position = "identity",
  width = 1/3,
  knot.pos = 1/4,
  knot.prop = TRUE,
  curve_type = NULL,
  curve_range = NULL,
  segments = NULL,
  outline.type = "both",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  ...
)

data_to_alluvium(
  data,
  knot.prop = TRUE,
  curve_type = "spline",
  curve_range = NULL,
  segments = NULL
)

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)`).
`stat`	The statistical transformation to use on the data; override the default.
`position`	Position adjustment, either as a string naming the adjustment (e.g. `"jitter"` to use `position_jitter`), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.
`width`	Numeric; the width of each stratum, as a proportion of the distance between axes. Defaults to 1/3.
`knot.pos`	The horizontal distance of x-spline knots from each stratum (`width/2` from its axis), either (if `knot.prop = TRUE`, the default) as a proportion of the length of the x-spline, i.e. of the gap between adjacent strata, or (if `knot.prop = FALSE`) on the scale of the `x` direction.
`knot.prop`	Logical; whether to interpret `knot.pos` as a proportion of the length of each flow (the default), rather than on the `x` scale.
`curve_type`	Character; the type of curve used to produce flows. Defaults to `"xspline"` and can be alternatively set to one of `"linear"`, `"cubic"`, `"quintic"`, `"sine"`, `"arctangent"`, and `"sigmoid"`. `"xspline"` produces approximation splines using 4 points per curve; the alternatives produce interpolation splines between points along the graphs of functions of the associated type. See the Curves section.
`curve_range`	For alternative `curve_type`s based on asymptotic functions, the value along the asymptote at which to truncate the function to obtain the shape that will be scaled to fit between strata. See the Curves section.
`segments`	The number of segments to be used in drawing each alternative curve (each curved boundary of each flow). If less than 3, will be silently changed to 3.
`outline.type`	Type of outline of each alluvium; one of `"both"`, `"lower"`, `"upper"`, and `"full"`.
`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()`.

Details

The helper function data_to_alluvium() takes internal ggplot2 data (mapped aesthetics) and curve parameters for a single alluvium as input and returns a data frame of x, y, and shape used by grid::xsplineGrob() to render the alluvium.

Aesthetics

geom_alluvium, geom_flow, geom_lode, and geom_stratum understand the following aesthetics (required aesthetics are in bold):

x
y
ymin
ymax
alpha
colour
fill
linetype
size
group

group is used internally; arguments are ignored.

Alluvium, flow, and lode geoms default to alpha = 0.5. Learn more about setting these aesthetics in vignette("ggplot2-specs", package = "ggplot2").

Curves

By default, geom_alluvium() and geom_flow() render flows between lodes as filled regions between parallel x-splines. These graphical elements, generated using grid::xsplineGrob(), are parameterized by the relative location of the knot (knot.pos). They are quick to render and clear to read, but users may prefer plots that use differently-shaped ribbons.

A variety of such options are documented at, e.g., this easing functions cheat sheet and this blog post by Jeffrey Shaffer. Easing functions are not (yet) used in ggalluvial, but several alternative curves are available. Each is encoded as a continuous, increasing, bijective function from the unit interval $[0,1]$ to itself, and each is rescaled so that its endpoints meet the corresponding lodes. They are rendered piecewise-linearly, by default using segments = 48. Summon each curve type by passing one of the following strings to curve_type:

"linear": $f(x)=x$ , the unique degree-1 polynomial that takes 0 to 0 and 1 to 1
"cubic": $f(x)=3x^{2}-2x^{3}$ , the unique degree-3 polynomial that also is flat at both endpoints
"quintic": $f(x)=10x^{3}-15x^{4}+6x^{5}$ , the unique degree-5 polynomial that also has zero curvature at both endpoints
"sine": the unique sinusoidal function that is flat at both endpoints
"arctangent": the inverse tangent function, scaled and re-centered to the unit interval from the interval centered at zero with radius curve_range
"sigmoid": the sigmoid function, scaled and re-centered to the unit interval from the interval centered at zero with radius curve_range

Only the (default) "xspline" option uses the ⁠knot.*⁠ parameters, while only the alternative curves use the segments parameter, and only "arctangent" and "sigmoid" use the curve_range parameter. (Both are ignored if not needed.) Larger values of curve_range result in greater compression and steeper slopes. The NULL default will be changed to 2+sqrt(3) for "arctangent" and to 6 for "sigmoid".

These package-specific options set global values for curve_type, curve_range, and segments that will be defaulted to when not manually set:

ggalluvial.curve_type: defaults to "xspline".
ggalluvial.curve_range: defaults to NA, which triggers the curve-specific default values.
ggalluvial.segments: defaults to 48L.

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

Defunct parameters

The previously defunct parameters axis_width and ribbon_bend have been discontinued. Use width and knot.pos instead.

Examples

# basic
ggplot(as.data.frame(Titanic),
       aes(y = Freq,
           axis1 = Class, axis2 = Sex, axis3 = Age,
           fill = Survived)) +
  geom_alluvium() +
  scale_x_discrete(limits = c("Class", "Sex", "Age"))

gg <- ggplot(alluvial::Refugees,
             aes(y = refugees, x = year, alluvium = country))
# time series bump chart (sigmoid flows)
gg + geom_alluvium(aes(fill = country, colour = country),
                   width = 1/4, alpha = 2/3, decreasing = FALSE,
                   curve_type = "sigmoid")
# time series line plot of refugees data, sorted by country
gg + geom_alluvium(aes(fill = country, colour = country),
                   decreasing = NA, width = 0, knot.pos = 0)


# irregular spacing between axes of a continuous variable
refugees_sub <- subset(alluvial::Refugees, year %in% c(2003, 2005, 2010, 2013))
gg <- ggplot(data = refugees_sub,
             aes(x = year, y = refugees, alluvium = country)) +
  theme_bw() +
  scale_fill_brewer(type = "qual", palette = "Set3")
# proportional knot positioning (default)
gg +
  geom_alluvium(aes(fill = country),
                alpha = .75, decreasing = FALSE, width = 1/2) +
  geom_stratum(aes(stratum = country), decreasing = FALSE, width = 1/2)
# constant knot positioning
gg +
  geom_alluvium(aes(fill = country),
                alpha = .75, decreasing = FALSE, width = 1/2,
                knot.pos = 1, knot.prop = FALSE) +
  geom_stratum(aes(stratum = country), decreasing = FALSE, width = 1/2)
# coarsely-segmented curves
gg +
  geom_alluvium(aes(fill = country),
                alpha = .75, decreasing = FALSE, width = 1/2,
                curve_type = "arctan", segments = 6) +
  geom_stratum(aes(stratum = country), decreasing = FALSE, width = 1/2)
# custom-ranged curves
gg +
  geom_alluvium(aes(fill = country),
                alpha = .75, decreasing = FALSE, width = 1/2,
                curve_type = "arctan", curve_range = 1) +
  geom_stratum(aes(stratum = country), decreasing = FALSE, width = 1/2)

# basic
ggplot(as.data.frame(Titanic),
       aes(y = Freq,
           axis1 = Class, axis2 = Sex, axis3 = Age,
           fill = Survived)) +
  geom_alluvium() +
  scale_x_discrete(limits = c("Class", "Sex", "Age"))

gg <- ggplot(alluvial::Refugees,
             aes(y = refugees, x = year, alluvium = country))
# time series bump chart (sigmoid flows)
gg + geom_alluvium(aes(fill = country, colour = country),
                   width = 1/4, alpha = 2/3, decreasing = FALSE,
                   curve_type = "sigmoid")
# time series line plot of refugees data, sorted by country
gg + geom_alluvium(aes(fill = country, colour = country),
                   decreasing = NA, width = 0, knot.pos = 0)


# irregular spacing between axes of a continuous variable
refugees_sub <- subset(alluvial::Refugees, year %in% c(2003, 2005, 2010, 2013))
gg <- ggplot(data = refugees_sub,
             aes(x = year, y = refugees, alluvium = country)) +
  theme_bw() +
  scale_fill_brewer(type = "qual", palette = "Set3")
# proportional knot positioning (default)
gg +
  geom_alluvium(aes(fill = country),
                alpha = .75, decreasing = FALSE, width = 1/2) +
  geom_stratum(aes(stratum = country), decreasing = FALSE, width = 1/2)
# constant knot positioning
gg +
  geom_alluvium(aes(fill = country),
                alpha = .75, decreasing = FALSE, width = 1/2,
                knot.pos = 1, knot.prop = FALSE) +
  geom_stratum(aes(stratum = country), decreasing = FALSE, width = 1/2)
# coarsely-segmented curves
gg +
  geom_alluvium(aes(fill = country),
                alpha = .75, decreasing = FALSE, width = 1/2,
                curve_type = "arctan", segments = 6) +
  geom_stratum(aes(stratum = country), decreasing = FALSE, width = 1/2)
# custom-ranged curves
gg +
  geom_alluvium(aes(fill = country),
                alpha = .75, decreasing = FALSE, width = 1/2,
                curve_type = "arctan", curve_range = 1) +
  geom_stratum(aes(stratum = country), decreasing = FALSE, width = 1/2)

Flows between lodes or strata

Description

geom_flow receives a dataset of the horizontal (x) and vertical (y, ymin, ymax) positions of the lodes of an alluvial plot, the intersections of the alluvia with the strata. It reconfigures these into alluvial segments connecting pairs of corresponding lodes in adjacent strata and plots filled x-splines between each such pair, using a provided knot position parameter knot.pos, and filled rectangles at either end, using a provided width.

Usage

geom_flow(
  mapping = NULL,
  data = NULL,
  stat = "flow",
  position = "identity",
  width = 1/3,
  knot.pos = 1/4,
  knot.prop = TRUE,
  curve_type = NULL,
  curve_range = NULL,
  segments = NULL,
  outline.type = "both",
  aes.flow = "forward",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  ...
)

positions_to_flow(
  x0,
  x1,
  ymin0,
  ymax0,
  ymin1,
  ymax1,
  kp0,
  kp1,
  knot.prop,
  curve_type,
  curve_range,
  segments
)
geom_flow(
  mapping = NULL,
  data = NULL,
  stat = "flow",
  position = "identity",
  width = 1/3,
  knot.pos = 1/4,
  knot.prop = TRUE,
  curve_type = NULL,
  curve_range = NULL,
  segments = NULL,
  outline.type = "both",
  aes.flow = "forward",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  ...
)

positions_to_flow(
  x0,
  x1,
  ymin0,
  ymax0,
  ymin1,
  ymax1,
  kp0,
  kp1,
  knot.prop,
  curve_type,
  curve_range,
  segments
)

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)`).
`stat`	The statistical transformation to use on the data; override the default.
`position`	Position adjustment, either as a string naming the adjustment (e.g. `"jitter"` to use `position_jitter`), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.
`width`	Numeric; the width of each stratum, as a proportion of the distance between axes. Defaults to 1/3.
`knot.pos`	The horizontal distance of x-spline knots from each stratum (`width/2` from its axis), either (if `knot.prop = TRUE`, the default) as a proportion of the length of the x-spline, i.e. of the gap between adjacent strata, or (if `knot.prop = FALSE`) on the scale of the `x` direction.
`knot.prop`	Logical; whether to interpret `knot.pos` as a proportion of the length of each flow (the default), rather than on the `x` scale.
`curve_type`	Character; the type of curve used to produce flows. Defaults to `"xspline"` and can be alternatively set to one of `"linear"`, `"cubic"`, `"quintic"`, `"sine"`, `"arctangent"`, and `"sigmoid"`. `"xspline"` produces approximation splines using 4 points per curve; the alternatives produce interpolation splines between points along the graphs of functions of the associated type. See the Curves section.
`curve_range`	For alternative `curve_type`s based on asymptotic functions, the value along the asymptote at which to truncate the function to obtain the shape that will be scaled to fit between strata. See the Curves section.
`segments`	The number of segments to be used in drawing each alternative curve (each curved boundary of each flow). If less than 3, will be silently changed to 3.
`outline.type`	Type of outline of each alluvium; one of `"both"`, `"lower"`, `"upper"`, and `"full"`.
`aes.flow`	Character; how inter-lode flows assume aesthetics from lodes. Options are "forward" and "backward".
`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()`.
`x0`, `x1`, `ymin0`, `ymax0`, `ymin1`, `ymax1`, `kp0`, `kp1`	Numeric corner and knot position data for the ribbon of a single flow.

Details

The helper function positions_to_flow() takes the corner and knot positions and curve parameters for a single flow as input and returns a data frame of x, y, and shape used by grid::xsplineGrob() to render the flow.

Aesthetics

geom_alluvium, geom_flow, geom_lode, and geom_stratum understand the following aesthetics (required aesthetics are in bold):

x
y
ymin
ymax
alpha
colour
fill
linetype
size
group

group is used internally; arguments are ignored.

Alluvium, flow, and lode geoms default to alpha = 0.5. Learn more about setting these aesthetics in vignette("ggplot2-specs", package = "ggplot2").

Curves

"linear": $f(x)=x$ , the unique degree-1 polynomial that takes 0 to 0 and 1 to 1
"cubic": $f(x)=3x^{2}-2x^{3}$ , the unique degree-3 polynomial that also is flat at both endpoints
"quintic": $f(x)=10x^{3}-15x^{4}+6x^{5}$ , the unique degree-5 polynomial that also has zero curvature at both endpoints
"sine": the unique sinusoidal function that is flat at both endpoints
"arctangent": the inverse tangent function, scaled and re-centered to the unit interval from the interval centered at zero with radius curve_range
"sigmoid": the sigmoid function, scaled and re-centered to the unit interval from the interval centered at zero with radius curve_range

These package-specific options set global values for curve_type, curve_range, and segments that will be defaulted to when not manually set:

ggalluvial.curve_type: defaults to "xspline".
ggalluvial.curve_range: defaults to NA, which triggers the curve-specific default values.
ggalluvial.segments: defaults to 48L.

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

Defunct parameters

The previously defunct parameters axis_width and ribbon_bend have been discontinued. Use width and knot.pos instead.

Examples

# use of strata and labels
ggplot(as.data.frame(Titanic),
       aes(y = Freq,
           axis1 = Class, axis2 = Sex, axis3 = Age)) +
  geom_flow() +
  scale_x_discrete(limits = c("Class", "Sex", "Age")) +
  geom_stratum() +
  geom_text(stat = "stratum", aes(label = after_stat(stratum))) +
  ggtitle("Alluvial plot of Titanic passenger demographic data")

# use of facets, with quintic flows
ggplot(as.data.frame(Titanic),
       aes(y = Freq,
           axis1 = Class, axis2 = Sex)) +
  geom_flow(aes(fill = Age), width = .4, curve_type = "quintic") +
  geom_stratum(width = .4) +
  geom_text(stat = "stratum", aes(label = after_stat(stratum)), size = 3) +
  scale_x_discrete(limits = c("Class", "Sex")) +
  facet_wrap(~ Survived, scales = "fixed")

# time series alluvia of WorldPhones data
wph <- as.data.frame(as.table(WorldPhones))
names(wph) <- c("Year", "Region", "Telephones")
ggplot(wph,
       aes(x = Year, alluvium = Region, y = Telephones)) +
  geom_flow(aes(fill = Region, colour = Region),
            width = 0, outline.type = "full")
# treat 'Year' as a number rather than as a factor
wph$Year <- as.integer(as.character(wph$Year))
ggplot(wph,
       aes(x = Year, alluvium = Region, y = Telephones)) +
  geom_flow(aes(fill = Region, colour = Region),
            width = 0, outline.type = "upper")
# hold the knot positions fixed
ggplot(wph,
       aes(x = Year, alluvium = Region, y = Telephones)) +
  geom_flow(aes(fill = Region, colour = Region),
            width = 0, outline.type = "lower", knot.prop = FALSE)


# rightward flow aesthetics for vaccine survey data, with cubic flows
data(vaccinations)
vaccinations$response <- factor(vaccinations$response,
                                rev(levels(vaccinations$response)))
# annotate with proportional counts
ggplot(vaccinations,
       aes(x = survey, stratum = response, alluvium = subject,
           y = freq, fill = response)) +
  geom_lode() + geom_flow(curve_type = "cubic") +
  geom_stratum(alpha = 0) +
  geom_text(stat = "stratum", aes(label = round(after_stat(prop), 3)))
# annotate fixed-width ribbons with counts
ggplot(vaccinations,
       aes(x = survey, stratum = response, alluvium = subject,
           weight = freq, fill = response)) +
  geom_lode() + geom_flow(curve_type = "cubic") +
  geom_stratum(alpha = 0) +
  geom_text(stat = "flow",
            aes(label = after_stat(n),
                hjust = (after_stat(flow) == "to")))

# use of strata and labels
ggplot(as.data.frame(Titanic),
       aes(y = Freq,
           axis1 = Class, axis2 = Sex, axis3 = Age)) +
  geom_flow() +
  scale_x_discrete(limits = c("Class", "Sex", "Age")) +
  geom_stratum() +
  geom_text(stat = "stratum", aes(label = after_stat(stratum))) +
  ggtitle("Alluvial plot of Titanic passenger demographic data")

# use of facets, with quintic flows
ggplot(as.data.frame(Titanic),
       aes(y = Freq,
           axis1 = Class, axis2 = Sex)) +
  geom_flow(aes(fill = Age), width = .4, curve_type = "quintic") +
  geom_stratum(width = .4) +
  geom_text(stat = "stratum", aes(label = after_stat(stratum)), size = 3) +
  scale_x_discrete(limits = c("Class", "Sex")) +
  facet_wrap(~ Survived, scales = "fixed")

# time series alluvia of WorldPhones data
wph <- as.data.frame(as.table(WorldPhones))
names(wph) <- c("Year", "Region", "Telephones")
ggplot(wph,
       aes(x = Year, alluvium = Region, y = Telephones)) +
  geom_flow(aes(fill = Region, colour = Region),
            width = 0, outline.type = "full")
# treat 'Year' as a number rather than as a factor
wph$Year <- as.integer(as.character(wph$Year))
ggplot(wph,
       aes(x = Year, alluvium = Region, y = Telephones)) +
  geom_flow(aes(fill = Region, colour = Region),
            width = 0, outline.type = "upper")
# hold the knot positions fixed
ggplot(wph,
       aes(x = Year, alluvium = Region, y = Telephones)) +
  geom_flow(aes(fill = Region, colour = Region),
            width = 0, outline.type = "lower", knot.prop = FALSE)


# rightward flow aesthetics for vaccine survey data, with cubic flows
data(vaccinations)
vaccinations$response <- factor(vaccinations$response,
                                rev(levels(vaccinations$response)))
# annotate with proportional counts
ggplot(vaccinations,
       aes(x = survey, stratum = response, alluvium = subject,
           y = freq, fill = response)) +
  geom_lode() + geom_flow(curve_type = "cubic") +
  geom_stratum(alpha = 0) +
  geom_text(stat = "stratum", aes(label = round(after_stat(prop), 3)))
# annotate fixed-width ribbons with counts
ggplot(vaccinations,
       aes(x = survey, stratum = response, alluvium = subject,
           weight = freq, fill = response)) +
  geom_lode() + geom_flow(curve_type = "cubic") +
  geom_stratum(alpha = 0) +
  geom_text(stat = "flow",
            aes(label = after_stat(n),
                hjust = (after_stat(flow) == "to")))

Lodes at intersections of alluvia and strata

Description

Usage

geom_lode(
  mapping = NULL,
  data = NULL,
  stat = "alluvium",
  position = "identity",
  width = 1/3,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  ...
)
geom_lode(
  mapping = NULL,
  data = NULL,
  stat = "alluvium",
  position = "identity",
  width = 1/3,
  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)`).
`stat`	The statistical transformation to use on the data; override the default.
`position`	Position adjustment, either as a string naming the adjustment (e.g. `"jitter"` to use `position_jitter`), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.
`width`	Numeric; the width of each stratum, as a proportion of the distance between axes. Defaults to 1/3.
`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

geom_alluvium, geom_flow, geom_lode, and geom_stratum understand the following aesthetics (required aesthetics are in bold):

x
y
ymin
ymax
alpha
colour
fill
linetype
size
group

group is used internally; arguments are ignored.

Alluvium, flow, and lode geoms default to alpha = 0.5. Learn more about setting these aesthetics in vignette("ggplot2-specs", package = "ggplot2").

Defunct parameters

The previously defunct parameters axis_width and ribbon_bend have been discontinued. Use width and knot.pos instead.

Examples

# one axis
ggplot(as.data.frame(Titanic),
       aes(y = Freq,
           axis = Class)) +
  geom_lode(aes(fill = Class, alpha = Survived)) +
  scale_x_discrete(limits = c("Class")) +
  scale_alpha_manual(values = c(.25, .75))

gg <- ggplot(as.data.frame(Titanic),
             aes(y = Freq,
                 axis1 = Class, axis2 = Sex, axis3 = Age,
                 fill = Survived))
# alluvia and lodes
gg + geom_alluvium() + geom_lode()
# lodes as strata
gg + geom_alluvium() +
  geom_stratum(stat = "alluvium")
# one axis
ggplot(as.data.frame(Titanic),
       aes(y = Freq,
           axis = Class)) +
  geom_lode(aes(fill = Class, alpha = Survived)) +
  scale_x_discrete(limits = c("Class")) +
  scale_alpha_manual(values = c(.25, .75))

gg <- ggplot(as.data.frame(Titanic),
             aes(y = Freq,
                 axis1 = Class, axis2 = Sex, axis3 = Age,
                 fill = Survived))
# alluvia and lodes
gg + geom_alluvium() + geom_lode()
# lodes as strata
gg + geom_alluvium() +
  geom_stratum(stat = "alluvium")

Strata at axes

Description

geom_stratum receives a dataset of the horizontal (x) and vertical (y, ymin, ymax) positions of the strata of an alluvial plot. It plots rectangles for these strata of a provided width.

Usage

geom_stratum(
  mapping = NULL,
  data = NULL,
  stat = "stratum",
  position = "identity",
  show.legend = NA,
  inherit.aes = TRUE,
  width = 1/3,
  na.rm = FALSE,
  ...
)
geom_stratum(
  mapping = NULL,
  data = NULL,
  stat = "stratum",
  position = "identity",
  show.legend = NA,
  inherit.aes = TRUE,
  width = 1/3,
  na.rm = FALSE,
  ...
)

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)`).
`stat`	The statistical transformation to use on the data; override the default.
`position`	Position adjustment, either as a string naming the adjustment (e.g. `"jitter"` to use `position_jitter`), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.
`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()`.
`width`	Numeric; the width of each stratum, as a proportion of the distance between axes. Defaults to 1/3.
`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).
`...`	Additional arguments passed to `ggplot2::layer()`.

Aesthetics

geom_alluvium, geom_flow, geom_lode, and geom_stratum understand the following aesthetics (required aesthetics are in bold):

x
y
ymin
ymax
alpha
colour
fill
linetype
size
group

group is used internally; arguments are ignored.

Alluvium, flow, and lode geoms default to alpha = 0.5. Learn more about setting these aesthetics in vignette("ggplot2-specs", package = "ggplot2").

Defunct parameters

The previously defunct parameters axis_width and ribbon_bend have been discontinued. Use width and knot.pos instead.

Examples

# full axis width
ggplot(as.data.frame(Titanic),
       aes(y = Freq,
           axis1 = Class, axis2 = Sex, axis3 = Age, axis4 = Survived)) +
  geom_stratum(width = 1) +
  geom_text(stat = "stratum", aes(label = after_stat(stratum))) +
  scale_x_discrete(limits = c("Class", "Sex", "Age", "Survived"))
  
# use of facets
ggplot(as.data.frame(Titanic),
       aes(y = Freq,
           axis1 = Class, axis2 = Sex)) +
  geom_flow(aes(fill = Survived)) +
  geom_stratum() +
  geom_text(stat = "stratum", aes(label = after_stat(stratum))) +
  scale_x_discrete(limits = c("Class", "Sex")) +
  facet_wrap(~ Age, scales = "free_y")
# full axis width
ggplot(as.data.frame(Titanic),
       aes(y = Freq,
           axis1 = Class, axis2 = Sex, axis3 = Age, axis4 = Survived)) +
  geom_stratum(width = 1) +
  geom_text(stat = "stratum", aes(label = after_stat(stratum))) +
  scale_x_discrete(limits = c("Class", "Sex", "Age", "Survived"))
  
# use of facets
ggplot(as.data.frame(Titanic),
       aes(y = Freq,
           axis1 = Class, axis2 = Sex)) +
  geom_flow(aes(fill = Survived)) +
  geom_stratum() +
  geom_text(stat = "stratum", aes(label = after_stat(stratum))) +
  scale_x_discrete(limits = c("Class", "Sex")) +
  facet_wrap(~ Age, scales = "free_y")

Lode guidance functions

Description

These functions control the order of lodes within strata in an alluvial diagram. They are invoked by stat_alluvium() and can be passed to the lode.guidance parameter.

Usage

lode_zigzag(n, i)

lode_zagzig(n, i)

lode_forward(n, i)

lode_rightward(n, i)

lode_backward(n, i)

lode_leftward(n, i)

lode_frontback(n, i)

lode_rightleft(n, i)

lode_backfront(n, i)

lode_leftright(n, i)
lode_zigzag(n, i)

lode_zagzig(n, i)

lode_forward(n, i)

lode_rightward(n, i)

lode_backward(n, i)

lode_leftward(n, i)

lode_frontback(n, i)

lode_rightleft(n, i)

lode_backfront(n, i)

lode_leftright(n, i)

Arguments

`n`	Numeric, a positive integer
`i`	Numeric, a positive integer at most `n`

Details

Each function orders the numbers 1 through n, starting at index i. The choice of function made in stat_alluvium() determines the order in which the other axes contribute to the sorting of lodes within each index axis. After starting at i, the functions order the remaining axes as follows:

zigzag: Zigzag outward from i, starting in the outward direction
zigzag: Zigzag outward from i, starting in the inward direction
forward: Increasing order (alias rightward)
backward: Decreasing order (alias leftward)
frontback: Proceed forward from i to n, then backward to 1 (alias rightleft)
backfront: Proceed backward from i to 1, then forward to n (alias leftright)

An extended discussion of how strata and lodes are arranged in alluvial plots, including the effects of different lode guidance functions, can be found in the vignette "The Order of the Rectangles" via vignette("order-rectangles", package = "ggalluvial").

Students' declared majors across several semesters

Description

This data set follows the major curricula of 10 students across 8 academic semesters. Missing values indicate undeclared majors. The data were kindly contributed by Dario Bonaretti.

Format

A data frame with 80 rows and 3 variables:

student: student identifier
semester: character tag for odd-numbered semesters
curriculum: declared major program

Adjoin a dataset to itself

Description

This function binds a dataset to itself along adjacent pairs of a key variable. It is invoked by geom_flow() to convert data in lodes form to something similar to alluvia form.

Usage

self_adjoin(
  data,
  key,
  by = NULL,
  link = NULL,
  keep.x = NULL,
  keep.y = NULL,
  suffix = c(".x", ".y")
)
self_adjoin(
  data,
  key,
  by = NULL,
  link = NULL,
  keep.x = NULL,
  keep.y = NULL,
  suffix = c(".x", ".y")
)

Arguments

`data`	A data frame in lodes form (repeated measures data; see `alluvial-data`).
`key`	Column of `data` indicating sequential collection; handled as in `tidyr::spread()`.
`by`	Character vector of variables to self-adjoin by; passed to `dplyr::mutate-joins` functions.
`link`	Character vector of variables to adjoin. Will be replaced by pairs of variables suffixed by `suffix`.
`keep.x`, `keep.y`	Character vector of variables to associate with the first (respectively, second) copy of `data` after adjoining. These variables can overlap with each other but cannot overlap with `by` or `link`.
`suffix`	Suffixes to add to the adjoined `link` variables; passed to `dplyr::mutate-joins` functions.

Details

self_adjoin invokes dplyr::mutate-joins functions in order to convert a dataset with measures along a discrete key variable into a dataset consisting of column bindings of these measures (by any by variables) along adjacent values of key.

Examples

# self-adjoin `majors` data
data(majors)
major_changes <- self_adjoin(majors, key = semester,
                             by = "student", link = c("semester", "curriculum"))
major_changes$change <- major_changes$curriculum.x == major_changes$curriculum.y
head(major_changes)

# self-adjoin `vaccinations` data
data(vaccinations)
vaccination_steps <- self_adjoin(vaccinations, key = survey, by = "subject",
                                 link = c("survey", "response"),
                                 keep.x = c("freq"))
head(vaccination_steps)
vaccination_steps <- self_adjoin(vaccinations, key = survey, by = "subject",
                                 link = c("survey", "response"),
                                 keep.x = c("freq"),
                                 keep.y = c("start_date", "end_date"))
head(vaccination_steps)
# self-adjoin `majors` data
data(majors)
major_changes <- self_adjoin(majors, key = semester,
                             by = "student", link = c("semester", "curriculum"))
major_changes$change <- major_changes$curriculum.x == major_changes$curriculum.y
head(major_changes)

# self-adjoin `vaccinations` data
data(vaccinations)
vaccination_steps <- self_adjoin(vaccinations, key = survey, by = "subject",
                                 link = c("survey", "response"),
                                 keep.x = c("freq"))
head(vaccination_steps)
vaccination_steps <- self_adjoin(vaccinations, key = survey, by = "subject",
                                 link = c("survey", "response"),
                                 keep.x = c("freq"),
                                 keep.y = c("start_date", "end_date"))
head(vaccination_steps)

Alluvial positions

Description

Given a dataset with alluvial structure, stat_alluvium calculates the centroids (x and y) and heights (ymin and ymax) of the lodes, the intersections of the alluvia with the strata. It leverages the group aesthetic for plotting purposes (for now).

Usage

stat_alluvium(
  mapping = NULL,
  data = NULL,
  geom = "alluvium",
  position = "identity",
  decreasing = NULL,
  reverse = NULL,
  absolute = NULL,
  discern = FALSE,
  negate.strata = NULL,
  aggregate.y = NULL,
  cement.alluvia = NULL,
  lode.guidance = NULL,
  lode.ordering = NULL,
  aes.bind = NULL,
  infer.label = FALSE,
  min.y = NULL,
  max.y = NULL,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  ...
)
stat_alluvium(
  mapping = NULL,
  data = NULL,
  geom = "alluvium",
  position = "identity",
  decreasing = NULL,
  reverse = NULL,
  absolute = NULL,
  discern = FALSE,
  negate.strata = NULL,
  aggregate.y = NULL,
  cement.alluvia = NULL,
  lode.guidance = NULL,
  lode.ordering = NULL,
  aes.bind = NULL,
  infer.label = FALSE,
  min.y = NULL,
  max.y = NULL,
  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)`).
`geom`	The geometric object to use display the data; override the default.
`position`	Position adjustment, either as a string naming the adjustment (e.g. `"jitter"` to use `position_jitter`), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.
`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.
`negate.strata`	A vector of values of the `stratum` aesthetic to be treated as negative (will ignore missing values with a warning).
`aggregate.y`	Deprecated alias for `cement.alluvia`.
`cement.alluvia`	Logical value indicating whether to aggregate `y` values over equivalent alluvia before computing lode and flow positions.
`lode.guidance`	The function to prioritize the axis variables for ordering the lodes within each stratum, or else a character string identifying the function. Character options are "zigzag", "frontback", "backfront", "forward", and "backward" (see `lode-guidance-functions`).
`lode.ordering`	Deprecated in favor of the `order` aesthetic. A list (of length the number of axes) of integer vectors (each of length the number of rows of `data`) or NULL entries (indicating no imposed ordering), or else a numeric matrix of corresponding dimensions, giving the preferred ordering of alluvia at each axis. This will be used to order the lodes within each stratum by sorting the lodes first by stratum, then by the provided vectors, and lastly by remaining factors (if the vectors contain duplicate entries and therefore do not completely determine the lode orderings).
`aes.bind`	At what grouping level, if any, to prioritize differentiation aesthetics when ordering the lodes within each stratum. Defaults to `"none"` (no aesthetic binding) with intermediate option `"flows"` to bind aesthetics after stratifying by axes linked to the index axis (the one adjacent axis in `stat_flow()`; all remaining axes in `stat_alluvium()`) and strongest option `"alluvia"` to bind aesthetics after stratifying by the index axis but before stratifying by linked axes (only available for `stat_alluvium()`). Stratification by any axis is done with respect to the strata at that axis, after separating positive and negative strata, consistent with the values of `decreasing`, `reverse`, and `absolute`. Thus, if `"none"`, then lode orderings will not depend on aesthetic variables. All aesthetic variables are used, in the order in which they are specified in `aes()`.
`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.
`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()`.
`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

# illustrate positioning
ggplot(as.data.frame(Titanic),
       aes(y = Freq,
           axis1 = Class, axis2 = Sex, axis3 = Age,
           color = Survived)) +
  stat_stratum(geom = "errorbar") +
  geom_line(stat = "alluvium") +
  stat_alluvium(geom = "pointrange") +
  geom_text(stat = "stratum", aes(label = after_stat(stratum))) +
  scale_x_discrete(limits = c("Class", "Sex", "Age"))

# lode ordering examples
gg <- ggplot(as.data.frame(Titanic),
             aes(y = Freq,
                 axis1 = Class, axis2 = Sex, axis3 = Age)) +
  geom_stratum() +
  geom_text(stat = "stratum", aes(label = after_stat(stratum))) +
  scale_x_discrete(limits = c("Class", "Sex", "Age"))
# use of lode controls
gg + geom_flow(aes(fill = Survived, alpha = Sex), stat = "alluvium",
               lode.guidance = "forward")
# prioritize aesthetic binding
gg + geom_flow(aes(fill = Survived, alpha = Sex), stat = "alluvium",
               aes.bind = "alluvia", lode.guidance = "forward")
# use of custom lode order
gg + geom_flow(aes(fill = Survived, alpha = Sex, order = sample(x = 32)),
               stat = "alluvium")
# use of custom luide guidance function
lode_custom <- function(n, i) {
  stopifnot(n == 3)
  switch(
    i,
    `1` = 1:3,
    `2` = c(2, 3, 1),
    `3` = 3:1
  )
}
gg + geom_flow(aes(fill = Survived, alpha = Sex), stat = "alluvium",
               aes.bind = "flow", lode.guidance = lode_custom)

# omit missing elements & reverse the `y` axis
ggplot(ggalluvial::majors,
       aes(x = semester, stratum = curriculum, alluvium = student, y = 1)) +
  geom_alluvium(fill = "darkgrey", na.rm = TRUE) +
  geom_stratum(aes(fill = curriculum), color = NA, na.rm = TRUE) +
  theme_bw() +
  scale_y_reverse()


# alluvium cementation examples
gg <- ggplot(ggalluvial::majors,
             aes(x = semester, stratum = curriculum, alluvium = student,
                 fill = curriculum)) +
  geom_stratum()
# diagram with outlined alluvia and labels
gg + geom_flow(stat = "alluvium", color = "black") +
  geom_text(aes(label = after_stat(lode)), stat = "alluvium")
# cemented diagram with default distillation (first most common alluvium)
gg +
  geom_flow(stat = "alluvium", color = "black", cement.alluvia = TRUE) +
  geom_text(aes(label = after_stat(lode)), stat = "alluvium",
            cement.alluvia = TRUE)
# cemented diagram with custom label distillation
gg +
  geom_flow(stat = "alluvium", color = "black", cement.alluvia = TRUE) +
  geom_text(aes(label = after_stat(lode)), stat = "alluvium",
            cement.alluvia = TRUE,
            distill = function(x) paste(x, collapse = "; "))



data(babynames, package = "babynames")
# a discontiguous alluvium
bn <- subset(babynames, prop >= .01 & sex == "F" & year > 1962 & year < 1968)
ggplot(data = bn,
       aes(x = year, alluvium = name, y = prop)) +
  geom_alluvium(aes(fill = name, color = name == "Tammy"),
                decreasing = TRUE, show.legend = FALSE) +
  scale_color_manual(values = c("#00000000", "#000000"))
# expanded to include missing values
bn2 <- merge(bn,
             expand.grid(year = unique(bn$year), name = unique(bn$name)),
             all = TRUE)
ggplot(data = bn2,
       aes(x = year, alluvium = name, y = prop)) +
  geom_alluvium(aes(fill = name, color = name == "Tammy"),
                decreasing = TRUE, show.legend = FALSE) +
  scale_color_manual(values = c("#00000000", "#000000"))
# with missing values filled in with zeros
bn2$prop[is.na(bn2$prop)] <- 0
ggplot(data = bn2,
       aes(x = year, alluvium = name, y = prop)) +
  geom_alluvium(aes(fill = name, color = name == "Tammy"),
                decreasing = TRUE, show.legend = FALSE) +
  scale_color_manual(values = c("#00000000", "#000000"))


# use negative y values to encode deaths versus survivals
titanic <- as.data.frame(Titanic)
titanic <- transform(titanic, Lives = Freq * (-1) ^ (Survived == "No"))
ggplot(subset(titanic, Class != "Crew"),
       aes(axis1 = Class, axis2 = Sex, axis3 = Age, y = Lives)) +
  geom_alluvium(aes(alpha = Survived, fill = Class), absolute = FALSE) +
  geom_stratum(absolute = FALSE) +
  geom_text(stat = "stratum", aes(label = after_stat(stratum)),
            absolute = FALSE) +
  scale_x_discrete(limits = c("Class", "Sex", "Age"), expand = c(.1, .05)) +
  scale_alpha_discrete(range = c(.25, .75), guide = "none")

# faceting with common alluvia
ggplot(titanic, aes(y = Freq, axis1 = Class, axis2 = Sex, axis3 = Age)) +
  facet_wrap(~ Survived) +
  geom_alluvium() +
  geom_stratum() +
  geom_text(stat = "stratum", aes(label = after_stat(stratum)))
ggplot(transform(alluvial::Refugees, id = 1),
       aes(y = refugees, x = year, alluvium = id)) +
  facet_wrap(~ country) +
  geom_alluvium(alpha = .75, color = "darkgrey") +
  scale_x_continuous(breaks = seq(2004, 2012, 4))
# illustrate positioning
ggplot(as.data.frame(Titanic),
       aes(y = Freq,
           axis1 = Class, axis2 = Sex, axis3 = Age,
           color = Survived)) +
  stat_stratum(geom = "errorbar") +
  geom_line(stat = "alluvium") +
  stat_alluvium(geom = "pointrange") +
  geom_text(stat = "stratum", aes(label = after_stat(stratum))) +
  scale_x_discrete(limits = c("Class", "Sex", "Age"))

# lode ordering examples
gg <- ggplot(as.data.frame(Titanic),
             aes(y = Freq,
                 axis1 = Class, axis2 = Sex, axis3 = Age)) +
  geom_stratum() +
  geom_text(stat = "stratum", aes(label = after_stat(stratum))) +
  scale_x_discrete(limits = c("Class", "Sex", "Age"))
# use of lode controls
gg + geom_flow(aes(fill = Survived, alpha = Sex), stat = "alluvium",
               lode.guidance = "forward")
# prioritize aesthetic binding
gg + geom_flow(aes(fill = Survived, alpha = Sex), stat = "alluvium",
               aes.bind = "alluvia", lode.guidance = "forward")
# use of custom lode order
gg + geom_flow(aes(fill = Survived, alpha = Sex, order = sample(x = 32)),
               stat = "alluvium")
# use of custom luide guidance function
lode_custom <- function(n, i) {
  stopifnot(n == 3)
  switch(
    i,
    `1` = 1:3,
    `2` = c(2, 3, 1),
    `3` = 3:1
  )
}
gg + geom_flow(aes(fill = Survived, alpha = Sex), stat = "alluvium",
               aes.bind = "flow", lode.guidance = lode_custom)

# omit missing elements & reverse the `y` axis
ggplot(ggalluvial::majors,
       aes(x = semester, stratum = curriculum, alluvium = student, y = 1)) +
  geom_alluvium(fill = "darkgrey", na.rm = TRUE) +
  geom_stratum(aes(fill = curriculum), color = NA, na.rm = TRUE) +
  theme_bw() +
  scale_y_reverse()


# alluvium cementation examples
gg <- ggplot(ggalluvial::majors,
             aes(x = semester, stratum = curriculum, alluvium = student,
                 fill = curriculum)) +
  geom_stratum()
# diagram with outlined alluvia and labels
gg + geom_flow(stat = "alluvium", color = "black") +
  geom_text(aes(label = after_stat(lode)), stat = "alluvium")
# cemented diagram with default distillation (first most common alluvium)
gg +
  geom_flow(stat = "alluvium", color = "black", cement.alluvia = TRUE) +
  geom_text(aes(label = after_stat(lode)), stat = "alluvium",
            cement.alluvia = TRUE)
# cemented diagram with custom label distillation
gg +
  geom_flow(stat = "alluvium", color = "black", cement.alluvia = TRUE) +
  geom_text(aes(label = after_stat(lode)), stat = "alluvium",
            cement.alluvia = TRUE,
            distill = function(x) paste(x, collapse = "; "))



data(babynames, package = "babynames")
# a discontiguous alluvium
bn <- subset(babynames, prop >= .01 & sex == "F" & year > 1962 & year < 1968)
ggplot(data = bn,
       aes(x = year, alluvium = name, y = prop)) +
  geom_alluvium(aes(fill = name, color = name == "Tammy"),
                decreasing = TRUE, show.legend = FALSE) +
  scale_color_manual(values = c("#00000000", "#000000"))
# expanded to include missing values
bn2 <- merge(bn,
             expand.grid(year = unique(bn$year), name = unique(bn$name)),
             all = TRUE)
ggplot(data = bn2,
       aes(x = year, alluvium = name, y = prop)) +
  geom_alluvium(aes(fill = name, color = name == "Tammy"),
                decreasing = TRUE, show.legend = FALSE) +
  scale_color_manual(values = c("#00000000", "#000000"))
# with missing values filled in with zeros
bn2$prop[is.na(bn2$prop)] <- 0
ggplot(data = bn2,
       aes(x = year, alluvium = name, y = prop)) +
  geom_alluvium(aes(fill = name, color = name == "Tammy"),
                decreasing = TRUE, show.legend = FALSE) +
  scale_color_manual(values = c("#00000000", "#000000"))


# use negative y values to encode deaths versus survivals
titanic <- as.data.frame(Titanic)
titanic <- transform(titanic, Lives = Freq * (-1) ^ (Survived == "No"))
ggplot(subset(titanic, Class != "Crew"),
       aes(axis1 = Class, axis2 = Sex, axis3 = Age, y = Lives)) +
  geom_alluvium(aes(alpha = Survived, fill = Class), absolute = FALSE) +
  geom_stratum(absolute = FALSE) +
  geom_text(stat = "stratum", aes(label = after_stat(stratum)),
            absolute = FALSE) +
  scale_x_discrete(limits = c("Class", "Sex", "Age"), expand = c(.1, .05)) +
  scale_alpha_discrete(range = c(.25, .75), guide = "none")

# faceting with common alluvia
ggplot(titanic, aes(y = Freq, axis1 = Class, axis2 = Sex, axis3 = Age)) +
  facet_wrap(~ Survived) +
  geom_alluvium() +
  geom_stratum() +
  geom_text(stat = "stratum", aes(label = after_stat(stratum)))
ggplot(transform(alluvial::Refugees, id = 1),
       aes(y = refugees, x = year, alluvium = id)) +
  facet_wrap(~ country) +
  geom_alluvium(alpha = .75, color = "darkgrey") +
  scale_x_continuous(breaks = seq(2004, 2012, 4))

Flow positions

Description

Given a dataset with alluvial structure, stat_flow calculates the centroids (x and y) and heights (ymin and ymax) of the flows between each pair of adjacent axes.

Usage

stat_flow(
  mapping = NULL,
  data = NULL,
  geom = "flow",
  position = "identity",
  decreasing = NULL,
  reverse = NULL,
  absolute = NULL,
  discern = FALSE,
  negate.strata = NULL,
  aes.bind = NULL,
  infer.label = FALSE,
  min.y = NULL,
  max.y = NULL,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  ...
)
stat_flow(
  mapping = NULL,
  data = NULL,
  geom = "flow",
  position = "identity",
  decreasing = NULL,
  reverse = NULL,
  absolute = NULL,
  discern = FALSE,
  negate.strata = NULL,
  aes.bind = NULL,
  infer.label = FALSE,
  min.y = NULL,
  max.y = NULL,
  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)`).
`geom`	The geometric object to use display the data; override the default.
`position`	Position adjustment, either as a string naming the adjustment (e.g. `"jitter"` to use `position_jitter`), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.
`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.
`negate.strata`	A vector of values of the `stratum` aesthetic to be treated as negative (will ignore missing values with a warning).
`aes.bind`	At what grouping level, if any, to prioritize differentiation aesthetics when ordering the lodes within each stratum. Defaults to `"none"` (no aesthetic binding) with intermediate option `"flows"` to bind aesthetics after stratifying by axes linked to the index axis (the one adjacent axis in `stat_flow()`; all remaining axes in `stat_alluvium()`) and strongest option `"alluvia"` to bind aesthetics after stratifying by the index axis but before stratifying by linked axes (only available for `stat_alluvium()`). Stratification by any axis is done with respect to the strata at that axis, after separating positive and negative strata, consistent with the values of `decreasing`, `reverse`, and `absolute`. Thus, if `"none"`, then lode orderings will not depend on aesthetic variables. All aesthetic variables are used, in the order in which they are specified in `aes()`.
`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.
`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()`.
`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.)

y
weight
order
group
label

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)

Package options

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

# illustrate positioning
ggplot(as.data.frame(Titanic),
       aes(y = Freq,
           axis1 = Class, axis2 = Sex, axis3 = Age,
           color = Survived)) +
  stat_stratum(geom = "errorbar") +
  geom_line(stat = "flow") +
  stat_flow(geom = "pointrange") +
  geom_text(stat = "stratum", aes(label = after_stat(stratum))) +
  scale_x_discrete(limits = c("Class", "Sex", "Age"))

# alluvium--flow comparison
data(vaccinations)
gg <- ggplot(vaccinations,
             aes(x = survey, stratum = response, alluvium = subject,
                 y = freq, fill = response)) +
  geom_stratum(alpha = .5) +
  geom_text(aes(label = response), stat = "stratum")
# rightward alluvial aesthetics for vaccine survey data
gg + geom_flow(stat = "alluvium", lode.guidance = "forward")
# memoryless flows for vaccine survey data
gg + geom_flow()

# size filter examples
gg <- ggplot(vaccinations,
       aes(y = freq,
           x = survey, stratum = response, alluvium = subject,
           fill = response, label = response)) +
  stat_stratum(alpha = .5) +
  geom_text(stat = "stratum")
# omit small flows
gg + geom_flow(min.y = 50)
# omit large flows
gg + geom_flow(max.y = 100)

# negate missing entries
ggplot(vaccinations,
       aes(y = freq,
           x = survey, stratum = response, alluvium = subject,
           fill = response, label = response,
           alpha = response != "Missing")) +
  stat_stratum(negate.strata = "Missing") +
  geom_flow(negate.strata = "Missing") +
  geom_text(stat = "stratum", alpha = 1, negate.strata = "Missing") +
  scale_alpha_discrete(range = c(.2, .6)) +
  guides(alpha = "none")


# aesthetics that vary betwween and within strata
data(vaccinations)
vaccinations$subgroup <- LETTERS[1:2][rbinom(
  n = length(unique(vaccinations$subject)), size = 1, prob = .5
) + 1][vaccinations$subject]
ggplot(vaccinations,
       aes(x = survey, stratum = response, alluvium = subject,
           y = freq, fill = response, label = response)) +
  geom_flow(aes(alpha = subgroup)) +
  scale_alpha_discrete(range = c(1/3, 2/3)) +
  geom_stratum(alpha = .5) +
  geom_text(stat = "stratum")
# can even set aesthetics that vary both ways
ggplot(vaccinations,
       aes(x = survey, stratum = response, alluvium = subject,
           y = freq, label = response)) +
  geom_flow(aes(fill = interaction(response, subgroup)), aes.bind = "flows") +
  scale_alpha_discrete(range = c(1/3, 2/3)) +
  geom_stratum(alpha = .5) +
  geom_text(stat = "stratum")

# illustrate positioning
ggplot(as.data.frame(Titanic),
       aes(y = Freq,
           axis1 = Class, axis2 = Sex, axis3 = Age,
           color = Survived)) +
  stat_stratum(geom = "errorbar") +
  geom_line(stat = "flow") +
  stat_flow(geom = "pointrange") +
  geom_text(stat = "stratum", aes(label = after_stat(stratum))) +
  scale_x_discrete(limits = c("Class", "Sex", "Age"))

# alluvium--flow comparison
data(vaccinations)
gg <- ggplot(vaccinations,
             aes(x = survey, stratum = response, alluvium = subject,
                 y = freq, fill = response)) +
  geom_stratum(alpha = .5) +
  geom_text(aes(label = response), stat = "stratum")
# rightward alluvial aesthetics for vaccine survey data
gg + geom_flow(stat = "alluvium", lode.guidance = "forward")
# memoryless flows for vaccine survey data
gg + geom_flow()

# size filter examples
gg <- ggplot(vaccinations,
       aes(y = freq,
           x = survey, stratum = response, alluvium = subject,
           fill = response, label = response)) +
  stat_stratum(alpha = .5) +
  geom_text(stat = "stratum")
# omit small flows
gg + geom_flow(min.y = 50)
# omit large flows
gg + geom_flow(max.y = 100)

# negate missing entries
ggplot(vaccinations,
       aes(y = freq,
           x = survey, stratum = response, alluvium = subject,
           fill = response, label = response,
           alpha = response != "Missing")) +
  stat_stratum(negate.strata = "Missing") +
  geom_flow(negate.strata = "Missing") +
  geom_text(stat = "stratum", alpha = 1, negate.strata = "Missing") +
  scale_alpha_discrete(range = c(.2, .6)) +
  guides(alpha = "none")


# aesthetics that vary betwween and within strata
data(vaccinations)
vaccinations$subgroup <- LETTERS[1:2][rbinom(
  n = length(unique(vaccinations$subject)), size = 1, prob = .5
) + 1][vaccinations$subject]
ggplot(vaccinations,
       aes(x = survey, stratum = response, alluvium = subject,
           y = freq, fill = response, label = response)) +
  geom_flow(aes(alpha = subgroup)) +
  scale_alpha_discrete(range = c(1/3, 2/3)) +
  geom_stratum(alpha = .5) +
  geom_text(stat = "stratum")
# can even set aesthetics that vary both ways
ggplot(vaccinations,
       aes(x = survey, stratum = response, alluvium = subject,
           y = freq, label = response)) +
  geom_flow(aes(fill = interaction(response, subgroup)), aes.bind = "flows") +
  scale_alpha_discrete(range = c(1/3, 2/3)) +
  geom_stratum(alpha = .5) +
  geom_text(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,
  ...
)
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()`. 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 naming the adjustment (e.g. `"jitter"` to use `position_jitter`), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.
`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()`). It recognizes three character values: `"first"` (the default) and `"last"` as defined in dplyr; 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.)

y
weight
order
group
label

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)

Package options

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))
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))

Influenza vaccination survey responses

Description

This data set is aggregated from three RAND American Life Panel (ALP) surveys that asked respondents their probability of vaccinating for influenza. Their responses were discretized to "Never" (0%), "Always" (100%), or "Sometimes" (any other value). After merging, missing responses were coded as "Missing" and respondents were grouped and counted by all three coded responses. The pre-processed data were kindly contributed by Raffaele Vardavas, and the complete surveys are freely available at the ALP website.

Usage

vaccinations
vaccinations

Format

A data frame with 117 rows and 5 variables:

freq: number of respondents represented in each row
subject: identifier linking respondents across surveys
survey: survey designation from the ALP website
start_date: start date of survey
end_date: end date of survey
response: discretized probability of vaccinating for influenza

Source

https://alpdata.rand.org/

Package 'ggalluvial'

Help Index

Check for alluvial structure and convert between alluvial formats

Description

Usage

Arguments

Details

See Also

Examples

Alluvia across strata

Description

Usage

Arguments

Details

Aesthetics

Curves

Defunct parameters

See Also

Examples

Flows between lodes or strata

Description

Usage

Arguments

Details

Aesthetics

Curves

Defunct parameters

See Also

Examples

Lodes at intersections of alluvia and strata

Description

Usage

Arguments

Aesthetics

Defunct parameters

See Also

Examples

Strata at axes

Description

Usage

Arguments

Aesthetics

Defunct parameters

See Also

Examples

Lode guidance functions

Description

Usage

Arguments

Details

Students' declared majors across several semesters

Description

Format

Adjoin a dataset to itself

Description

Usage

Arguments

Details

See Also

Examples

Alluvial positions

Description

Usage

Arguments

Aesthetics

Computed variables

Package options

Defunct parameters

See Also

Examples

Flow positions

Description

Usage

Arguments

Aesthetics

Computed variables

Package options

Defunct parameters

See Also

Examples