R: Check for alluvial structure and convert between alluvial...

alluvial-data {ggalluvial}

R Documentation

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)

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)