% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/sankeyplot.R
\name{SankeyPlot}
\alias{SankeyPlot}
\alias{AlluvialPlot}
\title{Sankey / Alluvial Plot}
\usage{
SankeyPlot(
  data,
  in_form = c("auto", "long", "lodes", "wide", "alluvia", "counts"),
  x,
  x_sep = "_",
  y = NULL,
  stratum = NULL,
  stratum_sep = "_",
  alluvium = NULL,
  alluvium_sep = "_",
  split_by = NULL,
  split_by_sep = "_",
  keep_empty = TRUE,
  flow = FALSE,
  expand = c(0, 0, 0, 0),
  nodes_legend = c("auto", "separate", "merge", "none"),
  nodes_color = "grey30",
  links_fill_by = NULL,
  links_fill_by_sep = "_",
  links_name = NULL,
  links_color = "gray80",
  nodes_palette = "Paired",
  nodes_palcolor = NULL,
  nodes_alpha = 1,
  nodes_label = FALSE,
  nodes_label_miny = 0,
  nodes_width = 0.25,
  links_palette = "Paired",
  links_palcolor = NULL,
  palreverse = FALSE,
  links_alpha = 0.6,
  legend.box = "vertical",
  x_text_angle = 0,
  aspect.ratio = 1,
  legend.position = "right",
  legend.direction = "vertical",
  flip = FALSE,
  theme = "theme_this",
  theme_args = list(),
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  facet_by = NULL,
  facet_scales = "fixed",
  facet_ncol = NULL,
  facet_nrow = NULL,
  facet_byrow = TRUE,
  seed = 8525,
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  axes = NULL,
  axis_titles = axes,
  guides = NULL,
  design = NULL,
  ...
)

AlluvialPlot(
  data,
  in_form = c("auto", "long", "lodes", "wide", "alluvia", "counts"),
  x,
  x_sep = "_",
  y = NULL,
  stratum = NULL,
  stratum_sep = "_",
  alluvium = NULL,
  alluvium_sep = "_",
  split_by = NULL,
  split_by_sep = "_",
  keep_empty = TRUE,
  flow = FALSE,
  expand = c(0, 0, 0, 0),
  nodes_legend = c("auto", "separate", "merge", "none"),
  nodes_color = "grey30",
  links_fill_by = NULL,
  links_fill_by_sep = "_",
  links_name = NULL,
  links_color = "gray80",
  nodes_palette = "Paired",
  nodes_palcolor = NULL,
  nodes_alpha = 1,
  nodes_label = FALSE,
  nodes_label_miny = 0,
  nodes_width = 0.25,
  links_palette = "Paired",
  links_palcolor = NULL,
  palreverse = FALSE,
  links_alpha = 0.6,
  legend.box = "vertical",
  x_text_angle = 0,
  aspect.ratio = 1,
  legend.position = "right",
  legend.direction = "vertical",
  flip = FALSE,
  theme = "theme_this",
  theme_args = list(),
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  facet_by = NULL,
  facet_scales = "fixed",
  facet_ncol = NULL,
  facet_nrow = NULL,
  facet_byrow = TRUE,
  seed = 8525,
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  axes = NULL,
  axis_titles = axes,
  guides = NULL,
  design = NULL,
  ...
)
}
\arguments{
\item{data}{A data frame.}

\item{in_form}{A character string specifying the input data format.
One of \code{"auto"} (default), \code{"long"}, \code{"lodes"},
\code{"wide"}, \code{"alluvia"}, or \code{"counts"}.
\code{"long"} is an alias for \code{"lodes"}; \code{"wide"} is an alias for
\code{"alluvia"}.  See the \code{data} parameter of \code{\link{SankeyPlot}}
for format descriptions.}

\item{x}{A character string specifying the column name of the data frame to plot for the x-axis.}

\item{x_sep}{A character string to join multiple \code{x} columns when
\code{in_form} is \code{"lodes"} or auto-determined as lodes.
Default \code{"_"}.}

\item{y}{A character string specifying the column name of the data frame to plot for the y-axis.}

\item{stratum}{A character string specifying the column that defines the
node categories at each x-axis position.  Each unique value becomes a
stratum (node block) at each x position.  When \code{NULL}, defaults to
\code{links_fill_by}.  Multiple columns are concatenated with
\code{stratum_sep}.  Ignored in \code{"alluvia"} format.}

\item{stratum_sep}{A character string to join multiple \code{stratum}
columns.  Default \code{"_"}.}

\item{alluvium}{A character string specifying the column that identifies
individual flows (alluvia) across x-axis positions.  Each unique value
represents a single observational unit tracked across positions.  When
\code{NULL} in \code{"counts"} format, an auto-generated identifier is
created.  Multiple columns are concatenated with \code{alluvium_sep}.
Ignored in \code{"alluvia"} format.}

\item{alluvium_sep}{A character string to join multiple \code{alluvium}
columns.  Default \code{"_"}.}

\item{split_by}{The column(s) to split data by and plot separately.
When \code{combine = TRUE}, the combined plot's data (\code{p$data})
contains the rows of every split, tagged with the \code{split_by}
column. For ggraph-based plots (e.g. \code{\link{Network}},
\code{\link{ClustreePlot}}), the node layout of every split is
exposed with the split column, and the original link rows (also
tagged with the \code{split_by} column) are available as the
\code{"edges"} attribute of the data.}

\item{split_by_sep}{The separator for multiple split_by columns. See \code{split_by}}

\item{keep_empty}{One of FALSE, TRUE and "level". It can also take a named list to specify
different behavior for different columns. Without a named list, the behavior applies to the
categorical/character columns used on the plot, for example, the \code{x}, \code{group_by}, \code{fill_by}, etc.
\itemize{
\item{\code{FALSE} (default): Drop empty factor levels from the data before plotting.}
\item{\code{TRUE}: Keep empty factor levels and show them as a separate category in the plot.}
\item{\code{"level"}: Keep empty factor levels, but do not show them in the plot.
But they will be assigned colors from the palette to maintain consistency across multiple plots.
Alias: \code{levels}}
}}

\item{flow}{A logical value.  When \code{FALSE} (default),
\code{\link[ggalluvial]{geom_alluvium}()} is used for the links.  When
\code{TRUE}, \code{\link[ggalluvial]{geom_flow}()} is used instead, which
draws the flows with a directional gradient between x positions.}

\item{expand}{The values to expand the x and y axes. It is like CSS padding.
When a single value is provided, it is used for both axes on both sides.
When two values are provided, the first value is used for the top/bottom side and the second value is used for the left/right side.
When three values are provided, the first value is used for the top side, the second value is used for the left/right side, and the third value is used for the bottom side.
When four values are provided, the values are used for the top, right, bottom, and left sides, respectively.
You can also use a named vector to specify the values for each side.
When the axis is discrete, the values will be applied as 'add' to the 'expansion' function.
When the axis is continuous, the values will be applied as 'mult' to the 'expansion' function.
See also \url{https://ggplot2.tidyverse.org/reference/expansion.html}}

\item{nodes_legend}{Controls how the node legend is displayed.  One of:
\describe{
\item{\code{"auto"} (default)}{Automatically determined:
if \code{nodes_label = TRUE}, or if \code{stratum} is identical to
\code{links_fill_by} with matching colours, the legend is hidden.
Otherwise, overlapping stratum values across x positions are checked:
any overlap produces a merged legend; no overlap produces separate
legends per x position.}
\item{\code{"merge"}}{A single merged legend for all nodes.}
\item{\code{"separate"}}{One legend per x-axis position, generated via
separate \code{\link[ggplot2]{scale_fill_manual}()} layers.}
\item{\code{"none"}}{No node legend is shown.}
}}

\item{nodes_color}{A character string specifying the border colour of the
node (stratum) rectangles.  Use the special value \code{".fill"} to match
the border colour to the node fill colour.  Default \code{"grey30"}.}

\item{links_fill_by}{A character string specifying the column that
determines the fill colour of the links (alluvia / flows).  When
\code{NULL} in \code{"lodes"} format, defaults to \code{alluvium}.  In
\code{"counts"} format with the \code{"."} prefix, this parameter is
required.  Multiple columns are concatenated with
\code{links_fill_by_sep}.}

\item{links_fill_by_sep}{A character string to join multiple
\code{links_fill_by} columns.  Default \code{"_"}.}

\item{links_name}{A character string for the legend title of the link fill
scale.  When \code{NULL} (default), the \code{links_fill_by} column name
is used.}

\item{links_color}{A character string specifying the border colour of the
links (alluvia / flows).  Use the special value \code{".fill"} to match
the link border colour to the link fill colour.  Default \code{"gray80"}.}

\item{nodes_palette}{A character string specifying the colour palette for
the node (stratum) fill.  Passed to \code{\link{palette_this}()}.
Default \code{"Paired"}.}

\item{nodes_palcolor}{A character vector of custom colours for the node
fill, used as \code{palcolor} in \code{\link{palette_this}()}.  When
\code{NULL} (default), the palette colours are used directly.}

\item{nodes_alpha}{A numeric value in \eqn{[0, 1]} controlling the
transparency of the node (stratum) fill.  Default \code{1}.}

\item{nodes_label}{A logical value.  When \code{TRUE}, stratum labels are
drawn inside each node using \code{\link[ggplot2]{geom_label}()} with
\code{\link[ggalluvial]{StatStratum}}.  Default \code{FALSE}.}

\item{nodes_label_miny}{A numeric value specifying the minimum y
(frequency) threshold for displaying node labels.  Nodes with y-values
below this threshold are not labelled.  Default \code{0}.}

\item{nodes_width}{A numeric value (typically 0–1) specifying the width of
the node (stratum) rectangles as a fraction of the x-axis spacing.
Default \code{0.25}.}

\item{links_palette}{A character string specifying the colour palette for
the link fill.  Passed to \code{\link{palette_this}()}.
Default \code{"Paired"}.}

\item{links_palcolor}{A character vector of custom colours for the link
fill, used as \code{palcolor} in \code{\link{palette_this}()}.  When
\code{NULL} (default), the palette colours are used directly.}

\item{palreverse}{A logical value indicating whether to reverse the palette. Default is FALSE.}

\item{links_alpha}{A numeric value in \eqn{[0, 1]} controlling the
transparency of the link fill.  Default \code{0.6}.}

\item{legend.box}{A character string specifying the arrangement of legend
boxes, either \code{"vertical"} (default) or \code{"horizontal"}.}

\item{x_text_angle}{A numeric value specifying the angle of the x-axis text.}

\item{aspect.ratio}{A numeric value specifying the aspect ratio of the plot.}

\item{legend.position}{A character string specifying the position of the legend.
if \code{waiver()}, for single groups, the legend will be "none", otherwise "right".}

\item{legend.direction}{A character string specifying the direction of the legend.}

\item{flip}{A logical value.  When \code{TRUE},
\code{\link[ggplot2]{coord_flip}()} is applied to swap the x and y axes.
Default \code{FALSE}.}

\item{theme}{A character string or a theme class (i.e. ggplot2::theme_classic) specifying the theme to use.
Default is "theme_this".}

\item{theme_args}{A list of arguments to pass to the theme function.}

\item{title}{A character string specifying the title of the plot.
A function can be used to generate the title based on the default title.
This is useful when split_by is used and the title needs to be dynamic.}

\item{subtitle}{A character string specifying the subtitle of the plot.}

\item{xlab}{A character string specifying the x-axis label.}

\item{ylab}{A character string specifying the y-axis label.}

\item{facet_by}{A character string specifying the column name of the data frame to facet the plot.
Otherwise, the data will be split by \code{split_by} and generate multiple plots
and combine them into one using \code{patchwork::wrap_plots}}

\item{facet_scales}{Whether to scale the axes of facets. Default is "fixed"
Other options are "free", "free_x", "free_y". See \code{ggplot2::facet_wrap}}

\item{facet_ncol}{A numeric value specifying the number of columns in the facet.
When facet_by is a single column and facet_wrap is used.}

\item{facet_nrow}{A numeric value specifying the number of rows in the facet.
When facet_by is a single column and facet_wrap is used.}

\item{facet_byrow}{A logical value indicating whether to fill the plots by row. Default is TRUE.}

\item{seed}{The random seed to use. Default is 8525.}

\item{combine}{Whether to combine the plots into one when facet is FALSE. Default is TRUE.}

\item{nrow}{A numeric value specifying the number of rows in the facet.}

\item{ncol}{A numeric value specifying the number of columns in the facet.}

\item{byrow}{A logical value indicating whether to fill the plots by row.}

\item{axes}{A string specifying how axes should be treated. Passed to \code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}}.
Only relevant when \code{split_by} is used and \code{combine} is TRUE.
Options are:
\itemize{
\item 'keep' will retain all axes in individual plots.
\item 'collect' will remove duplicated axes when placed in the same run of rows or columns of the layout.
\item 'collect_x' and 'collect_y' will remove duplicated x-axes in the columns or duplicated y-axes in the rows respectively.
}}

\item{axis_titles}{A string specifying how axis titltes should be treated. Passed to \code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}}.
Only relevant when \code{split_by} is used and \code{combine} is TRUE.
Options are:
\itemize{
\item 'keep' will retain all axis titles in individual plots.
\item 'collect' will remove duplicated titles in one direction and merge titles in the opposite direction.
\item 'collect_x' and 'collect_y' control this for x-axis titles and y-axis titles respectively.
}}

\item{guides}{A string specifying how guides should be treated in the layout. Passed to \code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}}.
Only relevant when \code{split_by} is used and \code{combine} is TRUE.
Options are:
\itemize{
\item 'collect' will collect guides below to the given nesting level, removing duplicates.
\item 'keep' will stop collection at this level and let guides be placed alongside their plot.
\item 'auto' will allow guides to be collected if a upper level tries, but place them alongside the plot if not.
}}

\item{design}{Specification of the location of areas in the layout, passed to \code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}}.
Only relevant when \code{split_by} is used and \code{combine} is TRUE. When specified, \code{nrow}, \code{ncol}, and \code{byrow} are ignored.
See \code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}} for more details.}

\item{...}{Additional arguments.}
}
\value{
A \code{ggplot} object (single panel, no \code{split_by}), a
\code{patchwork} object (when \code{combine = TRUE} and
\code{split_by} is used), or a named list of \code{ggplot} objects
(when \code{combine = FALSE}).  Each plot carries \code{height} and
\code{width} attributes in inches.
}
\description{
Draws Sankey (alluvial) diagrams to visualise flow, movement, or change
from one categorical state to another across discrete positions (time
points, stages, or groups).  The plot consists of \strong{nodes} (vertical
blocks, or strata) representing categories at each position, and
\strong{links} (alluvia / flows) representing the observation units that
move between categories across positions.

The function accepts data in several formats, controlled by \code{in_form}:
\describe{
\item{\code{"lodes"} / \code{"long"}}{Each row is an observation at one
x-position, with columns for \code{x}, \code{stratum}, \code{alluvium},
and optionally \code{y}.}
\item{\code{"alluvia"} / \code{"wide"}}{Each row is an observation unit
tracked across all positions; \code{x} columns represent the categories
at each position.  Converted internally via
\code{\link[ggalluvial]{to_lodes_form}()}.}
\item{\code{"counts"}}{Numeric columns under each \code{x} represent
frequencies.  When the first element of \code{x} is \code{"."}, the
\code{links_fill_by} values are injected as an additional first column
of nodes, visualising the source distribution of flows.}
\item{\code{"auto"} (default)}{Automatically detects the format:
numeric multi-column \code{x} → \code{"counts"};
multi-column \code{x} passing \code{is_alluvia_form} → \code{"alluvia"};
otherwise → \code{"lodes"}.}
}

Supports \strong{split_by} to produce separate sub-plots for different
subsets of the data, \strong{facet_by} for within-plot faceting, and
independent styling of nodes and links (colours, alpha, borders, labels,
and legend behaviour).

\code{AlluvialPlot} is an alias of \code{SankeyPlot}.
}
\section{split_by workflow}{

When \code{split_by} is provided:
\enumerate{
\item The \code{split_by} column(s) are validated and coerced to factors
via \code{\link{check_columns}()}.  Multi-column \code{split_by}
is concatenated with \code{split_by_sep}.
\item Empty factor levels are dropped from \code{split_by}.
\item The data is split by \code{split_by} level (preserving level order).
If \code{split_by} is \code{NULL}, the data is wrapped in a
single-element list with name \code{"..."}.
\item \code{\link{SankeyPlotAtomic}()} is called for each split, with
\code{title} resolved per level (supports function-valued titles).
\item Results are combined via \code{\link{combine_plots}()} (when
\code{combine = TRUE}) or returned as a named list.
}
}

\examples{
\donttest{
# Examples from ggalluvial datasets
set.seed(8525)

data(UCBAdmissions, package = "datasets")
UCBAdmissions <- as.data.frame(UCBAdmissions)
SankeyPlot(as.data.frame(UCBAdmissions), x = c("Gender", "Dept"),
    y = "Freq", nodes_width = 1/12, links_fill_by = "Admit", nodes_label = TRUE,
    nodes_palette = "simspec", links_palette = "Set1", links_alpha = 0.5,
    nodes_palcolor = "black", links_color = "transparent")

data(HairEyeColor, package = "datasets")
SankeyPlot(as.data.frame(HairEyeColor), x = c("Hair", "Eye", "Sex"),
    y = "Freq", links_fill_by = "Eye", nodes_width = 1/8, nodes_alpha = 0.4,
    flip = TRUE, reverse = FALSE, knot.pos = 0, links_color = "transparent",
    ylab = "Freq", links_alpha = 0.5, links_name = "Eye (links)", links_palcolor = c(
        Brown = "#70493D", Hazel = "#E2AC76", Green = "#3F752B", Blue = "#81B0E4"))

data(Refugees, package = "alluvial")
country_regions <- c(
    Afghanistan = "Middle East",
    Burundi = "Central Africa",
    `Congo DRC` = "Central Africa",
    Iraq = "Middle East",
    Myanmar = "Southeast Asia",
    Palestine = "Middle East",
    Somalia = "Horn of Africa",
    Sudan = "Central Africa",
    Syria = "Middle East",
    Vietnam = "Southeast Asia"
)
Refugees$region <- country_regions[Refugees$country]
SankeyPlot(Refugees, x = "year", y = "refugees", alluvium = "country",
    links_fill_by = "country", links_color = ".fill", links_alpha = 0.75,
    links_palette = "Set3", facet_by = "region", x_text_angle = -45, nodes_legend = "none",
    theme_args = list(strip.background = ggplot2::element_rect(fill="grey80")),
    decreasing = FALSE, nodes_width = 0, nodes_color = "transparent", ylab = "refugees",
    title = "Refugee volume by country and region of origin")

data(majors, package = "ggalluvial")
majors$curriculum <- as.factor(majors$curriculum)
SankeyPlot(majors, x = "semester", stratum = "curriculum", alluvium = "student",
    links_fill_by = "curriculum", flow = TRUE, stat = "alluvium", nodes_palette = "Set2",
    links_palette = "Set2")

data(vaccinations, package = "ggalluvial")
vaccinations <- transform(vaccinations,
    response = factor(response, rev(levels(response))))
SankeyPlot(vaccinations, x = "survey", stratum = "response", alluvium = "subject",
    y = "freq", links_fill_by = "response", nodes_label = TRUE, nodes_alpha = 0.5,
    nodes_palette = "seurat", links_palette = "seurat", links_alpha = 0.5,
    legend.position = "none", flow = TRUE, expand = c(0, 0, 0, .15), stat = "alluvium",
    title = "vaccination survey responses at three points in time")

data(Titanic, package = "datasets")
SankeyPlot(as.data.frame(Titanic), x = c("Class", "Sex"), y = "Freq",
    links_fill_by = "Survived", flow = TRUE, facet_by = "Age", facet_scales = "free_y",
    nodes_label = TRUE, expand = c(0.05, 0), xlab = "", links_palette = "Set1",
    nodes_palcolor = "white", nodes_label_miny = 10)

# Simulated examples
df <- data.frame(
    Clone = paste0("clone", 1:10),
    Timepoint1 = sample(c(rep(0, 30), 1:100), 10),
    Timepoint2 = sample(c(rep(0, 30), 1:100), 10)
)
SankeyPlot(df, x = c("Timepoint1", "Timepoint2"), alluvium = "Clone",
    links_color = ".fill")

df <- data.frame(
    Clone = rep(paste0("clone", 1:6), each = 2),
    Timepoint1 = sample(c(rep(0, 30), 1:100), 6),
    Timepoint2 = sample(c(rep(0, 30), 1:100), 6),
    Group = rep(c("A", "B"), 6)
)
SankeyPlot(df, x = c(".", "Timepoint1", "Timepoint2"),
    stratum = "Group", links_fill_by = "Clone", links_color = ".fill")
}
}
