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Sankey / Alluvial Plot

Source: R/sankeyplot.R
sankeyplot.Rd

A plot visualizing flow/movement/change from one state to another or one time to another. AlluvialPlot is an alias of SankeyPlot.

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,
  links_alpha = 0.6,
  legend.box = "vertical",
  x_text_angle = 0,
  aspect.ratio = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  flip = FALSE,
  theme = "theme_ggforge",
  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,
  links_alpha = 0.6,
  legend.box = "vertical",
  x_text_angle = 0,
  aspect.ratio = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  flip = FALSE,
  theme = "theme_ggforge",
  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

data

A data frame in following possible formats:

  • "long" or "lodes": A long format with columns for x, stratum, alluvium, and y. x (required, single columns or concatenated by x_sep) is the column name to plot on the x-axis, stratum (defaults to links_fill_by) is the column name to group the nodes for each x, alluvium (required) is the column name to define the links, and y is the frequency of each x, stratum, and alluvium.

  • "wide" or "alluvia": A wide format with columns for x. x (required, multiple columns, x_sep won't be used) are the columns to plot on the x-axis, stratum and alluvium will be ignored. See ggalluvial::to_lodes_form for more details.

  • "counts": A format with counts being provides under each x. x (required, multiple columns, x_sep won't be used) are the columns to plot on the x-axis. When the first element of x is ".", values of links_fill_by (required) will be added to the plot as the first column of nodes. It is useful to show how the links are flowed from the source to the targets.

  • "auto" (default): Automatically determine the format based on the columns provided. When the length of x is greater than 1 and all x columns are numeric, "counts" format will be used. When the length of x is greater than 1 and ggalluvial::is_alluvia_form returns TRUE, "alluvia" format will be used. Otherwise, "lodes" format will be tried.

in_form

A character string to specify the format of the data. Possible values are "auto", "long", "lodes", "wide", "alluvia", and "counts".

x

A character string of the column name to plot on the x-axis. See data for more details.

x_sep

A character string to concatenate the columns in x, if multiple columns are provided.

y

A character string of the column name to plot on the y-axis. When in_form is "counts", y will be ignored. Otherwise, it defaults to the count of each x, stratum, alluvium and links_fill_by.

stratum

A character string of the column name to group the nodes for each x. See data for more details.

stratum_sep

A character string to concatenate the columns in stratum, if multiple columns are provided.

alluvium

A character string of the column name to define the links. See data for more details.

alluvium_sep

A character string to concatenate the columns in alluvium, if multiple columns are provided.

split_by

Column name(s) to split data into multiple plots

split_by_sep

Separator when concatenating multiple split_by columns

keep_empty

A logical value to keep the empty nodes.

flow

A logical value to use ggalluvial::geom_flow instead of ggalluvial::geom_alluvium.

expand

Expansion values for axes (CSS-like: top, right, bottom, left)

nodes_legend

Controls how the legend of nodes will be shown. Possible values are:

  • "merge": Merge the legends of nodes. That is only one legend will be shown for all nodes.

  • "separate": Show the legends of nodes separately. That is, nodes on each x will have their own legend.

  • "none": Do not show the legend of nodes.

  • "auto": Automatically determine how to show the legend. When nodes_label is TRUE, "none" will apply. When nodes_label is FALSE, and if stratum is the same as links_fill_by, "none" will apply. If there is any overlapping values between the nodes on different x, "merge" will apply. Otherwise, "separate" will apply.

nodes_color

A character string to color the nodes. Use a special value ".fill" to use the same color as the fill.

A character string of the column name to fill the links.

A character string to concatenate the columns in links_fill_by, if multiple columns are provided.

A character string to name the legend of links.

A character string to color the borders of links. Use a special value ".fill" to use the same color as the fill.

nodes_palette

A character string to specify the palette of nodes fill.

nodes_palcolor

A character vector to specify the colors of nodes fill.

nodes_alpha

A numeric value to specify the transparency of nodes fill.

nodes_label

A logical value to show the labels on the nodes.

nodes_label_miny

A numeric value to specify the minimum y (frequency) to show the labels.

nodes_width

A numeric value to specify the width of nodes.

A character string to specify the palette of links fill.

A character vector to specify the colors of links fill.

A numeric value to specify the transparency of links fill.

legend.box

A character string to specify the box of the legend, either "vertical" or "horizontal".

x_text_angle

Angle for x-axis text

aspect.ratio

Aspect ratio of plot panel

legend.position

Legend position: "none", "left", "right", "bottom", "top"

legend.direction

Legend direction: "horizontal" or "vertical"

flip

A logical value to flip the plot.

theme

Theme name (string) or theme function

theme_args

List of arguments passed to theme function

title

Plot title

subtitle

Plot subtitle

xlab

X-axis label

ylab

Y-axis label

facet_by

Column name(s) for faceting the plot

facet_scales

Scales for facets: "fixed", "free", "free_x", "free_y"

facet_ncol

Number of columns in facet layout

facet_nrow

Number of rows in facet layout

facet_byrow

Fill facets by row (TRUE) or column (FALSE)

seed

Random seed for reproducibility

combine

Whether to combine split plots into one

nrow

Number of rows when combining plots

ncol

Number of columns when combining plots

byrow

Fill combined plots by row

axes

How to handle axes in combined plots ("keep", "collect", "collect_x", "collect_y")

axis_titles

How to handle axis titles in combined plots

guides

How to handle guides in combined plots ("collect", "keep", "auto")

design

Custom layout design for combined plots

...

Other arguments to pass to ggalluvial::geom_alluvium or ggalluvial::geom_flow.

Value

A ggplot object or wrap_plots object or a list of ggplot objects

Examples

# \donttest{
# Reproduce the examples in ggalluvial
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"
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.

# }