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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 = 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,
  ...
)

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 = 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,
  ...
)

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 specifying the column name of the data frame to plot for the x-axis.

x_sep

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

y

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

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

The column(s) to split data by and plot separately.

split_by_sep

The separator for multiple split_by columns. See split_by

keep_empty

A logical value indicating whether to keep empty groups. If FALSE, empty groups will be removed.

flow

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

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 https://ggplot2.tidyverse.org/reference/expansion.html

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

A numeric value specifying the angle of the x-axis text.

aspect.ratio

A numeric value specifying the aspect ratio of the plot.

legend.position

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

legend.direction

A character string specifying the direction of the legend.

flip

A logical value to flip the plot.

theme

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

theme_args

A list of arguments to pass to the theme function.

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.

subtitle

A character string specifying the subtitle of the plot.

xlab

A character string specifying the x-axis label.

ylab

A character string specifying the y-axis label.

facet_by

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

facet_scales

Whether to scale the axes of facets. Default is "fixed" Other options are "free", "free_x", "free_y". See ggplot2::facet_wrap

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.

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.

facet_byrow

A logical value indicating whether to fill the plots by row. Default is TRUE.

seed

The random seed to use. Default is 8525.

combine

Whether to combine the plots into one when facet is FALSE. Default is TRUE.

nrow

A numeric value specifying the number of rows in the facet.

ncol

A numeric value specifying the number of columns in the facet.

byrow

A logical value indicating whether to fill the plots by row.

...

Additional arguments.

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")

# }