Create a Sequence Index Plot or a Distribution Plot

Usage

plot_sequences(x, ...)

# S3 method for class 'tna'
plot_sequences(
  x,
  group,
  type = "index",
  scale = "proportion",
  geom = "bar",
  include_na = TRUE,
  na_color = "white",
  sort_by,
  show_n = TRUE,
  border,
  title,
  legend_title,
  xlab,
  ylab,
  tick = 1,
  ...
)

# S3 method for class 'tna_data'
plot_sequences(
  x,
  group,
  type = "index",
  scale = "proportion",
  geom = "bar",
  include_na = FALSE,
  colors,
  na_color = "white",
  sort_by,
  show_n = TRUE,
  border,
  title,
  legend_title,
  xlab,
  ylab,
  tick = 1,
  ...
)

# Default S3 method
plot_sequences(
  x,
  cols,
  group,
  type = "index",
  scale = "proportion",
  geom = "bar",
  include_na = FALSE,
  colors,
  na_color = "white",
  sort_by,
  show_n = TRUE,
  border,
  title,
  legend_title,
  xlab,
  ylab,
  tick = 1,
  ...
)

# S3 method for class 'group_tna'
plot_sequences(
  x,
  type = "index",
  scale = "proportion",
  geom = "bar",
  include_na = FALSE,
  na_color = "white",
  sort_by,
  show_n = TRUE,
  border,
  title,
  legend_title,
  xlab,
  ylab,
  tick = 1,
  ...
)

Arguments

x: A tna, group_tna, tna_data or a data.frame object with sequence data in wide format.
...: Ignored.
group: A vector indicating the group assignment of each row of the data. Must have the same length as the number of rows of x. Alternatively, a single character string giving the column name of the data that defines the group when x is a wide format data.frame or a tna_data object. Used for faceting the plot.
type: A character string for the type of plot to generate. The available options are "index" (the default) for a sequence index plot, and "distribution" showing the distribution of the states over time.
scale: A character string that determines the scaling of the vertical axis for distribution plots. The options are "proportion" (the default) and "count" for proportions and raw counts of states, respectively.
geom: A character string for the type of geom to use for distribution plots. The options are "bar" (the default) and "area".
include_na: A logical value for whether to include missing values for distribution plots. The default is TRUE: missing values are converted to a new state and included in the plot.
na_color: A character string giving the color to use for missing values. The default is "white".
sort_by: Either a character vector of column names of x to sort by or "everything" to sort by every column. If missing, no sorting is done.
show_n: A logical value for whether to add the number of observations (total or by group) to the plot title.
border: A character string giving the color for borders. For index plots, this is the color of borders between cells (tiles). For distribution plot with geom = "bar", this is the color of bar outlines. Not applicable to geom = "area".
title: An optional character string providing a title for the plot.
legend_title: An optional character string providing a title for the legend.
xlab: A character string giving the label for the horizontal axis. The default is "Time".
ylab: A character string giving the label for the vertical axis. The default is "Sequence" for index plots, and "Proportion" or "Count" based on scale for distribution plots.
tick: An integer specifying the horizontal axis label interval, e.g., tick = 5 would show every 5th label. The default is 1 showing every label.
colors: A named character vector mapping states to colors, or an unnamed character vector. If missing, a default palette is used.
cols: A character Vector of column names to be treated as time points. If missing, all columns will be used.

Examples

# Sequence index plot (default)
plot_sequences(
  group_regulation,
  group = rep(1:2, each = 1000),
  tick = 5
)

# State distribution plot
plot_sequences(
  group_regulation,
  group = rep(1:2, each = 1000),
  type = "distribution",
  tick = 5
)