tna (version 1.0.0)

plot_sequences: Create a Sequence Index Plot or a Distribution Plot

Description

Create a Sequence Index Plot or a Distribution Plot

Usage

plot_sequences(x, ...)
# S3 method for tna
plot_sequences(
  x,
  group,
  type = "index",
  scale = "proportion",
  geom = "bar",
  include_na = FALSE,
  na_color = "white",
  sort_by,
  show_n = TRUE,
  border,
  title,
  legend_title,
  xlab,
  ylab,
  tick = 5,
  ncol = 2L,
  ...
)
# S3 method for 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 = 5,
  ncol = 2L,
  ...
)
# S3 method for default
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 = 5,
  ncol = 2L,
  ...
)
# S3 method for 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,
  ncol = 2L,
  ...
)

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 FALSE. If TRUE, the 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. The default value tick = 5 shows every 5th label. Setting this to 1 will show every label.

ncol

Number of columns to use for the facets. The default is 2.

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