Plot VaSSTra Trajectories with Nestimate

Delegates grouped sequence index, distribution, and heatmap rendering to Nestimate::sequence_plot() and per-trajectory transition networks to transition_plot().

Usage

# S3 method for class 'vasstra_trajectories'
plot(
  x,
  type = c("index", "distribution", "heatmap", "transition"),
  colors = NULL,
  main = NULL,
  sort = "start",
  na = x$source$diagnostics$n_missing > 0L,
  ...
)

Arguments

x

A vasstra_trajectories object.

type

One or more of "index" (the default), "distribution", "heatmap", and "transition". A character vector requests several views and switches to the per-trajectory grid described above; for example type = c("transition", "index", "distribution").

colors

Optional colors, one per state, passed to Nestimate as state_colors and to transition_plot() as node fills.

main

Plot title for the single faceted view. Ignored by the grid, where each row is titled with its trajectory label.

sort

Sequence ordering passed to Nestimate::sequence_plot(). The default is "start" for robust within-trajectory index plots, including trajectories containing one sequence.

na

Show missing cells as a separate distribution band. By default, this is TRUE only when the sequence data contain NA.

...

Additional arguments passed to the sequence panels (Nestimate::sequence_plot()). In the grid, legend = "none" or legend = FALSE suppresses the shared bottom legend.

Value

For a single view, the value returned by Nestimate::sequence_plot(). For the grid, NULL invisibly.

Details

A single view (the default) is drawn as one faceted figure with a panel per trajectory. Passing several views, or the "transition" network, instead lays out a grid with one row per trajectory and one column per requested view (in the order given), which reproduces the familiar per-cluster VaSSTra figure of a transition network beside its sequence index and state-distribution plots. A single shared legend is drawn along the bottom; pass legend = "none" (or legend = FALSE) to omit it.

See also

flow_plot() for alluvial and individual flow views, transition_plot() for a single transition network.

Examples

data("engagement", package = "VaSSTra")
fit <- vasstra(engagement, n_states = 3, n_trajectories = 3)
plot(fit$trajectories)

plot(fit$trajectories, type = "distribution")

# \donttest{
if (requireNamespace("cograph", quietly = TRUE)) {
  # One row per trajectory; columns are the requested views.
  plot(fit$trajectories, type = c("transition", "index", "distribution"))
}

# }