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Extract Trajectories for a Given Gradient Flow Cell (gfc.flow)

Source: R/gfc_flow.R
cell.trajectories.gfc.flow.Rd

Extracts all stored trajectories connecting a specified minimum and maximum (a gradient-flow cell) from a gfc.flow object.

Usage

# S3 method for class 'gfc.flow'
cell.trajectories(
  x,
  min.id,
  max.id,
  map = NULL,
  trajectory.format = c("vertices", "with.y.hat.modified"),
  gfc.flow = x,
  ...
)

Arguments

x

A gfc.flow object from compute.gfc() trajectory modes (or compute.gfc.trajectory() / deprecated compute.gfc.flow()).

min.id

Minimum identifier: label (character) or vertex index (numeric/integer).

max.id

Maximum identifier: label (character) or vertex index (numeric/integer).

map

Optional integer vector giving a vertex mapping (domain vertex IDs); if provided, returned trajectory vertices are mapped to indices via match().

trajectory.format

Output format for result$trajectories.

"vertices"

(Default) List of integer vectors (vertex indices).

"with.y.hat.modified"

List of lists with $vertices and $y.hat.modified (NULL if not available).

gfc.flow

Backward-compatible alias for x.

...

Additional arguments (currently ignored).

Value

An object of class gfc_cell_trajectories with components:

  • min.vertex, max.vertex, min.label, max.label

  • min.value, max.value

  • min.is.spurious, max.is.spurious

  • trajectories (format controlled by trajectory.format)

  • n.trajectories

  • mapped, original.min.vertex, original.max.vertex