add_cell_waypoints: Add or select waypoint cells of a trajectory

In dynwrap: Representing and Inferring Single-Cell Trajectories

Add or select waypoint cells of a trajectory

Description

Waypoint cells are cells spread across all of the trajectory such that there is no other cell that has a large geodesic distance to any of the waypoint cells.

Usage

add_cell_waypoints(trajectory, num_cells_selected = 100)

is_wrapper_with_waypoint_cells(trajectory)

determine_cell_trajectory_positions(
  milestone_ids,
  milestone_network,
  milestone_percentages,
  progressions,
  divergence_regions
)

select_waypoint_cells(
  milestone_ids,
  milestone_network,
  milestone_percentages,
  progressions,
  divergence_regions,
  num_cells_selected = 100
)

Arguments

trajectory	The trajectory as created by infer_trajectory() or add_trajectory()
num_cells_selected	About the number of cells selected as waypoints
milestone_ids	The ids of the milestones in the trajectory. Type: Character vector.
milestone_network	The network of the milestones. Type: Data frame(from = character, to = character, length = numeric, directed = logical).
milestone_percentages	A data frame specifying what percentage milestone each cell consists of. Type: Data frame(cell_id = character, milestone_id = character, percentage = numeric).
progressions	Specifies the progression of a cell along a transition in the milestone_network. Type: Data frame(cell_id = character, from = character, to = character, percentage = numeric).
divergence_regions	A data frame specifying the divergence regions between milestones (e.g. a bifurcation). Type: Data frame(divergence_id = character, milestone_id = character, is_start = logical).

Value

add_cell_waypoints returns a trajectory with waypoint_cells, a character vector containing the cell ids of the waypoint cells

select_waypoint_cells returns a character vector containing the cell ids of the waypoint cells

A dynwrap object with the waypoint cells added.

dynwrap documentation built on July 26, 2023, 5:15 p.m.