add_cell_graph: Constructs a trajectory using a graph between cells, by...

In dynwrap: Representing and Inferring Single-Cell Trajectories

Constructs a trajectory using a graph between cells, by mapping cells onto a set of backbone cells.

Description

The cells that are part of the backbone will form the trajectory. All other cells are moved towards the nearest cell that is part of the backbone.

Usage

add_cell_graph(
  dataset,
  cell_graph,
  to_keep,
  milestone_prefix = "milestone_",
  ...
)

Arguments

dataset	A dataset created by wrap_data() or wrap_expression()
cell_graph	The edges between cells, a dataframe containing the from and to cells, the *length, and whether this edge is directed
to_keep	Whether a cells is part of the backbone. May be a character vector with the identifiers of the backbone cells, or a named boolean vector whether a cell is from the backbone
milestone_prefix	A prefix to add to the id of the cell ids when they are used as milestones, in order to avoid any naming conflicts,
...	extra information to be stored in the wrapper.

Value

A trajectory object

Examples

library(dplyr)
dataset <- wrap_data(cell_ids = letters)

backbone_cell_graph <- tibble::tibble(
  from = letters[1:10],
  to = letters[2:11],
  length = 1,
  directed = TRUE
)
leaves_cell_graph <- tibble::tibble(
  from = letters[12:26],
  to = sample(letters[1:11], 15, replace = TRUE),
  length = 1,
  directed = TRUE
)
cell_graph <- bind_rows(backbone_cell_graph, leaves_cell_graph)
cell_graph
to_keep <- letters[1:11]
to_keep

trajectory <- add_cell_graph(dataset, cell_graph, to_keep)

# for plotting the result, install dynplot
#- dynplot::plot_graph(trajectory)

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