getTrajectories: Reconstructing cell trajectories following a specific lineage...

In minzheguo/SLICE: Determining Cell Differentiation and Lineage based on Single Cell Entropy

Reconstructing cell trajectories following a specific lineage (start -> end) in the inferred lineage model

Description

This function implements both shortest-path based and principal-curve based cell transitional path reconstruction.

Usage

getTrajectories(
  object,
  method = "sp",
  start,
  end,
  network = "mst",
  NN.threshold = 0.7,
  do.trim = F,
  do.stepwise = F,
  ...
)

Arguments

object	Slice object
method	Select either "sp" (shortest-path based) method or "pc" (principal-curve based) method to reconstruct cell trajectories following a lineage in the infered lineage model
start	The numeric ID of the stable state from which the cell transition starts
end	The numeric ID of the stable state at which the cell transition ends
network	Used in the shortest path based method; "mst" means the shortest path will be explored on the minimum spanning tree of cells, while "csn" means on the cell similarity network (i.e., mst + local wiring)
NN.threshold	Used in the shortest path based method, specifies the distance threshold for determining neighbors of each cell in the path. Default is 0.7 quantile of all edge weights in the network
do.trim	Used in the principal curve based method. When set to TRUE, only the curve between the start and end stable states will be returned; otherwise, the whole curve will be returned.

Details

Prerequisite: the "model" slot of the input slice object must be set

Value

updated slice object with reconstructed cell trajectories in the "transitions" slot.

minzheguo/SLICE documentation built on June 5, 2023, 11:56 a.m.