Add a Slingshot Trajectories to an ArchR Project #NEW

This function will fit a supervised trajectory in a lower dimensional space that can then be used for downstream analyses.

addSlingShotTrajectories(
  ArchRProj = NULL,
  name = "SlingShot",
  useGroups = NULL,
  principalGroup = NULL,
  groupBy = NULL,
  embedding = NULL,
  reducedDims = NULL,
  force = FALSE,
  seed = 1
)

Arguments

ArchRProj	An ArchRProject object.
name	A string indicating the name of the fitted trajectory to be added in cellColData.
useGroups	A character vector that is used to select a subset of groups by name from the designated groupBy column in cellColData. This limits the groups used to identify trajectories.
principalGroup	The principal group which represents the group that will be the starting point for all trajectories.
groupBy	A string indicating the column name from cellColData that contains the cell group definitions used in useGroups to constrain trajectory analysis.
embedding	A string indicating the name of the embedding object from the ArchRProject that should be used for trajectory analysis.
reducedDims	A string indicating the name of the reducedDims object from the ArchRProject that should be used for trajectory analysis. embedding must equal NULL to use.
force	A boolean value indicating whether to force the trajactory indicated by name to be overwritten if it already exists in the given ArchRProject.
seed	A number to be used as the seed for random number generation for trajectory creation.