addSlingShotTrajectories: Add a Slingshot Trajectories to an ArchR Project #NEW
In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

addSlingShotTrajectories

R Documentation

Add a Slingshot Trajectories to an ArchR Project #NEW

Description

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

Usage

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.