addTrajectory: Add a Supervised Trajectory to an ArchR Project
In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

addTrajectory

R Documentation

Add a Supervised Trajectory to an ArchR Project

Description

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

Usage

addTrajectory(
  ArchRProj = NULL,
  name = "Trajectory",
  trajectory = NULL,
  groupBy = "Clusters",
  reducedDims = "IterativeLSI",
  embedding = NULL,
  preFilterQuantile = 0.9,
  postFilterQuantile = 0.9,
  useAll = FALSE,
  dof = 250,
  spar = 1,
  force = FALSE,
  seed = 1,
  logFile = createLogFile("addTrajectory")
)

Arguments

`ArchRProj`	An `ArchRProject` object.
`name`	A string indicating the name of the fitted trajectory to be added in `cellColData`.
`trajectory`	The order of cell groups to be used for constraining the initial supervised fitting procedure. For example, to get a trajectory from Cluster1 to Cluster2 to Cluster3, input should be c("Cluster1", "Cluster2", "Cluster3"). Cells will then be used from these 3 groups to constrain an initial fit in the group order.
`groupBy`	A string indicating the column name from `cellColData` that contains the cell group definitions used in `trajectory` to constrain the initial supervised fitting procedure.
`reducedDims`	A string indicating the name of the `reducedDims` object from the `ArchRProject` that should be used for distance computation.
`embedding`	A string indicating the name of the `embedding` object from the `ArchRProject` that should be used for distance computation.
`preFilterQuantile`	Prior to the initial supervised trajectory fitting, cells whose euclidean distance from the cell-grouping center is above the provided quantile will be excluded.
`postFilterQuantile`	After initial supervised trajectory fitting, cells whose euclidean distance from the cell-grouping center is above the provided quantile will be excluded.
`useAll`	A boolean describing whether to use cells outside of trajectory groups for post-fitting procedure.
`dof`	The number of degrees of freedom to be used in the spline fit. See `stats::smooth.spline()` for more information.
`spar`	The sparsity to be used in the spline fit. See `stats::smooth.spline()` for more information.
`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.
`logFile`	The path to a file to be used for logging ArchR output.