getMonocleTrajectories: Get a Monocle CDS of Trajectories that can be added to an...
In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

getMonocleTrajectories

R Documentation

Get a Monocle CDS of Trajectories that can be added to an ArchRProject #NEW

Description

This function will use monocle3 to find trajectories and then returns a monocle CDS object that can be used as input for addMonocleTrajectory.

Usage

getMonocleTrajectories(
  ArchRProj = NULL,
  name = "Trajectory",
  useGroups = NULL,
  principalGroup = NULL,
  groupBy = NULL,
  embedding = NULL,
  clusterParams = list(),
  graphParams = list(),
  seed = 1
)

Arguments

`ArchRProj`	An `ArchRProject` object.
`name`	A string indicating the name of the fitted trajectory.
`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.
`clusterParams`	A list of parameters to be added when clustering cells for monocle3 with `monocle3::cluster_cells`.
`graphParams`	A list of parameters to be added when learning graphs for monocle3 with `monocle3::learn_graph`.
`seed`	A number to be used as the seed for random number generation for trajectory creation.