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

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

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.

Examples

# Get Test ArchR Project
proj <- getTestProject()

#Create Monocole Trajectory
cds <- getMonocleTrajectories(
  ArchRProj = proj, 
  useGroups = c("C1", "C2", "C3"), 
  principalGroup = "C1", 
  groupBy = "Clusters", 
  embedding = "UMAP"
)