Add a Monocle Trajectory to an ArchR Project — addMonocleTrajectory • ArchR

This function will add a trajectory from a monocle CDS created from getMonocleTrajectories to an ArchRProject.

addMonocleTrajectory(
  ArchRProj = NULL,
  name = "Trajectory",
  useGroups = NULL,
  groupBy = "Clusters",
  monocleCDS = NULL,
  force = FALSE
)

Arguments

ArchRProj: An ArchRProject object.
name: A string indicating the name of the fitted trajectory to be added in cellColData.
useGroups: The cell groups to be used for creating trajectory analysis.
groupBy: A string indicating the column name from cellColData that contains the cell group definitions used in useGroups to constrain trajectory analysis.
monocleCDS: A monocle CDS object created from getMonocleTrajectories.
force: A boolean value indicating whether to force the trajactory indicated by name to be overwritten if it already exists in the given ArchRProject.

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"
)

# Add Monocole Trajectory
proj <- addMonocleTrajectory(
  ArchRProj = proj, 
  name = "Trajectory_Monocole",
  useGroups = c("C1", "C2", "C3"),
  monocleCDS = cds
)