addMonocleTrajectory: Add a Monocle Trajectory to an ArchR Project

In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

Add a Monocle Trajectory to an ArchR Project

Description

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

Usage

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
)

GreenleafLab/ArchR documentation built on Feb. 21, 2025, 3:05 p.m.