Add a Slingshot Trajectories to an ArchR Project — addSlingShotTrajectories • ArchR

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

addSlingShotTrajectories(
  ArchRProj = NULL,
  name = "SlingShot",
  useGroups = NULL,
  principalGroup = NULL,
  groupBy = NULL,
  embedding = NULL,
  reducedDims = NULL,
  force = FALSE,
  seed = 1
)

Arguments

ArchRProj: An ArchRProject object.
name: A string indicating the name of the fitted trajectory to be added in cellColData.
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.
reducedDims: A string indicating the name of the reducedDims object from the ArchRProject that should be used for trajectory analysis. embedding must equal NULL to use.
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.

Examples


# Get Test ArchR Project
proj <- getTestProject()

#Add SlingShot Trajectory
proj <- addSlingShotTrajectories(
  ArchRProj = proj,
  name = "Trajectory_SlingShot", 
  useGroups = c("C1", "C2", "C3"), 
  principalGroup = "C1", 
  groupBy = "Clusters", 
  embedding = "UMAP"
)