addTrajectory: Add a Supervised Trajectory to an ArchR Project

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

Add a Supervised Trajectory to an ArchR Project

Description

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

Usage

addTrajectory(
  ArchRProj = NULL,
  name = "Trajectory",
  trajectory = NULL,
  groupBy = "Clusters",
  reducedDims = "IterativeLSI",
  embedding = NULL,
  preFilterQuantile = 0.9,
  postFilterQuantile = 0.9,
  useAll = FALSE,
  dof = 250,
  spar = 1,
  saveDF = NULL,
  force = FALSE,
  seed = 1,
  logFile = createLogFile("addTrajectory")
)

Arguments

ArchRProj	An ArchRProject object.
name	A string indicating the name of the fitted trajectory to be added in cellColData.
trajectory	The order of cell groups to be used for constraining the initial supervised fitting procedure. For example, to get a trajectory from Cluster1 to Cluster2 to Cluster3, input should be c("Cluster1", "Cluster2", "Cluster3"). Cells will then be used from these 3 groups to constrain an initial fit in the group order.
groupBy	A string indicating the column name from cellColData that contains the cell group definitions used in trajectory to constrain the initial supervised fitting procedure.
reducedDims	A string indicating the name of the reducedDims object from the ArchRProject that should be used for distance computation.
embedding	A string indicating the name of the embedding object from the ArchRProject that should be used for distance computation.
preFilterQuantile	Prior to the initial supervised trajectory fitting, cells whose euclidean distance from the cell-grouping center is above the provided quantile will be excluded.
postFilterQuantile	After initial supervised trajectory fitting, cells whose euclidean distance from the cell-grouping center is above the provided quantile will be excluded.
useAll	A boolean describing whether to use cells outside of trajectory groups for post-fitting procedure.
dof	The number of degrees of freedom to be used in the spline fit. See stats::smooth.spline() for more information.
spar	The sparsity to be used in the spline fit. See stats::smooth.spline() for more information.
saveDF	A full or relative path to use for creating a .RDS R object file containing a DataFrame with additional information about the trajectory. This includes the distance of each cell to the splines of the trajectory and the corresponding indicies returned by nabor::knn.
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.
logFile	The path to a file to be used for logging ArchR output.

Examples

# Get Test ArchR Project
proj <- getTestProject()

#Add Trajectory
proj <- addTrajectory(proj, trajectory = c("C1", "C2", "C3"), embedding = "UMAP", force = TRUE)

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