Get data along the trajectory — GetTrajectory • scMEGA

This function collects and smooths data along the trajectory using Seurat object as input. It was modified from the package ArchR getTrajectory to use a Seurat object as input. For more details, check here https://www.archrproject.com/reference/getTrajectory.html.

GetTrajectory(
  object = NULL,
  trajectory.name = "Trajectory",
  assay = NULL,
  slot = "counts",
  groupEvery = 1,
  log2Norm = TRUE,
  scaleTo = 10000,
  smoothWindow = 11
)

Arguments

object: Seurat object
trajectory.name: The name of trajectory inferred by AddTrajectory
assay: Which assay is used for data collection
slot: Name of slot used to collect data. Usually set as "counts" or "data".
groupEvery: The number of sequential percentiles to group together when generating a trajectory. This is similar to smoothing via a non-overlapping sliding window across pseudo-time.
log2Norm: Whether or not the data should be log2 transformed. This can be set to TRUE if gene expression or chromatin accessibility data is used, otherwise FALSE if data from TF activity is used.
scaleTo: Once the sequential trajectory matrix is created, each column in that matrix will be normalized to a column sum indicated by scaleTo.
smoothWindow: An integer value indicating the smoothing window in size (relative to groupEvery) for the sequential trajectory matrix to better reveal temporal dynamics.

Value

A SummarizedExperiment object

Examples

if (FALSE) {
trajRNA <- GetTrajectory(
   object = obj,
   assay = "RNA",
   slot = "data",
   smoothWindow = 7,
   log2Norm = TRUE
)
}