AddTrajectory: Add trajectory

In CostaLab/scMEGA: Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference

Add trajectory

Description

This function infers a pseudo-time trajectory based on the supervised input. It was modified from the package ArchR addTrajectory to use a Seurat object as input. For more details, check here https://www.archrproject.com/reference/addTrajectory.html.
Author: Jeffrey Granja

Usage

AddTrajectory(
  object,
  name = "Trajectory",
  trajectory = NULL,
  group.by = NULL,
  reduction = NULL,
  dims = NULL,
  pre.filter.quantile = 0.9,
  post.filter.quantile = 0.9,
  use.all = FALSE,
  dof = 250,
  spar = 1,
  seed = 42
)

Arguments

object	A Seurat object
name	A string indicating the name of the fitted trajectory to be added in meta.data
trajectory	The order of cell groups to be used for constraining the initial supervised fitting procedure
group.by	The column name in metadata that contains the cell group definitions used in trajectory
reduction	Name of dimension reduction used to infer the trajectory
dims	How many dimensions to use
pre.filter.quantile	Prior to the initial supervised trajectory fitting, cells whose euclidean distance from the cell-grouping center is above the provided quantile will be excluded.
post.filter.quantile	After initial supervised trajectory fitting, cells whose euclidean distance from the cell-grouping center is above the provided quantile will be excluded.
use.all	Whether or not to use cells ourside of trajectory groups for post-fitting procedure
dof	The number of degrees of freedom to be used in the spline fit
spar	The sparsity to be used in the spline fit.
seed	Random seed

Value

Seurat object with inferred trajectory

Examples

## Not run: 
obj <- AddTrajectory(
   object = obj,
   trajectory = c(2, 1),
   group.by = "RNA_snn_res.0.2",
   reduction = "dm",
   dims = 1:3,
   use.all = FALSE
)

## End(Not run)

CostaLab/scMEGA documentation built on Sept. 25, 2024, 6:11 a.m.