extractMonocleTrajectory: Extract trajectory from Monocle and add to Seurat object.

In romanhaa/cerebroPrepare: Export data for visualization in Cerebro.

Description

This function takes a Monocle object, extracts a trajectory that was calculated, and stores it in the specified Seurat object. Trajectory info (state, pseudotime, projection and tree) will be stored in seurat@misc$trajectory under the specified name.

Usage

extractMonocleTrajectory(monocle, seurat, trajectory_name,
  column_state = "State", column_pseudotime = "Pseudotime")

Arguments

monocle	Monocle object to extract trajectory from.
seurat	Seurat object to transfer trajectory to.
trajectory_name	Name of trajectory.
column_state	Name of meta data column that holds info about the state of a cell; defaults to 'State'.
column_pseudotime	Name of meta data column that holds info about the pseudotime of a cell; defaults to 'Pseudotime'.

Details

Extract trajectory from Monocle and add to Seurat object.

Value

Returns Seurat object with added trajectory. Trajectory info (state, pseudotime, projection and tree) will be stored in seurat@misc$trajectory under the specified name.

Examples

seurat <- extractMonocleTrajectory(
  monocle = monocle,
  seurat = seurat,
  name = 'trajectory_1'
  column_state = 'State',
  column_pseudotime = 'Pseudotime'
)

romanhaa/cerebroPrepare documentation built on Oct. 17, 2019, 4:01 p.m.