R/extractMonocleTrajectory.R
extractMonocleTrajectory.Rd
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
object@misc$trajectories$monocle2
under the specified name.
extractMonocleTrajectory( monocle, seurat, trajectory_name, column_state = "State", column_pseudotime = "Pseudotime" )
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'. |
Returns Seurat object with added trajectory. Trajectory info (state,
pseudotime, projection and tree) will be stored in
object@misc$trajectories$monocle2
` under the specified name.
if (FALSE) { seurat <- extractMonocleTrajectory( monocle = monocle, seurat = seurat, name = 'trajectory_1', column_state = 'State', column_pseudotime = 'Pseudotime' ) }