Description Usage Arguments Details Value Examples
View source: R/extractMonocleTrajectory.R
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$trajectory under the specified name.
1 2 | extractMonocleTrajectory(monocle, seurat, trajectory_name,
column_state = "State", column_pseudotime = "Pseudotime")
|
monocle |
Monocle object to extract trajectory from. |
seurat |
Seurat object to transfer trajectory to. |
trajectory_name |
Name of trajectory. |
column_state |
Name of meta data column that holds info about the state of a cell; defaults to 'State'. |
column_pseudotime |
Name of meta data column that holds info about the pseudotime of a cell; defaults to 'Pseudotime'. |
Extract trajectory from Monocle and add to Seurat object.
Returns Seurat object with added trajectory. Trajectory info (state, pseudotime, projection and tree) will be stored in seurat@misc$trajectory under the specified name.
1 2 3 4 5 6 7 | seurat <- extractMonocleTrajectory(
monocle = monocle,
seurat = seurat,
name = 'trajectory_1'
column_state = 'State',
column_pseudotime = 'Pseudotime'
)
|
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