View source: R/perform.slingshot.trajectory.R
perform.slingshot.trajectory | R Documentation |
Generates slingshot trajectory inference on the defined reduction and clustering
perform.slingshot.trajectory( object, reduction, assay, clust.method, column, start.clus = NULL, end.clus = NULL, verbose = FALSE, seed = 1234, ... )
object |
IBRAP S4 class object |
reduction |
Character. String defining which reduction to supply to the clustering algorithm. Default = NULL |
assay |
Character. String containing indicating which assay to use |
clust.method |
Character. Which cluster method should be used utilised from clustering results, if ''metadata'' is supplied, you will access the metadata. |
column |
Character. Which column within the isolated clust.method should be used to define cell type annoation. |
start.clus |
Character. Which cluster should start the trajectory, if NULL then slingshot will attempt to discover this. Default = NULL |
end.clus |
Character. Which cluster should end the trajectory, if NULL then slingshot will attempt to discover this. Default = NULL |
verbose |
Logical Should function messages be printed? |
seed |
Numeric. What should the seed be set as. Default = 1234 |
... |
arguments to be passed to slingshot::slingshot |
A SingleshotDataSet class results object containing cellular lineages/curves
traj_res <- perform.slingshot.trajectory(object = object, reduction = 'pca_umap', assay = 'SCT', clust.method = 'metadata', column = 'celltype') plot.slingshot(result = traj_red, object = traj, assay = 'SCT', relevant = F, Pseudotime = T)
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