addTrajectory | R Documentation |
This function will fit a supervised trajectory in a lower dimensional space that can then be used for downstream analyses.
addTrajectory(
ArchRProj = NULL,
name = "Trajectory",
trajectory = NULL,
groupBy = "Clusters",
reducedDims = "IterativeLSI",
embedding = NULL,
preFilterQuantile = 0.9,
postFilterQuantile = 0.9,
useAll = FALSE,
dof = 250,
spar = 1,
force = FALSE,
seed = 1,
logFile = createLogFile("addTrajectory")
)
ArchRProj |
An |
name |
A string indicating the name of the fitted trajectory to be added in |
trajectory |
The order of cell groups to be used for constraining the initial supervised fitting procedure. For example, to get a trajectory from Cluster1 to Cluster2 to Cluster3, input should be c("Cluster1", "Cluster2", "Cluster3"). Cells will then be used from these 3 groups to constrain an initial fit in the group order. |
groupBy |
A string indicating the column name from |
reducedDims |
A string indicating the name of the |
embedding |
A string indicating the name of the |
preFilterQuantile |
Prior to the initial supervised trajectory fitting, cells whose euclidean distance from the cell-grouping center is above the provided quantile will be excluded. |
postFilterQuantile |
After initial supervised trajectory fitting, cells whose euclidean distance from the cell-grouping center is above the provided quantile will be excluded. |
useAll |
A boolean describing whether to use cells outside of trajectory groups for post-fitting procedure. |
dof |
The number of degrees of freedom to be used in the spline fit. See |
spar |
The sparsity to be used in the spline fit. See |
force |
A boolean value indicating whether to force the trajactory indicated by |
seed |
A number to be used as the seed for random number generation for trajectory creation. |
logFile |
The path to a file to be used for logging ArchR output. |
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