addTrajectory.Rd
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 |
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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. |