getTrajectory.Rd
This function will get a supervised trajectory from an ArchRProject
(see addTrajectory
), get data
from a desired matrix, and smooth each value across the input trajectory.
getTrajectory( ArchRProj = NULL, name = "Trajectory", useMatrix = "GeneScoreMatrix", groupEvery = 1, log2Norm = TRUE, scaleTo = 10000, smoothWindow = 11, threads = getArchRThreads() )
ArchRProj | An |
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name | A string indicating the name of the fitted trajectory in |
useMatrix | The name of the data matrix from the |
groupEvery | The number of sequential percentiles to group together when generating a trajectory. This is similar to smoothing
via a non-overlapping sliding window across pseudo-time. If |
log2Norm | A boolean value that indicates whether the summarized trajectory matrix should be log2 transformed. If you are using a "MotifMatrix" set to FALSE. |
scaleTo | Once the sequential trajectory matrix is created, each column in that matrix will be normalized to a column sum
indicated by |
smoothWindow | An integer value indicating the smoothing window in size (relaive to |
threads | The number of threads to be used for parallel computing. |