getTrajectory | R Documentation |
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 |
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. |
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