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()
)

## Arguments

ArchRProj |
An `ArchRProject` object. |

name |
A string indicating the name of the fitted trajectory in `cellColData` to retrieve from the given `ArchRProject` . |

useMatrix |
The name of the data matrix from the `ArrowFiles` to get numerical values for each cell from. Recommended
matrices are "GeneScoreMatrix", "PeakMatrix", or "MotifMatrix". |

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 `groupEvery = 2` , the values for percentiles 1 and 2, 3 and 4,
5 and 6, etc. will be grouped together. |

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 `scaleTo` . Setting this to `NULL` will prevent any normalization and should be done in certain circumstances
(for ex. if you are using a "MotifMatrix"). |

smoothWindow |
An integer value indicating the smoothing window in size (relaive to `groupEvery` ) for the sequential
trajectory matrix to better reveal temporal dynamics. |

threads |
The number of threads to be used for parallel computing. |