processTrajectories-methods: Process trajectories.

In edroaldo/fusca: Framework for Unified Single-Cell Analysis

Process trajectories.

Description

Process trajectories found in findPaths.

Usage

processTrajectories(
  object,
  assay.type = "RNA",
  genes,
  path.rank,
  num.cells,
  neighs,
  column.ann = "population",
  column.color = "colors"
)

## S4 method for signature 'CellRouter'
processTrajectories(
  object,
  assay.type = "RNA",
  genes,
  path.rank,
  num.cells,
  neighs,
  column.ann = "population",
  column.color = "colors"
)

Arguments

object	CellRouter object.
assay.type	character; the type of data to use.
genes	character vector; gene names that are used for trajectory analysis.
path.rank	character; method to rank paths: path_cost, path_flow, rank, length. Available ranks are 'path_cost', 'path_flow', 'rank', 'length'.
num.cells	numeric; minimum of cells contained in the trajectories.
neighs	numeric; the size of the neighborhood in kNN graph used to smoothen kinetic profiles.
column.ann	character; transitions between the cell states provided here are identified, such as clusters or sorted populations.
column.color	character; the colors corresponding to the annotation in column.ann.

Value

CellRouter object with the paths, the networks and the pathsinfo slots updated.

edroaldo/fusca documentation built on March 1, 2023, 1:43 p.m.