findPaths-methods: Identify trajectories connecting source and target...

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

Identify trajectories connecting source and target populations.

Description

Identify trajectories based on euclidean, maximum, manhattan, canberra, binary or graph network. Writes to the computer terminal calling a java code and that saves the data in files which address is stored in assay@sampTab. These files will be processed by the processTrajectories function. The java code is written in the CellRouterJava folder in the package directory. The java folder in the package directory has the code with some modifications to be used in the findPathsRJava function.

Usage

findPaths(
  object,
  assay.type = "RNA",
  sources,
  targets,
  column = "population",
  maindir,
  method
)

## S4 method for signature 'CellRouter'
findPaths(
  object,
  assay.type = "RNA",
  sources,
  targets,
  column = "population",
  maindir,
  method
)

Arguments

object	CellRouter object.
assay.type	character; the type of data to use.
sources	character vector; names of the source populations.
targets	character vector; names of the target populations.
column	character; column in the metadata table specifying whether transitions are between clusters or other annotations, such as sorted populations.
maindir	character; directory where the files will be saved.
method	character; method used to determine the source and target cells based on the source and target populations.

Value

CellRouter object with the directory slot updated.

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