findPathsRJava-methods: Identify trajectories connecting source and target...
In edroaldo/fusca: Framework for Unified Single-Cell Analysis

findPathsRJava

R Documentation

Identify trajectories connecting source and target populations.

Description

Identify trajectories based on euclidean, maximum, manhattan, canberra, binary or graph network. The code uses the rJava library and does not communicate with the terminal as the findPaths function does. The computations are stored in the specified directories and can be read using the summarize function. This function uses the java code stored in the java folder in the package directory. If you are a linux user and the rJava library is not installed, please check the topic at https://stackoverflow.com/questions/12872699/error-unable-to-load-installed-packages-just-now.

Usage

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

## S4 method for signature 'CellRouter'
findPathsRJava(
  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. The available methods are 'euclidean', 'maximum', 'manhattan', 'canberra', 'binary', 'graph'.