computeMST: Comptute Minimum Spanning Tree

In PFPrzytycki/CellWalkR: An R Package for Integrating and Visualizing Single-Cell and Bulk Data to Resolve Regulatory Elements

Comptute Minimum Spanning Tree

Description

computeMST() computes a minimum spanning tree based on cell-to-cell influence

Usage

computeMST(
  cellWalk,
  cellTypes,
  labelThreshold,
  recompute = FALSE,
  plot = TRUE,
  seed
)

Arguments

cellWalk	a cellWalk object
cellTypes	character, optional vector of labels to use, all labels used by default. Most likely label among those listed will be used. If only a single label is provided, all cells will be colored by their score for that label. If two labels are given, the difference in score for each cell is shown.
labelThreshold	numeric, set a threshold below which cells aren't labeled (e.g. 0)
recompute	boolean, recompute layout for MST plot
plot	boolean, optionally don't plot output and only compute the embedding
seed	numeric, random seed

Value

cellWalk object with MST stored in "MST" and layout stored in "MST_layout"

Examples

data("SampleCellWalkRData")
cellWalk <- computeMST(SampleCellWalkRData$cellWalk, plot=FALSE)

PFPrzytycki/CellWalkR documentation built on Oct. 26, 2023, 1:50 p.m.