plotCells: Plot Cells

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

Plot Cells

Description

plotCells() generates a tSNE plot based on cell-to-cell influence

Usage

plotCells(
  cellWalk,
  cellTypes,
  labelThreshold,
  embedding = "tSNE",
  initial_dims = 10,
  perplexity = 50,
  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)
embedding	method with which to embed data, either "tSNE" or "UMAP"
initial_dims	numeric, number of PCA dims to use for tSNE
perplexity	numeric, perplexity parameter for tSNE
recompute	boolean, recompute tSNE
plot	boolean, optionally don't plot output and only compute the embedding
seed	numeric, random seed

Value

cellWalk object with embedding stored in "tSNE" or "UMAP"

Examples

data("SampleCellWalkRData")
cellWalk <- plotCells(SampleCellWalkRData$cellWalk, perplexity=3, plot=FALSE)

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