regulon_plotExpression: regulon_plotExpression

In aertslab/SCENIC: SCENIC (Single Cell rEgulatory Network Inference and Clustering)

regulon_plotExpression

Description

Plots the expression of the genes in the regulon (as heatmap)

Usage

regulon_plotExpression(
  exprMat,
  regulonsSelected,
  nCells = 500,
  cellInfo = NULL,
  colVars = NULL,
  color = c("black", "goldenrod", "yellow"),
  ...
)

Arguments

exprMat	Expression matrix
regulonsSelected	Regulons to plot
nCells	Number of cells to plot (random subset of cells for faster plotting)
cellInfo	Cell labels to plot in the heatmap (data.frame)
colVars	Colors for the cell labels
color	Expression color range
...	Other arguments to pass to NMF::aheatmap

Value

Plots the heatmap

Examples

loomPath <- system.file(package="SCENIC", "examples/mouseBrain_toy.loom")
exprMat <- SCopeLoomR::get_dgem(SCopeLoomR::open_loom(loomPath)) # normalized preferred
dim(exprMat)

cellInfo <- data.frame(loadFile(scenicOptions, getDatasetInfo(scenicOptions, "cellInfo")))
colVars <- loadFile(scenicOptions, getDatasetInfo(scenicOptions, "colVars"))

exprMat_log <- log2(exprMat+1)
regulons <- loadInt(scenicOptions, "regulons")
regulonNames <- getRegulonName(c("Dlx1") , names(regulons))
regulon_plotExpression(exprMat_log, regulons[regulonNames], cellInfo=cellInfo, colVars=colVars) #, filename="regulonExpression.pdf")

aertslab/SCENIC documentation built on April 7, 2024, 10 a.m.