SCENIC (version 1.1.2-01)

regulon_plotExpression: 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

# NOT RUN {
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")
# }