plotTsne_AUCellApp: plotTsne_AUCellApp

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

plotTsne_AUCellApp

Description

Creates the AUCell shiny app to visualize the regulon activities on the t-SNE

Usage

plotTsne_AUCellApp(
  scenicOptions,
  exprMat,
  tSNE_fileName = NULL,
  skipDuplicatedExtended = TRUE
)

Arguments

scenicOptions	Fields used: aucell_regulonAUC, aucell_thresholds, cellInfo, and default tSNE
exprMat	Expression matrix
tSNE_fileName	tSNE file name. If null, the default t-SNE is used.
skipDuplicatedExtended	Skip extended regulons if there is a high-confidence regulon for the same TF

Value

Invisible: aucellApp

Examples

logMat <- exprMat # Better if it is logged/normalized
aucellApp <- plotTsne_AUCellApp(scenicOptions, logMat)
savedSelections <- shiny::runApp(aucellApp)

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