viewMotifs: viewMotifs

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

viewMotifs

Description

Shows the motif information table as HTML using DT::datatable()

Usage

viewMotifs(
  tableSubset,
  motifCol = c("motif", "bestMotif", "MotifID"),
  dbVersion = "v9",
  nSignif = 3,
  colsToShow = c(motifEnrichment = c("motifDb", "logo", "NES", "geneSet",
    "TF_highConf"), regulonTargets = c("TF", "gene", "nMotifs", "bestMotif", "logo",
    "NES", "highConfAnnot", "Genie3Weight")),
  options = list(pageLength = 50),
  ...
)

Arguments

tableSubset	Motif information table to show
motifCol	Column name containing the motif logo ID (to pass to RcisTarget::addLogo). If NULL the logo is not added.
dbVersion	Database version (to pass to RcisTarget::addLogo).
nSignif	Number of significant digits to show for numeric columns
colsToShow	(No warning is shown for missing columns)
options	argument to pass to DT::datatable()
...	Any other other arguments to pass to DT::datatable()

Value

Writes the output in the file name stored in: getIntName(scenicOptions, "corrMat")

See Also

?DT::datatable()

Examples

library(SCENIC)
scenicOptions <- readRDS("int/scenicOptions.Rds")

regulonTargetsInfo <- loadInt(scenicOptions, "regulonTargetsInfo")
tableSubset <- regulonTargetsInfo[TF=="Stat6" & highConfAnnot==TRUE]
viewMotifs(tableSubset)

motifEnrichment_selfMotifs_wGenes <- loadInt(scenicOptions, "motifEnrichment_selfMotifs_wGenes")
tableSubset <- motifEnrichment_selfMotifs_wGenes[highlightedTFs=="Sox8"]
viewMotifs(tableSubset)

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