SCENIC (version 1.1.2-01)

viewMotifs: 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

# NOT RUN {
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)
# }