addLogo: Add motif logo to RcisTarget results table

In aertslab/RcisTarget: RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions

Add motif logo to RcisTarget results table

Description

Adds a column containing the logo URL to RcisTarget results table.

Usage

addLogo(motifEnrDT, addHTML = TRUE, dbVersion = NULL, motifCol = "motif")

Arguments

motifEnrDT	Results from RcisTarget (data.table)
addHTML	Whether to add the HTML tag <img> around the URL or not (boolean).
dbVersion	The default value 'v10nr_clust' corresponds to the latest version of the databases (currently version 10). For previous databases use 'v8' or 'v9', as appropriate.
motifCol	Name of the column which contains the logo ID.

Value

Returns the results table with a new column: 'logo'. This column contains either a URL with the logo image, or the HTML code to show the logo [e.g. with datatable()].

See Also

vignette("showLogo") to directly show the table as HTML. See the package vignette for more examples: vignette("RcisTarget")

Examples

# Run the enrichment (or load previous results)
load(paste(file.path(system.file('examples', package='RcisTarget')),
           "motifEnrichmentTable_wGenes.RData", sep="/"))

# Add link to logo
newMotifErnTable <- addLogo(motifEnrichmentTable_wGenes)

# Show table
library(DT)
datatable(newMotifErnTable[,-c("enrichedGenes"), with=FALSE],
          escape = FALSE,
          filter="top",
          options=list(pageLength=5))

aertslab/RcisTarget documentation built on March 7, 2024, 11:21 p.m.