plotTopMotifsSequence,MotifEnrichmentResults-method {PWMEnrich} | R Documentation

## Plot the top N enrichment motifs in a single sequence

### Description

Plot the top N enrichment motifs in a single sequence

### Usage

    ## S4 method for signature 'MotifEnrichmentResults'
    plotTopMotifsSequence(obj, seq.id, n, bg = TRUE, id = FALSE, ...)

### Arguments

`obj` | a MotifEnrichmentResults object
`seq.id` | either the sequence number or sequence name
`n` | the number of top ranked motifs to plot
`bg` | if to use background corrected P-values to do the ranking (if available)
`id` | if to show PWM IDs instead of target TF names
`...` | other parameters passed to `plotMultipleMotifs()`

### Examples

    if(requireNamespace("PWMEnrich.Dmelanogaster.background")){
       ###
       # load the pre-compiled lognormal background
       data(PWMLogn.dm3.MotifDb.Dmel, package = "PWMEnrich.Dmelanogaster.background")

       # scan two sequences for motif enrichment
       sequences = list(DNAString("GAAGTATCAAGTGACCAGTAAGTCCCAGATGA"),
         DNAString("AGGTAGATAGAACAGTAGGCAATGAAGCCGATG"))

       res = motifEnrichment(sequences, PWMLogn.dm3.MotifDb.Dmel)

       # plot the top 4 motifs in a 2x2 grid
       plotTopMotifsSequence(res, 1, 4)

       # plot top 3 motifs in a single row
       plotTopMotifsSequence(res, 1, 3, row=1, cols=3)
    }

[Package PWMEnrich version 4.26.0 Index]