plot {PWMEnrich} | R Documentation

## Plotting for the PWM class

### Description

This function produces a sequence logo (via package seqLogo).

Plots a graphical version of the motif enrichment report. Note that all values are plotted, if you want to plot only a subset of a report, first select this subset (see examples).

### Arguments

`x` | the PWM object
`y` | unused
`...` | other parameters to pass to seqLogo's `plot` function
`x` | a MotifEnrichmentReport object
`y` | unused
`fontsize` | font size to use in the plot
`header.fontsize` | font size of the header
`widths` | the relative widths of columns
`...` | unused if(require("PWMEnrich.Dmelanogaster.background")) ### # load the pre-compiled lognormal background data(PWMLogn.dm3.MotifDb.Dmel) # scan two sequences for motif enrichment sequences = list(DNAString("GAAGTATCAAGTGACCAGTAAGTCCCAGATGA"), DNAString("AGGTAGATAGAACAGTAGGCAATGAAGCCGATG")) res = motifEnrichment(sequences, PWMLogn.dm3.MotifDb.Dmel) # produce a report for all sequences taken together r = groupReport(res) # plot the top 10 most enriched motifs plot(r[1:10])

### Examples

    if(require("PWMEnrich.Dmelanogaster.background")){
      data(MotifDb.Dmel)

      # plot the tinman motif from MotifDb
      plot(MotifDb.Dmel[["tin"]])
    }

[Package PWMEnrich version 4.20.0 Index]