plot {PWMEnrich} | R Documentation |
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).
x |
the PWM object |
y |
unused |
... |
other parameters to pass to seqLogo's
|
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]) |
if(require("PWMEnrich.Dmelanogaster.background")){ data(MotifDb.Dmel) # plot the tinman motif from MotifDb plot(MotifDb.Dmel[["tin"]]) }