motifRG (version 1.16.0)

plotMotif: plot motif sequence matches

Description

plot aligned sequences, revealing the independent position specificity and dependency among adjacent positions.

Usage

plotMotif(match, logodds=F, entropy=F, bg.ld=NULL,  alphabet=c("A", "C", "G", "T"),has.box=T,...)

Arguments

match

motif match to be plotted. character or DNAStringSet object

logodds

logical; if true, plot the enrichment/depletion of a adjacent pair relative to the independent model.

entropy

logical; if true, areas outside the core region of the motif are dimmed

bg.ld

Experimental features: background dinucleotide logodds against independent model. if logodds=T, then the background logodds will be substracted

alphabet

the alphabets used in the sequence. Do not change its value

has.box

logical; if true, plot the boundaries of the motif

...

other arguments passed to the lower level plot function

Details

X-axis refers to the positions of the motifs. Y-axis correspond to the alphabets. Letter sizes define the frequencies of the nucleotides at a given position. Edges between the letters specifiy the dinucleotide relationship. The depth of the color correspond to the dinucleotide frequency. If logodds=T, thinner edges will be plotted between dependent pairs. The edge is colored red if the pair is depleted (relative to the expected frequency if the pair is independent), and green if the pair is enriched. The gradient of color red/green correspond to the level of dependency.

Examples

data(ctcf.motifs)
### plot the dinucleotide representation of the first motif
plotMotif(ctcf.motifs$motifs[[1]]@match$pattern)
plotMotif(ctcf.motifs$motifs[[1]]@match$pattern, logodds=TRUE)
plotMotif(ctcf.motifs$motifs[[1]]@match$pattern, logodds=TRUE, entropy=TRUE)