Description Usage Arguments Examples
This function visualises the motif scores for one or more
sequences. Sequences are drawn as lines, and scores are
plotted as triangles at both sides of the line
(corresponding to the two strands). The width of the base
of the triangle corresponds to motif width and the height
to the motif log(score)
that is positive and
greater than the cutoff
parameter (if specified).
All scores have the same yaxis, so the heights of bars
are comparable between sequences and motifs.
1 2 3 4 5 6 
scores 
the list of motifs scores. Each element of
the list is a matrix of scores for one sequences. The
columns in the matrix correspond to different motifs.
Each column contains the odds (not logodds!) scores over
both strands. For example, for a sequence of length 5,
scores for a 3 bp motifs could be: 
sel.motifs 
a vector of motif names. Use this parameter to show the motif hits to only a subset of motifs for which the scores are available. 
seq.names 
a vector of sequence names to show in the graph. If none specified, the sequences will be named Sequence 1, Sequence 2, ... 
cols 
a vector of colours to use to colour code motif hits. If none are specified, the current palette will be used. 
cutoff 
either a single value, or a vector of
values. The values are PWM cutoffs after 
log.fun 
the logarithm function to use to calculate logodds. By default log2 is used for consistency with Biostrings. 
main 
the main title 
legend.space 
the proportion of horizontal space to reserve for the legend. The default is 30%. 
max.score 
the maximal logodds score used to scale all other scores. By default this values is automatically determined, but it can also be set manually to make multiple plots comparable. 
trans 
the level of transparency. By default 50% transparency to be able to see overlapping binding sites 
text.cex 
the scaling factor for sequence names 
legend.cex 
the scaling factor for the legend 
motif.names 
optional vector of motif names to show
instead of those present as column names in

seq.len.spacing 
the spacing (in bp units) between the end of the sequence line and the text showing the length in bp 
shape 
the shape to use to draw motif occurances, valid values are "rectangle" (default), "line" and "triangle" 
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18  if(require("PWMEnrich.Dmelanogaster.background")){
###
# Load Drosophila PWMs
data(MotifDb.Dmel)
# two sequences of interest
sequences = list(DNAString("GAAGTATCAAGTGACCAGGTGAAGTCCCAGATGA"), DNAString("AGGTAGATAGAACAGTAGGCAATGAAGCCGATG"))
# select the tinman and snail motifs
pwms = MotifDb.Dmel[c("tin", "sna")]
# get the raw score that will be plotted
scores = motifScores(sequences, pwms, raw.scores=TRUE)
# plot the scores in both sequences, green for tin and blue for sna
plotMotifScores(scores, cols=c("green", "blue"))
}

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