plotMotifScores {PWMEnrich} | R Documentation |
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 y-axis, so the heights of bars
are comparable between sequences and motifs.
plotMotifScores(scores, sel.motifs = NULL, seq.names = NULL, cols = NULL, cutoff = NULL, log.fun = log2, main = "", legend.space = 0.3, max.score = NULL, trans = 0.5, text.cex = 0.9, legend.cex = 0.9, motif.names = NULL, seq.len.spacing = 8, shape="rectangle")
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 log-odds!) 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 log-odds. 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 log-odds 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" |
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")) }