plotMotifScanScores {seqPattern} | R Documentation |
Plots heatmap of motif scanning scores for a set of sorted sequences of the same length in the form of a two dimensional map centered at a common reference position. Motif is specified by a position weight matrix (PWM) that contains estimated probability of base b at position i, and the percentage of the maximal PWM score is plotted for each position (nucleotide) in each sequence.
plotMotifScanScores(regionsSeq, motifPWM, seqOrder = c(1:length(regionsSeq)), flankUp = NULL, flankDown = NULL, xTicks = NULL, xTicksAt = NULL, xLabel = "", yTicks = NULL, yTicksAt = NULL, yLabel = "", cexAxis = 8, plotScale = TRUE, scaleLength = NULL, scaleWidth = 15, addReferenceLine = TRUE, plotColorLegend = TRUE, outFile = "MotifScanningScores.png", plotWidth = 2000, plotHeight = 2000)
regionsSeq |
A |
motifPWM |
A numeric matrix representing the Position Weight Matrix (PWM), such as
returned by |
seqOrder |
Integer vector specifying the order of the provided input sequences.
Must have the same length as the number of sequences in the
|
flankUp, flankDown |
The number of base-pairs upstream and downstream of the reference
position in the provided sequences, respectively.
|
xTicks |
Character vector of labels to be placed at the tick-marks on x-axis.
The default |
xTicksAt |
Numeric vector of positions of the tick-marks on the x-axis. The values
can range from 1 (the position of the first base-pair in the sequence)
to input sequence length. The default |
xLabel |
The label for the x-axis. The default is no label, i.e. empty string. |
yTicks |
Character vector of labels to be placed at the tick-marks on y-axis.
The default |
yTicksAt |
Numeric vector of positions of the tick-marks on the y-axis. The values
can range from 1 (the position of the last sequence on the bottom of the
plot) to input sequence length (the position of the first sequence on
the top of the plot). The default |
yLabel |
The label for the y-axis. The default is no label, i.e. empty string. |
cexAxis |
The magnification to be used for axis annotation. |
plotScale |
Logical, should the scale bar be plotted in the lower left corner of the plot. |
scaleLength |
The length of the scale bar to be plotted. Used only when
|
scaleWidth |
The width of the line for the scale bar. Used only when
|
addReferenceLine |
Logical, should the vertical dashed line be drawn at the reference point. |
plotColorLegend |
Logical, should the color legend for the scanning score be plotted on the right side of the plot. |
outFile |
Character vector specifying the base name of the output plot file. The
final name of the plot file for each pattern will be
|
plotWidth, plotHeight |
Width and height of the density plot in pixels. |
The function produces a PNG file in the working directory, visualising motif scanning scores in the set of ordered input sequences.
Vanja Haberle
motifScanScores
plotPatternDensityMap
library(GenomicRanges) load(system.file("data", "zebrafishPromoters.RData", package="seqPattern")) promoterWidth <- elementMetadata(zebrafishPromoters)$interquantileWidth load(system.file("data", "TBPpwm.RData", package="seqPattern")) plotMotifScanScores(regionsSeq=zebrafishPromoters, motifPWM = TBPpwm, seqOrder=order(promoterWidth), flankUp = 400, flankDown = 600)