seqPattern (version 1.4.0)

plotMotifScanScores: Plotting heatmap of motif scanning scores

Description

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.

Usage

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)

Arguments

regionsSeq

A DNAStringSet object. Set of sequences of the same length for which the motif occurrence density should be visualised.

motifPWM

A numeric matrix representing the Position Weight Matrix (PWM), such as returned by PWM function. Can contain either probabilities or log2 probability ratio of base b at position i.

seqOrder

Integer vector specifying the order of the provided input sequences. Must have the same length as the number of sequences in the regionSeq. Input sequences will be sorted according to this index in an ascending order form top to the bottom of the plot, i.e. the sequence labeled with the lowest number will appear at the top of the plot. The default value will order the sequences as they are ordered in the input regionSeq object.

flankUp, flankDown

The number of base-pairs upstream and downstream of the reference position in the provided sequences, respectively. flankUp + flankDown must sum up to the length of the sequences.

xTicks

Character vector of labels to be placed at the tick-marks on x-axis. The default NULL value produces five tick-marks: one at the reference point and two equally spaced tick-marks both upstream and downstream of the reference point.

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 NULL value produces five tick-marks: one at the reference point and two equally spaced tick-marks both upstream and downstream of the reference point.

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 NULL value produces no tick-marks and labels.

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 NULL value produces no tick-marks.

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 plotScale = TRUE. If no value is provided, it defaults to one fifth of the input sequence length.

scaleWidth

The width of the line for the scale bar. Used only when plotScale = TRUE.

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 outFile."pattern.jpg".

plotWidth, plotHeight

Width and height of the density plot in pixels.

Value

The function produces a PNG file in the working directory, visualising motif scanning scores in the set of ordered input sequences.

See Also

motifScanScores plotPatternDensityMap

Examples

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)