plotMotifScanScores: Plotting heatmap of motif scanning scores

In seqPattern: Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences

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.

Author(s)

Vanja Haberle

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)

Example output

Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb

Getting motif scanning scores...

Plotting heatmap...
png 
  2 
There were 12 warnings (use warnings() to see them)

seqPattern documentation built on Nov. 8, 2020, 7:52 p.m.