plotPatternOccurrenceAverage: Plotting average profile of sequence pattern occurrence

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

Description

Plots average profile of sequence pattern occurrence for a set of input sequences of the same length. Multiple sequence patterns can be processed at once and visualised in the same plot, allowing comparison across different patterns.

Usage

plotPatternOccurrenceAverage(regionsSeq, patterns, flankUp = NULL, 
    flankDown = NULL, smoothingWindow = 1, color = rainbow(length(patterns)),
    xLabel = "Distance to reference point (bp)", yLabel = "Relative frequency",
    cexAxis = 1, addReferenceLine = TRUE, plotLegend = TRUE, cexLegend = 1,
    useMulticore = FALSE, nrCores = NULL, add = FALSE, ...)

Arguments

regionsSeq	A DNAStringSet object. Set of sequences of the same length for which the patterns occurrence profile should be visualised.
patterns	Character vector specifying one or more DNA sequence patterns (oligonucleotides). IUPAC ambiguity codes can be used and will match any letter in the subject that is associated with the code.
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. If no values are provided both flankUp and flankDown are set to be half of the length of the input sequences, i.e. the reference position is assumed to be in the middle of the sequences.
smoothingWindow	Integer specifying the size of a window (in base-pairs) to be used for smoothing the signal. Default value of 1 corresponds to no smoothing.
color	A vector of values specifying the colors for plotting. Number of colors must match the number of patterns that should be plotted.
xLabel, yLabel	Character strings for x and y axis labels, respectively.
cexAxis	The magnification to be used for axis annotation relative to the current setting of cex.
addReferenceLine	Logical, should the vertical dashed line be drawn at the reference point.
plotLegend	Logical, should the legend be plotted at the top.
cexLegend	The magnification to be used for legend relative to the current setting of cex.
useMulticore	Logical, should multicore be used. useMulticore = TRUE is supported only on Unix-like platforms.
nrCores	Number of cores to use when useMulticore = TRUE. Default value NULL uses all detected cores.
add	Logical, should the pattern occurrence profiles be added to the existing plot.
...	Further arguments to be passed to plot() or lines() methods, such as lty, etc.

Value

The function finds all hits matching the specified patterns in the set of input sequences and plots one average profile per pattern reflecting the occurrence of patterns across sequences.

Author(s)

Vanja Haberle

See Also

getPatternOccurrenceList
plotPatternDensityMap

Examples

load(system.file("data", "zebrafishPromoters.RData", package="seqPattern"))

# dinucleotide patterns
plotPatternOccurrenceAverage(regionsSeq = zebrafishPromoters, patterns = c("AT", 
            "TA", "CG", "GC"), flankUp = 400, flankDown = 600, smoothingWindow = 
            3, color = c("gold", "darkred", "forestgreen", "navy"))

# motif consensus sequence
plotPatternOccurrenceAverage(regionsSeq = zebrafishPromoters, patterns = 
            "TATAWAWR", flankUp = 400, flankDown = 600, smoothingWindow = 3, 
            color = "gray")

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