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.
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.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(seqPattern)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/seqPattern/plotMotifScanScores.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotMotifScanScores
> ### Title: Plotting heatmap of motif scanning scores
> ### Aliases: plotMotifScanScores
> ### plotMotifScanScores,DNAStringSet,matrix-method
>
> ### ** Examples
>
> library(GenomicRanges)
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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
> 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)
Getting motif scanning scores...
Plotting heatmap...
png
2
There were 12 warnings (use warnings() to see them)
>
>
>
>
>
> dev.off()
null device
1
>