plotPeak: plot Peak
In dhelekal/mmdiff3: Statistical Testing for ChIP-Seq data sets

This function plots histograms of fragment positions over a pre defined regions of interests / peaks. Can also show occurences of Sequence motifs and annotated objects (e.g. genes).

plotPeak(MD, Peak.id, Sample.ids = NULL, NormMethod = NULL,
  plot.input = FALSE, strand.specific = FALSE, whichPos = "Center",
  whichContrast = NULL, Motifs = NULL, Motifcutoff = "80%",
  anno = NULL, xaxt = NULL, xlim = NULL, ylim = NULL)

`MD`	DBAmmd Object. This Object can be created using `DBAmmd()`.
`Peak.id`	Peak id to specify which Peak to plot. (coresponding to names of Regions(MD))
`Sample.ids`	which samples to draw. If NULL all samples are drawn. (DEFAULT: NULL)
`NormMethod`	whether to apply normailzation factors. currently no normalization method implemented (DEFAULT: None)
`plot.input`	whether to plot input controls (DEFAULT: TRUE)
`strand.specific`	if strand specific reads should be kept apart. (DEFAULT:FALSE)
`whichPos`	specifies which relative positions of mapped fragments should to be considered. Can be one of: 'Left.p', 'Right.p', 'Right.p' and 'Left.n': Start and end positions of fragments mapping to positive or negative strand, respectively ('Right.p' and 'Left.n' are not available for single-end reads). Additionally inferred positions: 'Center.n','Center.p','Center','Left','Right'. (DEFAULT: 'Center')
`whichContrast`	index determining which of the set contrast should be used. (DEFAULT: 1)
`Motifs`	TF binding sites (DEFAULT: NULL)
`Motifcutoff`	(Default: "80%")
`anno`	either a GRanges objects containing annotated objects, e.g. genes, or a list of GRanges Objects. (Default: NULL)
`xaxt`	(Default: NULL)
`xlim`	(Default: NULL)
`ylim`	(Default: NULL)

dev.off()
data("MMD")
plotPeak(MMD,Peak.id='6',plot.input=FALSE)

# add annotation (Overlapping genes)
data("mm9-Genes")
GR <- list(UCSCKnownGenes = GR)
plotPeak(MMD, Peak.id='6', plot.input = FALSE, anno=GR)

# add TF binding sites
library('MotifDb')
motifs <- query(query(MotifDb, 'Mmusculus'), 'E2F')
plotPeak(MMD, Peak.id='6', plot.input = FALSE,
       Motifs=motifs,Motifcutoff="80%")

# split peaks by contrast
plotPeak(MMD, Peak.id='6', plot.input = FALSE, whichContrast=1,
       Motifs=motifs,Motifcutoff="80%",anno=GR)