plotPeak {MMDiff2} | R Documentation |
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, 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 |
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) |
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)