plotPeaks {nucleR} | R Documentation |
Helper function for a quick and convenient overview of nucleosome calling data.
plotPeaks(peaks, data, ...) ## S4 method for signature 'numeric' plotPeaks( peaks, data, threshold = 0, scores = NULL, start = 1, end = length(data), xlab = "position", ylab = "coverage", type = 1, col.points = "red", thr.lty = 1, thr.lwd = 1, thr.col = "darkred", scor.col = col.points, scor.cex = 2.5, scor.digits = 2, scor.nudge = 2000 ) ## S4 method for signature 'data.frame' plotPeaks(peaks, data, ...) ## S4 method for signature 'GRanges' plotPeaks(peaks, data, ...) ## S4 method for signature 'IRanges' plotPeaks( peaks, data, threshold = 0, scores = NULL, start = 1, end = length(data), dyn.pos = TRUE, xlab = "position", ylab = "coverage", type = 1, col.points = "red", thr.lty = 1, thr.lwd = 1, thr.col = "darkred", rect.thick = 2, rect.lwd = 0.5, rect.border = "black", scor.col = col.points, scor.cex = 2.5, scor.digits = 2, indiv.scores = FALSE, scor.nudge = 2000 )
peaks |
|
data |
Coverage or Tiling Array intensities |
... |
Arguments to be passed to other methods. |
threshold |
Threshold applied in |
scores |
If |
start, end |
Start and end points defining a subset in the range of
|
xlab, ylab, type, col.points |
Default values with general properties of the plot |
thr.lty, thr.lwd, thr.col |
Default values with general properties for threshold representation |
scor.col, scor.nudge, scor.cex, scor.digits |
Default values for
|
dyn.pos |
If peaks are ranges, should they be positioned dynamicaly on
top of the peaks or staticaly at |
rect.thick, rect.lwd, rect.border |
Default values for
|
indiv.scores |
Show or hide individual scores for width and height in brakets besides the mixed score. |
This function is intended to plot data previously processed with nucleR
pipeline. It shows a coverage/intensity profile toghether with the
identified peaks. If available, score of each peak is also shown.
(none)
Ricard Illa ricard.illa@irbbarcelona.org
peakDetection()
, peakScoring()
, ggplot2::ggplot()
,
# Generate a random peaks profile reads <- syntheticNucMap(nuc.len=40, lin.len=130)$syn.reads cover <- coverage.rpm(reads) # Filter them cover_fft <- filterFFT(cover) # Detect peaks peaks <- peakDetection(cover_fft, threshold="40%", score=TRUE, width=140) # Plot peaks and coverage profile (show only a window) plotPeaks(peaks, cover_fft, threshold="40%", start=1000, end=6000)