plotPeaks: Nucleosome calling plot function

In nucleR: Nucleosome positioning package for R

Description

Helper function for a quick and convenient overview of nucleosome calling data.

Usage

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
)

Arguments

peaks	numeric, data.frame, IRanges or GRanges object containing the detected peaks information. See help of peakDetection() or peakScoring() for more details.
data	Coverage or Tiling Array intensities
...	Arguments to be passed to other methods.
threshold	Threshold applied in peakDetection
scores	If peaks is a data.frame or a GRanges it's obtained from 'score' column, otherwise, scores can be given here as a numeric vector.
start, end	Start and end points defining a subset in the range of data. This is a convenient way to plot only a small region of data, without dealing with subsetting of range or score objects.
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 ggplot2::geom_text() representation for score numbers, if available.
dyn.pos	If peaks are ranges, should they be positioned dynamicaly on top of the peaks or staticaly at threshold baseline. Spacing of overlapping ranges is automatically applied if FALSE.
rect.thick, rect.lwd, rect.border	Default values for ggplot2::geom_rect() representation of ranges. rect.thick indicates the thickness of the rectangles.
indiv.scores	Show or hide individual scores for width and height in brakets besides the mixed score.

Details

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.

Value

(none)

Author(s)

Ricard Illa [e-mail]

See Also

peakDetection(), peakScoring(), ggplot2::ggplot(),

Examples

# 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)

nucleR documentation built on Nov. 8, 2020, 8:24 p.m.