plotPeaks {nucleR} | R Documentation

## Nucleosome calling plot function

### 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 'RangedData'
    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 ricard.illa@irbbarcelona.org

### 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)

[Package nucleR version 2.14.0 Index]