plotSliceMS2: Plot "precursor ion scan"- or "neutral loss scan"-like...

Description Usage Arguments Value

Description

Note that multiple scans with the same precursor m/z values are averaged (after peak integration).

Usage

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plotSliceMS2(xraw, mz, ppm = 50, mzrange = NULL, ylim = NULL,
  slicemode = "FRAG", scanType = "profile", plotSpec = TRUE,
  type = c("h", "p"), col = c("blue", "red"), pch = 1, cex = 0.5,
  labelPeaks = TRUE, top = 5, SNR = 5, halfWindowSize = NULL,
  digits = 4, ...)

Arguments

xraw

xcmsRaw object.

mz

xcmsRaw object.

ppm

Numeric (default 10 ppm). Integration range. If mzabs is provided, this parameter will not be ignored.

slicemode

Character (default "FRAG").Select one from "FRAG" or "NL", to plot precursor ion spectrum with fragment or neutral loss intensity respectively.

scanType

Character (default "profile"). Either "profile" or "centroid".

plotSpec

Logical (default TRUE). Whether plot pseudo-precursor ion spectrum. If set to FALSE, only returns pseudo precursor ion spectrum as a matrix.

type

A character vector containing type argments that are used in standard plot(). For example, c("h", "p") results in points over vertical lines.

col

Colors used to plot multiple spectra. A character vector (default c("blue", "red"))

pch

Same as plot(). Type of points.

cex

Same as plot(). Size of points.

labelPeaks

Logical (default TRUE), that determines whether to plot peak labels.

top

The number of peak labels (default 5). By default, top 5 peaks in each spectrum will be labelled.

SNR

S/N ratio for peak picking (default 5).

halfWindowSize

A parameter for peak picking (default NULL). By default, automatically determined based on data. Larger value prevents peak labeling of nearer peaks.

digits

Digits of peak label (default 4).

Value

Plot spectrrum. Plus, if assigned to a variable, returns a data.frame with precursor m/z, and intensities (AUC for profile, sum for cetroid).


ohgane/ShotgunLipidomicsR documentation built on May 24, 2019, 11:55 a.m.