plotAvgMS1: A function to plot averaged MS1 spectrum from a 'xcmsRaw'...

In ohgane/ShotgunLipidomicsR: Utility Functions for Analysis/Visualization of ShotgunLipidomics Data.

Description

This function accepts xcmsRaw object with MS/MS data (direct infusion, data-dependent acquisition) and plot the spectrum and overlay colored lines over the precursors. Additionally, label some selected peaks.

Usage

plotAvgMS1(xcmsraw, normalization = "constant", int.divide = 1000,
  col = 1, type = "l", plot.precursor = TRUE, custom.precursor = NULL,
  col.precursor = "light blue", lwd.precursor = 2, lty.precursor = 1,
  baseline = FALSE, col.baseline = "gray50", lty.baseline = 1,
  scans = NULL, mzrange = NULL, ylim = NULL, ad.lab.mzrange = NA,
  ad.top = 3, top = 12, halfWindowSize = NULL, SNR = 50, digits = 4,
  ...)

Arguments

xcmsraw	xcmsRaw object.
normalization	Type of normalization for plotting. Default, "constant". Either "constant", "relative", or "TIC" (percent of total ion current).
int.divide	Intensity normalization factor (simple division). Default, 1000.
col	Default, 1 (=black).
type	Default, "l" (line).
plot.precursor	Logical (default, TRUE). If true, plot lines at the precursor m/z values.
custom.precursor	Default, NULL.
col.precursor	Default, "light blue".
lwd.precursor	Default, 2.
lty.precursor	Default, 1.
baseline	Logical (default TRUE)
col.baseline	The color of baseline. Default, "gray50"
lty.baseline	Line type of baseine. Default, 1.
scans	A numeric vector of scan indexes. If provided, only the indicated scans are averaged and plotted.
mzrange	m/z range to plot.
ylim	Y axis range to plot.
ad.top	The number of additional peak labels.
top	The number of peak labels.
halfWindowSize	See MALDIquant::labelPeaks() for detail.
SNR	See MALDIquant::labelPeaks() for detail.
digits	Digits for peak labels.
ad.lab.	mzrange m/z range to add additional peak labels.

Value

Plot spectrrum. Plus, if assigned to a variable (= invisibly), returns the averaged spectrum as a data frame.

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