PlotXIC: PlotXIC/EIC

In xia-lab/OptiLCMS: Optimized LC-MS Spectra Processing

PlotXIC/EIC

Description

This functionn creates an extracted ion chromatogram (XIC/EIC) for a specific m/z and retention time. This is used for quality-control of raw m/s data.

Usage

PlotXIC(
  mSet = NULL,
  featureNum,
  sample_labeled,
  Group_labeled,
  format,
  dpi,
  width,
  height,
  sample_filled,
  group_filled
)

Arguments

mSet	mSet Object. Should contain the spectra processing result.
featureNum	Numeric, Feature number in the feature table.
sample_labeled	Logical, whether to lable the sample name.
Group_labeled	Logical, whether to lable the group name.
format	Character, to give the format of BPI figures ploted. Can be "jpeg", "png", "pdf", "svg", "tiff" or "ps". Default is "png".
dpi	Numeric, to define the dpi of the figures. Default is 72.
width	Numeric, to define the width of the figure.
height	Numeric, to define the height of the figure.
sample_filled	Logical, to determine the EIC/XIC is filled or not for sample EIC
group_filled	Logical, to determine the EIC/XIC is filled or not for group EIC

Value

will return a figure of EIC/XIC

Examples

data(mSet);
newPath <- dir(system.file("mzData", package = "mtbls2"),
               full.names = TRUE, recursive = TRUE)[c(10, 11, 12)]
mSet <- updateRawSpectraPath(mSet, newPath);
#PlotXIC(mSet, 1, TRUE, TRUE);

xia-lab/OptiLCMS documentation built on Nov. 26, 2024, 3:50 a.m.