plotChr: Plotting sample chromatogram

In erah: Automated Spectral Deconvolution, Alignment, and Metabolite Identification in GC/MS-Based Untargeted Metabolomics

Description

Plot the sample chromatogram.

Usage

plotChr(Experiment, N.sample=1, type=c("BIC","TIC","EIC"), 
xlim=NULL, mz=NULL)

Arguments

Experiment	A 'MetaboSet' S4 object containing the experiment.
N.sample	Integer. The number of the sample to query.
type	The type of plotting, Base Ion Chromatogram (BIC), Total Ion Chromatogram (TIC), or Extracted Ion Chromatogram (EIC).
xlim	The range in minutes, separated by comas: c(rt.min, rt.max) of the limits of plotting. By default, all the chromatogram is plotted.
mz	Just when EIC is selected. The range separated by comas: c(mz.min, mz.max) or a vector of numbers: c(50,67,80), of the masses to be ploted.

See Also

sampleInfo

Examples

## Not run: 
# First, an experiment has to be already created by newExp()
# then, each sample chromatogram can be plotted by:

plotChr(Experiment, 1, "BIC")
plotChr(Experiment, 1, "TIC", xlim=c(5,7))  #Plots from minute 5 to 7.

plotChr(Experiment, 1, "EIC", mz=50:70, xlim=c(5,7))  #Plots 
# from minute 5 to 7, and only the masses from 50 to 70.

plotChr(Experiment, 1, "EIC", xlim=c(7,7.5), mz=c(50,54,70))  #Plots
# the EIC from minute 7 to 7.5, and only the masses 50, 54 and 70.


## End(Not run)

erah documentation built on May 11, 2021, 9:11 a.m.