QC_CV_specNMR: Plot NMR spectrum colored based on CV

In MWASTools: MWASTools: an integrated pipeline to perform metabolome-wide association studies

Description

This function allows plotting a reference NMR spectrum colored based on the coefficient of variation (CV) of each NMR signal. See function "QC_CV()".

Usage

QC_CV_specNMR (metabo_SE, ref_sample,  CV_th = 0.30, xlab = "ppm",
               ylab = "intensity", size_axis = 12, size_lab = 12, xlim = NULL,
               ylim = NULL, xbreaks = waiver (), xnames = waiver (),
               ybreaks = waiver (), ynames = waiver ())

Arguments

metabo_SE	SummarizedExperiment object. See "MWAS_SummarizedExperiment()".
ref_sample	character vector indicating the ID of the sample that will be used to plot the NMR spectrum.
CV_th	numeric value indicating the CV threshold. NMR signals with CV equal or above CV_th will be colored in red.
xlab	character vector specifying a title for the x-axis.
ylab	character vector specifying a title for the y-axis.
size_axis	numeric vector indicating the font size of x- and y-axis labels.
size_lab	numeric vector indicating the font size of x- and y-axis tittles.
xlim	numeric vector containing the minimum and maximum values of the x-axis. Notice that ppm is displayed in reverse scaled (e.g. xlim = c(10, 0)).
ylim	numeric vector containing the minimum and maximum values of the y-axis.
xbreaks	numeric vector indicating the positions of the breaks of the x-axis.
xnames	character vector (same length as xbreaks) containing the labels of each break of the x-axis.
ybreaks	numeric vector indicating the positions of the breaks of the y-axis.
ynames	character vector (same length as ybreaks) containing the labels of each break of the y-axis.

Value

An NMR spectrum plot colored based on the CV of each NMR signal.

References

Dumas ME, et al. (2006). Assessment of analytical reproducibility of 1H NMR spectroscopy based metabonomics for large-scale epidemiological research: the INTERMAP Study. Analytical Chemistry, 78, 2199-1208.

Examples

## Load data
data(metabo_SE)

## Plot NMR spectrum colored by CV
QC_CV_specNMR (metabo_SE, ref_sample = "QC1", CV_th = 0.30)
QC_CV_specNMR (metabo_SE, ref_sample = "QC1", CV_th = 0.30, xlim = c(1.1, 0.95))
QC_CV_specNMR (metabo_SE, ref_sample = "QC1", CV_th = 0.15)

MWASTools documentation built on Nov. 8, 2020, 5:07 p.m.