QC_CV_specNMR {MWASTools} | R Documentation |
This function allows plotting a reference NMR spectrum colored based on the coefficient of variation (CV) of each NMR signal. See function "QC_CV()".
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 ())
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. |
An NMR spectrum plot colored based on the CV of each NMR signal.
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.
## 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)