QC_CV_specNMR {MWASTools} | R Documentation

## Plot NMR spectrum colored based on CV

### 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)

[Package MWASTools version 1.16.0 Index]