JBA_plotBins: Visualization of JBA bins

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

Description

This function allows visualizing the bins generated by the JBA algorithm.

Usage

JBA_plotBins(NMR_JBA, NMR_data, ct = 0.85, ref_sample = 1, xlim = NULL, 
             ylim = NULL)

Arguments

NMR_JBA	list corresponding to the output of "JBA_binning()".
NMR_data	numeric matrix containing the NMR data (i.e. NMR peak intensities). The columns of the matrix must correspond to the metabolic variables (chemical shifts) and the rows to the samples. Column and row names must contain the metabolite IDs (i.e chemical shifts) and the sample IDs, respectively.
ct	numeric value indicating the correlation threshold. Bins with average correlation below ct will be neglected. This value can be established by comparing the distribution of average correlations in a spectral region dominated by electronic noise, and a spectral region dominated by metabolic signals. See function "JBA_corDistribution()".
ref_sample	numeric value indicating the index of the reference spectrum.
xlim	numeric vector containing the minimum and maximum values of the x axis.
ylim	numeric vector containing the minimum and maximum values of the y axis.

Value

A plot with two panels. The upper panel shows the reference spectrum with the bin edges (start: dark blue, end: light blue). The lowe panel shows the corresponding correlation-based spectrum.

Examples

## Not available.

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