NMR_plot_spectra_pval_stocsy: Plot one or multiple NMR spectra, colored by user defined...
In adwolfer/someRutils: A compilation of R data analysis functions

Description Usage Arguments Value Examples

Plot one or multiple NMR spectra with ppm as x-axis and intensity as y-axis; the colour of each spectra can be defined using spectraColour (default grey for one spectra, rainbow for multiple ones). If a vector of pval (one per ppm) is passed as input, each datapoint will be colored depending on the p-value. If a driver ppm is passed as input, the correlation of all variables to this driver will be calculated (statistical total correlation spectroscopy - STOCSY) and used to colour the median spectra. Only one colouring method (spectraColour, pval or driver) can be used at any given time). Require ggplot2, reshape2, scales, grDevices, stats

1 2	NMR_plot_spectra_pval_stocsy(ppm, data, spectraColour = NULL, pval = NULL, driver = NULL, verbose = TRUE, debug = FALSE)

`ppm`	(float) vector of ppm values (x-axis)
`data`	(data.frame) spectra intensity values matching `ppm` (spectra as rows, ppm as columns)
`spectraColour`	(str) NULL or vector of colour for each sample (same length as the number of row of `data`)
`pval`	(float) NULL or vector of p-value for each ppm (same length as `ppm` and the number of columns of `data`)
`driver`	(float) NULL or ppm value of the driver feature for STOCSY (the closest ppm value will be used)
`verbose`	(bool) If TRUE message progress
`debug`	(bool) If TRUE returns the data to plot instead of the ggplot object

Grob (ggplot object)

{
# load data (2.95 - 3.5 ppm)
inPPM  <- someRutils::exampleNMR$ppm[711:821]
inData <- someRutils::exampleNMR$data[,711:821]

# default plot
NMR_plot_spectra_pval_stocsy(ppm=inPPM, data=inData)

# set each spectra colour (3 spectra)
inSpectraColour <- c('blue', 'red', 'green')
NMR_plot_spectra_pval_stocsy(ppm=inPPM[1:3], data=inData[1:3], spectraColour=inSpectraColour)

# colour by p-value
inPval  <- rep(c(0.0000001, 0.001, 0.01, 0.05, 0.1, 0.25, 0.5, 1), 14)[1:111]
NMR_plot_spectra_pval_stocsy(ppm=inPPM, data=inData, pval=inPval)

# STOCSY (driver peak is 3.2765ppm)
NMR_plot_spectra_pval_stocsy(ppm=inPPM, data=inData, driver=3.2765)
}