plotEICs: Plot EICs from mz and RT List
In schymane/ReSOLUTION: SOLUTIONS for High ReSOLUTION Mass Spectrometry

Description Usage Arguments Value Author(s) See Also Examples

This plots EICs of given mz and from the mzML (or mzXML), with various options. Additional wrapper functions provide different ways of generating mz.

plotEICs(mzML_filePath, mz, rt, rt_in_sec=TRUE, names=NULL, smiles="", plot_title=NULL,
rt_window=NULL, mz_limit=0.001, ppm=10, isPos=TRUE, isLog=FALSE, isSwitching=FALSE,
greyscale=FALSE, colours = NULL, cpdID=NULL, ymin_log=3, switchShift=0,
kekulise=TRUE, addMSMS=TRUE, newRMB=TRUE, takePPM=TRUE)

`mzML_filePath`	Path to the mzML (or mzXML) file to extract the EICs.
`mz`	Vector of mz values to process.
`rt`	Vector of retention times to process. Set the unit with `rt_in_sec`.
`rt_in_sec`	Default `TRUE` indicates that `rt` is in seconds. If `FALSE`, `rt` is converted to seconds internally.
`names`	Optional names to belong to each `mz`. If `NULL`, `mz` is used.
`smiles`	SMILES code of the compound of interest.
`plot_title`	If `NULL`, title is autogenerated using `isPos`, `smiles` and `cpdID` if given.
`rt_window`	The retention time window (in seconds) for EIC extraction. This is added to `rt` to form the extraction window. Should not be zero! If `NULL`, the whole EIC is extracted.
`mz_limit`	Default 0.001. This controls the limits for EIC extraction. Choose between using `mz_limit` and `ppm` with `takePPM`.
`ppm`	Default 10 ppm is an alternative to `mz_limit` for EIC extraction.
`isPos`	`TRUE` indicates positive mode; `FALSE` negative mode. Only relevant for switching data.
`isLog`	If `TRUE`, EICs are plotted with a log scale; `FALSE` with absolute intensities. Zero intensities are lost with `TRUE`.
`isSwitching`	If `TRUE`, will split switching files assuming that the first scan is positive and that positive and negative alternate, unless `switchShift` is set. USE WITH CAUTION.
`greyscale`	If `TRUE`, greyscale plot will be produced. If `FALSE`, rainbow colours are assigned automatically.
`colours`	Used to define EIC colours. If `NULL`, rainbow or greyscale colours are used, depending on `greyscale`.
`cpdID`	If given, this is used in the output. Otherwise a value of 1 is assigned.
`ymin_log`	This defines the y axis intercept for log plots, for aesthetic reasons. Should be just under the `log(noise_intensity)` threshold. `3` is appropriate for Orbitraps.
`switchShift`	If `isSwitching` is `TRUE`, this can be used to shift the start scan between positive and negative mode. A `"quick fix"`, USE WITH CAUTION.
`kekulise`	Controls aromaticity detection in SMILES for plotting.
`addMSMS`	Indicates whether MSMS scans should be added to plot with default settings `TRUE`. `FALSE` does not attempt to add MSMS scans.
`newRMB`	Indicates whether new RMassBank version is used for MS/MS retrieval (`TRUE`). Set to `FALSE` for older versions (< 2.0.0) or if error is observed.
`takePPM`	Indicates whether ppm or mz_limit value should be used to extract EICs.

Returns a plot in the active device and a summary output.

Emma Schymanski <emma.schymanski@uni.lu>, Michael Stravs, Benedikt Lauper

findEIC.

library(RMassBank)
library(RMassBankData)
RmbDefaultSettings()
mzML_files <- list.files(system.file("spectra", package="RMassBankData"), ".mzML", full.names = TRUE)
mzML_file <- mzML_files[1]
cmpd_id <- "2818"
loadList(system.file("list/NarcoticsDataset.csv",package="RMassBankData"))
smiles <- findSmiles(cmpd_id)
mz <- as.numeric(findMz(cmpd_id, mode="pH")[3])
rt <- as.numeric(findRt(cmpd_id))
plotEICs(mzML_file, mz, rt, rt_in_sec=FALSE, smiles = smiles)
plotEICs(mzML_file, mz, rt, rt_in_sec=FALSE, smiles = smiles, addMSMS=TRUE)