plotAdductEICs: Plot EICs from Adduct List
In schymane/ReSOLUTION: SOLUTIONS for High ReSOLUTION Mass Spectrometry

Description Usage Arguments Value Author(s) See Also Examples

This plots EICs of adducts in adduct_list from the mzML (or mzXML) and smiles given, with various options. Adduct masses are calculated from the smiles using getSuspectMasses via rcdk. Labelling will not be processed correctly. Adducts that cannot be calculated (especially in negative mode) are automatically skipped. Uses plotEICs behind the scenes.

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plotAdductEICs(mzML_filePath, smiles, adduct_list, rt=0, rt_in_sec=TRUE, plot_title=NULL,
rt_window=NULL, mz_limit=0.001, isPos=TRUE, isLog=FALSE, isSwitching=FALSE, greyscale=FALSE,
colours=NULL, cpdID=NULL, ymin_log=3, switchShift=0, kekulise=TRUE,addMSMS=FALSE,newRMB=TRUE)

`mzML_filePath`	Path to the mzML (or mzXML) file to extract the EICs.
`smiles`	SMILES code of the compound of interest.
`adduct_list`	Vector of adducts to process, matching entries in the `adducts` table in `enviPat`. Used to fill `mz` and `names` in `plotEICs`.
`rt`	The retention time (in seconds) to centre EIC extraction. If unknown, set `rt_window` to `NULL`.
`rt_in_sec`	Default `TRUE` indicates that `rt` is in seconds. If `FALSE`, `rt` is converted to seconds internally.
`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.
`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`. Acting strangely.
`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.

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

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

getSuspectMasses, findEIC, plotEICs.

pos_add <- c("M+H", "M+", "M+Na", "M+K", "M+NH4")
neg_add <- c("M-H", "M-", "M+FA-H", "M+Cl", "M-H2O-H")
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"
mzML_file <- mzML_files[5]
cmpd_id <- "2822"
loadList(system.file("list/NarcoticsDataset.csv",package="RMassBankData"))
smiles <- findSmiles(cmpd_id)
rt <- as.numeric(findRt(cmpd_id))
plotAdductEICs(mzML_file, pos_add, rt, rt_in_sec=FALSE, smiles = smiles)
plotAdductEICs(mzML_file, pos_add, rt, rt_in_sec=FALSE, smiles = smiles, addMSMS=TRUE)
# at this stage, log plots are not working properly...
plotAdductEICs(mzML_file, pos_add, rt, rt_in_sec=FALSE, smiles = smiles, isLog=TRUE)