plotMS: Plot MS1 Spectrum
In schymane/ReSOLUTION: SOLUTIONS for High ReSOLUTION Mass Spectrometry

Description Usage Arguments Value Author(s) See Also Examples

This is a wrapper function for plotSpectra for backwards compatability with previous workflows/scripts. plotSpectra offers much more functionality. xlim and ylim are fixed suited to MS1 spectra.

1 2	plotMS(mz, int, main, labels=NULL, formatFormula=TRUE, absInt=FALSE,ylim_factor=2, smiles="")

`mz`	Vector containing mz values (x) to plot.
`int`	Vector containing intensity values (y) to plot.
`main`	Title for the plot.
`labels`	Vector containing labels for selected peaks. If `NULL`, no labels are plotted.
`formatFormula`	If `TRUE`, uses `chemistry2expression` to create subscript numbers. Any `+` or `-` are removed to avoid errors. If `FALSE`, `labels` are printed as is. This is passed to `chem2express` in `plotSpectra`.
`absInt`	If `TRUE`, absolute intensity values are used. If `FALSE`, relative intensities are calculated on individual spectra, scaled to 1000.
`ylim_factor`	Scaling factor for y-axis. Default `2.5` leaves ample space for structure, annotations and legend. Reduce for peaks only. Passed to `yfactor` in `plotSpectra`.

Returns a plot in the current plotting device.

Emma Schymanski <emma.schymanski@uni.lu>

plotSpectra, renderSMILES.rcdk, chemistry2expression, trimAnnotation.

ms1_mz <- c(210.1125, 211.1154, 212.1187)
ms1_int <- c(420889280, 52790856, 2265951.5)
ms1_labels <- c("[M+H]+", "13C-M+1", "13C-M+2")
smiles_1 <- "O=C(Oc1ccccc1OC(C)C)NC"
plotMS(ms1_mz, ms1_int, main="test MS1 spec",labels=ms1_labels, formatFormula=FALSE,
absInt=TRUE)
plotMS(ms1_mz, ms1_int, main="test MS1 spec",labels=ms1_labels, formatFormula=FALSE,
absInt=FALSE, smiles=smiles_1)