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.

1 2	plotAnnoSpectrum(mz, int, main, smiles="", labels=NULL,mz_a=NA,int_a=NA, formatFormula=TRUE, absInt=FALSE,ylim_factor=2.5,max_xlim=0,kekulise=TRUE,legend=c("spec1","spec2"))

`mz`	Vector containing mz values (x) to plot.
`int`	Vector containing intensity values (y) to plot.
`main`	Title for the plot.
`smiles`	SMILES code of the structure to plot. Leave empty for no structure.
`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`.
`mz_a`	Vector containing mz values for second spectrum.
`int_a`	Vector containing intensity values for second spectrum.
`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`.
`max_xlim`	Option to control the maximum value on the x axis. Passed to `xlim` in `plotSpectra` as `c(0,max_xlim)`
`kekulise`	Controls aromaticity detection of `smiles`. Default `TRUE` should work best with rcdk>3.4.1. Try `FALSE` if rings and double bonds appear together in aromatic rings.
`legend`	Vector containing legend entries for the two spectra.

Returns a plot in the current plotting device.

Emma Schymanski <emma.schymanski@uni.lu>

plotSpectra, renderSMILES.rcdk, chemistry2expression, trimAnnotation.

mz_1 <- c(58.0287, 111.0441, 168.0655, 210.1125)
int_1 <- c(23.0000, 999.0000, 843.5855, 999.0000)
labels_1 <- c("C2H4NO", "C6H7O2", "C8H10NO3", "C11H16NO3")
smiles_1 <- "O=C(Oc1ccccc1OC(C)C)NC"
plotAnnoSpectrum(mz_1, int_1, main="test spec",labels=labels_1, smiles=smiles_1, mz_a = mz_1,
int_a = int_1)