## AbstractMassObject
setMethod(f="plot",
signature=signature(x="AbstractMassObject", y="missing"),
definition=function(x, col="black",
xlab=expression(italic(m/z)), ylab="intensity",
type=ifelse(isMassPeaks(x), "h", "l"),
xlim=c(ifelse(length(x@mass),
min(x@mass, na.rm=TRUE), 0L),
ifelse(length(x@mass),
max(x@mass, na.rm=TRUE), 1L)),
ylim=c(0, ifelse(length(x@intensity),
max(x@intensity, na.rm=TRUE),
1L)),
main=x@metaData$name, sub=x@metaData$file,
cex.sub=0.75, col.sub="#808080", ...) {
if (all(sub == x@metaData$file) && length(x@metaData$file) > 1L) {
sub <- paste0(ifelse(isMassSpectrum(x),
"averaged spectrum", "merged peaks"),
" composed of ", length(x@metaData$file), " ",
ifelse(isMassSpectrum(x), "MassSpectrum", "MassPeaks"),
" objects")
}
plot(x=x@mass, y=x@intensity, col=col, type=type, xlab=xlab, ylab=ylab,
xlim=xlim, ylim=ylim, main=main, sub=sub, cex.sub=cex.sub,
col.sub=col.sub, ...)
})
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