Generic method for plot

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Description

Generic method for plot

Method defining plot() for the MassSpectra class plot has no generic by default

Usage

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plot(x, y, ...)

## S4 method for signature 'MassSpectra,missing'
plot(x, y, ..., mzRange = c(0, 200),
  normalize = FALSE)

## S4 method for signature 'PCA,ANY'
plot(x, ..., comps = c(1, 2), pcType = "pcaLoadings",
  label = FALSE, labelThreshold = 1)

Arguments

x

object of type MassSpectra

y

missing

...

further args

mzRange

vector or lenght two, indicating the mz range to be plotted

normalize

boolean should the mass spectra be normalized

comps

numeric vector of length two denominating the components to be plotted

pcType

character 'pcaLoadings' or pcaScores'

label

boolean plot label

labelThreshold

numeric threshhold on which values to plot a label

Details

The output of this method is adapted for plotting mass spectra. Uncalibrated data is plotted as xy plot while uncalibrated data is plotted as barplot. The parameter mzRange allows choosing the plot range directly according to the mz number (when calibrated). The argument lineplot, TRUE by default, allows to switch between line and barplot.

Value

graphical output

plot of mass spectra

scatter loading/score plot

Examples

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## plot method for MassSpectra objects
library(tofsimsData)
data(tofsimsData)
plot(testSpectra, mzRange=c(1,300),type='l')

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