plot: Generic method for plot

In tofsims: Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data

Description

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

Usage

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

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

tofsims documentation built on Nov. 8, 2020, 5:10 p.m.