Package 'xcms' - Bioconductor

42 plotRaw-methods
Arguments
object
peaks
figs
width
the xcmsRaw object
matrix with peak information as produced by findPeaks
two-element vector describing the number of rows and the number of columns
of peaks to plot, if missing then an approximately square grid that will fit the
number of peaks supplied
width of chromatogram retention time to plot for each peak
Details
This function is intended to help graphically analyze the results of peak picking. It can help estimate
the number of false positives and improper integration start and end points. Its output is very
compact and tries to waste as little space as possible. Each plot is labeled with rounded m/z and
retention time separated by a space.
Methods
See Also
object = "xcmsRaw" plotPeaks(object, peaks, figs, width = 200)
xcmsRaw-class, findPeaks, split.screen
plotRaw-methods
Scatterplot of raw data points
Description
Produce a scatterplot showing raw data point location in retention time and m/z. This plot is more
useful for centroided data than continuum data.
Arguments
object
mzrange
rtrange
scanrange
log
title
the xcmsRaw object
numeric vector of length >= 2 whose range will be used to select the masses to
plot
numeric vector of length >= 2 whose range will be used to select the retention
times to plot
numeric vector of length >= 2 whose range will be used to select scans to plot
logical, log transform intensity
main title of the plot
Value
A matrix with the points plotted.