plotChromPeaks: General visualizations of peak detection results

In sneumann/xcms: LC-MS and GC-MS Data Analysis

General visualizations of peak detection results

Description

'plotChromPeaks' plots the identified chromatographic peaks from one file into the plane spanned by the retention time (x-axis) and m/z (y-axis) dimension. Each chromatographic peak is plotted as a rectangle representing its width in RT and m/z dimension.

'plotChromPeakImage' plots the number of detected peaks for each sample along the retention time axis as an *image* plot, i.e. with the number of peaks detected in each bin along the retention time represented with the color of the respective cell.

Usage

plotChromPeaks(
  x,
  file = 1,
  xlim = NULL,
  ylim = NULL,
  add = FALSE,
  border = "#00000060",
  col = NA,
  xlab = "retention time",
  ylab = "mz",
  main = NULL,
  msLevel = 1L,
  ...
)

plotChromPeakImage(
  x,
  binSize = 30,
  xlim = NULL,
  log = FALSE,
  xlab = "retention time",
  yaxt = par("yaxt"),
  main = "Chromatographic peak counts",
  msLevel = 1L,
  ...
)

Arguments

x	A [XcmsExperiment()] or [XCMSnExp()] object.
file	For 'plotChromPeaks': 'integer(1)' specifying the index of the file within 'x' for which the plot should be created. Defaults to 'file = 1'.
xlim	'numeric(2)' specifying the x-axis limits (retention time dimension). Defaults to 'xlim = NULL' in which case the full retention time range of the file is used.
ylim	For 'plotChromPeaks': 'numeric(2)' specifying the y-axis limits (m/z dimension). Defaults to 'ylim = NULL' in which case the full m/z range of the file is used.
add	For 'plotChromPeaks': 'logical(1)' whether the plot should be added to an existing plot or if a new plot should be created.
border	For ‘plotChromPeaks': the color for the rectangles’ border.
col	For 'plotChromPeaks': the color to be used to fill the rectangles.
xlab	'character(1)' defining the x-axis label.
ylab	For 'plotChromPeaks': 'character(1)' defining the y-axis label.
main	'character(1)' defining the plot title. By default (i.e. 'main = NULL') the name of the file will be used as title.
msLevel	'integer(1)' defining the MS level from which the peaks should be visualized.
...	Additional arguments passed to the 'plot' (for 'plotChromPeaks') and 'image' (for 'plotChromPeakImage') functions. Ignored for 'add = TRUE'.
binSize	For 'plotChromPeakImage': 'numeric(1)' defining the size of the bins along the x-axis (retention time). Defaults to 'binSize = 30', peaks within each 30 seconds will thus counted and plotted.
log	For 'plotChromPeakImage': 'logical(1)' whether the peak counts should be log2 transformed before plotting.
yaxt	For 'plotChromPeakImage': 'character(1)' defining whether y-axis labels should be added. To disable the y-axis use 'yaxt = "n"'. For any other value of 'yaxt' the axis will be drawn. See [par()] help page for more details.

Details

The width and line type of the rectangles indicating the detected chromatographic peaks for the 'plotChromPeaks' function can be specified using the 'par' function, i.e. with 'par(lwd = 3)' and 'par(lty = 2)', respectively.

Author(s)

Johannes Rainer

Examples

## Load a test data set with detected peaks
faahko_sub <- loadXcmsData("faahko_sub2")

## plotChromPeakImage: plot an image for the identified peaks per file
plotChromPeakImage(faahko_sub)

## Show all detected chromatographic peaks from the first file
plotChromPeaks(faahko_sub)

## Plot all detected peaks from the second file and restrict the plot to a
## mz-rt slice
plotChromPeaks(faahko_sub, file = 2, xlim = c(3500, 3600), ylim = c(400, 600))

sneumann/xcms documentation built on Nov. 23, 2024, 6:53 p.m.