General visualizations of peak detection results

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

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))