plotChromPeaks: General visualizations of peak detection results
In yclement/xcms: LC-MS and GC-MS Data Analysis

Description Usage Arguments Details Author(s) See Also Examples

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

This plot is supposed to provide some initial overview of the chromatographic peak detection results.

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.

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

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

`x`	`XCMSnExp` object.
`file`	For `plotChromPeaks`: `numeric(1)` specifying the index of the file within `x` for which the plot should be created. Defaults to `1`.
`xlim`	`numeric(2)` specifying the x-axis limits (retention time dimension). Defaults to `NULL` in which case the full retention time range of the file is used.
`ylim`	For `plotChromPeaks`: `numeric(2)` specifying the y-axis limits (mz dimension). Defaults to `NULL` in which case the full mz range of the file is used.
`add`	For `plotChromPeaks`: `logical(1)` whether the plot should be added or created as a new plot.
`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.
`...`	Additional arguments passed to the `plot` (for `plotChromPeaks`) and `image` (for `plotChromPeakImage`) functions. Ignored if `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.

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.

Johannes Rainer

highlightChromPeaks for the function to highlight detected chromatographic peaks in extracted ion chromatogram plots.

## Perform peak detection on two files from the faahKO package.
library(xcms)
library(faahKO)
faahko_file <- c(system.file('cdf/KO/ko16.CDF', package = "faahKO"),
                 system.file('cdf/KO/ko18.CDF', package = "faahKO"))

od <- readMSData(faahko_file, mode = "onDisk")

## Peak detection using the 'matchedFilter' method. Note that we are using a
## larger binSize to reduce the runtime of the example.
xod <- findChromPeaks(od, param = MatchedFilterParam(binSize = 0.3, snthresh = 20))

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

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

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