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))