Plot chromatograms

Chromatograms() can be plotted with the following functions:

The plotChromatograms(): plots each chromatogram in its separate plot by splitting the plot area into as many panels as there are spectra.

Usage

# S4 method for class 'Chromatograms'
plotChromatograms(
  object,
  xlab = "rtime (s)",
  ylab = "intensity",
  type = "o",
  pch = 20,
  cex = 0.6,
  lwd = 1.5,
  xlim = numeric(),
  ylim = numeric(),
  main = character(),
  col = "#00000080",
  asp = 1,
  ...
)

# S4 method for class 'Chromatograms'
plotChromatogramsOverlay(
  object,
  xlab = "rtime (s)",
  ylab = "intensity",
  type = "o",
  pch = 20,
  cex = 0.6,
  lwd = 1.5,
  xlim = numeric(),
  ylim = numeric(),
  main = paste(length(object), "chromatograms"),
  col = "#00000080",
  axes = TRUE,
  frame.plot = axes,
  ...
)

Arguments

object

A Chromatograms object.

xlab

character(1) with the label for the x-axis (by default xlab = "rtime (s)").

ylab

character(1) with the label for the y-axis (by default ylab = "intensity").

type

character(1) specifying the type of plot. See plot.default() for details. Defaults to type = "l" which draws each peak as a line.

pch

integer(1) or character(1) specifying the plotting symbol (see plot.default()).

cex

numeric(1) specifying the size of the plotting symbol (see plot.default()).

lwd

numeric(1) specifying the line width (see plot.default()).

xlim

numeric(2) defining the x-axis limits. The range of m/z values are used by default.

ylim

numeric(2) defining the y-axis limits. The range of intensity values are used by default.

main

character(1) with the title for the plot. By default the spectrum's MS level and retention time (in seconds) is used.

col

color to be used to draw the peaks. Should be either of length 1, or equal to the number of chromatograms (to plot each chromatograms in a different color) or be a list with colors for each individual peak in each spectrum.

asp

numeric(1) the aspect ratio of the plot, i.e. the ratio of the y-axis to the x-axis. Defaults to 1.

...

Additional arguments to be passed to plot.default().

axes

logical(1) whether (x and y) axes should be drawn.

frame.plot

logical(1) whether a box should be drawn around the plotting area.

Value

These functions create a plot.

Refer to the individual function description for information on the return value.

Author

Philippine Louail, Johannes Rainer.

Examples

## Create a Chromatograms object
cdata <- data.frame(
    msLevel = c(1L, 1L, 1L),
    mz = c(112.2, 123.3, 134.4),
    chromIndex = c(1L, 2L, 3L)
)
pdata <- list(
    data.frame(
        rtime = c(12.4, 12.8, 13.2, 14.6),
        intensity = c(123.3, 153.6, 2354.3, 243.4)
    ),
    data.frame(
        rtime = c(45.1, 46.2),
        intensity = c(100, 80.1)
    ),
    data.frame(
        rtime = c(12.4, 12.8, 13.2, 14.6),
        intensity = c(123.3, 153.6, 2354.3, 243.4)
    )
)
chr <- backendInitialize(ChromBackendMemory(),
    chromData = cdata,
    peaksData = pdata
) |> Chromatograms()

## Plot one chromatogram
plotChromatograms(chr[1])

## Plot the full Chromatograms object
plotChromatograms(chr)


## Define a color for each peak in each chromatogram
plotChromatograms(chr[1:2], col = c("green", "blue"))


## Overlay all chromatograms
plotChromatogramsOverlay(chr[1:2], col = c("green", "blue"))