plotChromatograms: Plot chromatograms

In rformassspectrometry/Chromatograms: Infrastructure for Chromatographic Mass Spectrometry Data

Plot chromatograms

Description

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

plotChromatograms(
  x,
  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,
  ...
)

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

Arguments

x	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.

Author(s)

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"))

rformassspectrometry/Chromatograms documentation built on April 12, 2025, 6:53 p.m.