DEPRECATED: Create a plot that combines a XIC and a mz/rt 2D plot for one sample

UPDATE: please use plot() from the MsExperiment or plot(x, type = "XIC") from the MSnbase package instead. See examples in the vignette for more information.

The plotMsData creates a plot that combines an (base peak ) extracted ion chromatogram on top (rt against intensity) and a plot of rt against m/z values at the bottom.

Usage

plotMsData(
  x,
  main = "",
  cex = 1,
  mfrow = c(2, 1),
  grid.color = "lightgrey",
  colramp = colorRampPalette(rev(brewer.pal(9, "YlGnBu")))
)

Arguments

x

data.frame such as returned by the extractMsData() function. Only a single data.frame is supported.

main

character(1) specifying the title.

cex

numeric(1) defining the size of points. Passed directly to the plot function.

mfrow

numeric(2) defining the plot layout. This will be passed directly to par(mfrow = mfrow). See par for more information. Setting mfrow = NULL avoids calling par(mfrow = mfrow) hence allowing to pre-define the plot layout.

grid.color

a color definition for the grid line (or NA to skip creating them).

colramp

a color ramp palette to be used to color the data points based on their intensity. See argument col.regions in lattice::level.colors documentation.

Author

Johannes Rainer