R: Create a plot that combines a XIC and a mz/rt 2D plot for one...

plotMsData {xcms}

R Documentation

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

Description

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(s)

Johannes Rainer

Examples


## Read two files from the faahKO package
library(faahKO)
cdfs <- dir(system.file("cdf", package = "faahKO"), full.names = TRUE,
    recursive = TRUE)[1:2]
raw_data <- readMSData(cdfs, mode = "onDisk")
## Extract the MS data from a slice of data
msd <- extractMsData(raw_data, mz = c(334.9, 335.1), rt = c(2700, 2900))

## Plot the data for the first file
plotMsData(msd[[1]])

## To plot the data for both files:
layout(mat = matrix(1:4, ncol = 2))
plotMsData(msd[[1]], mfrow = NULL)
plotMsData(msd[[2]], mfrow = NULL)