xcms: LC-MS and GC-MS Data Analysis

Description Usage Arguments Author(s) Examples

UPDATE: please use plot(x, type = "XIC") from the MSnbase package instead. See examples below.

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.

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

`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.

Johannes Rainer

## Read two files from the faahKO package
library(faahKO)
library(magrittr)
cdfs <- dir(system.file("cdf", package = "faahKO"), full.names = TRUE,
    recursive = TRUE)[1:2]
raw_data <- readMSData(cdfs, mode = "onDisk")

## Subset the object to a rt and mz range and plot the data.
raw_data %>%
    filterRt(rt = c(2700, 2900)) %>%
    filterMz(mz = c(334.9, 335.1)) %>%
    plot(type = "XIC")