plotMsData {xcms} | R Documentation

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

### Description

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.

### 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)
    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")

[Package xcms version 3.16.1 Index]