plotMsData: DEPRECATED: Create a plot that combines a XIC and a mz/rt 2D...

In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

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")

xiaodfeng/DynamicXCMS documentation built on Aug. 6, 2023, 3:02 p.m.