plotFeatureGroups: Plot feature groups in the m/z-retention time space

In sneumann/xcms: LC-MS and GC-MS Data Analysis

Plot feature groups in the m/z-retention time space

Description

plotFeatureGroups visualizes defined feature groups in the m/z by retention time space. Features are indicated by points with features from the same feature group being connected by a line. See featureGroups() for details on and options for feature grouping.

Usage

plotFeatureGroups(
  x,
  xlim = numeric(),
  ylim = numeric(),
  xlab = "retention time",
  ylab = "m/z",
  pch = 4,
  col = "#00000060",
  type = "o",
  main = "Feature groups",
  featureGroups = character(),
  ...
)

Arguments

x	XcmsExperiment or XCMSnExp() object with grouped features (i.e. after calling groupFeatures().
xlim	numeric(2) with the lower and upper limit for the x-axis.
ylim	numeric(2) with the lower and upper limit for the y-axis.
xlab	character(1) with the label for the x-axis.
ylab	character(1) with the label for the y-axis.
pch	the plotting character. Defaults to pch = 4 i.e. plotting features as crosses. See par() for more information.
col	color to be used to draw the features. At present only a single color is supported.
type	plotting type (see par()). Defaults to type = "o" which draws each feature as a point and connecting the features of the same feature group with a line.
main	character(1) with the title of the plot.
featureGroups	optional character of feature group IDs to draw only specified feature group(s). If not provided, all feature groups are drawn.
...	additional parameters to be passed to the lines function.

Author(s)

Johannes Rainer

sneumann/xcms documentation built on April 26, 2024, 3:05 a.m.