ggChromPlot: Chromatogram plot

In jordirofes/OmniOmics: Analysis of metabolomics (LC-MS) and transcriptomics (Microarray) data

Chromatogram plot

Description

Creates a ggplot2 chromatogram or EIC from an XCMS object

Usage

ggChromPlot(
  object,
  filenum = NA,
  mz = NA,
  ppm = NA,
  rtint = NA,
  pheno_var = 1,
  chromtype = "max",
  logscale = TRUE,
  interactive = TRUE
)

Arguments

object	A OnDiskXCMSnExp or XCMSnExp object
filenum	An optional numeric vector indicating the files to plot
mz	A numeric indicating the mz value to plot (requires the ppm param) or a numeric two with the mz limits to plot
ppm	An optional numeric indicating the ppm error for the mz param
rtint	An optional length two numeric vector indicating the retention time interval to plot
pheno_var	A numeric or string indicating the variable from the phenodata to use as file groups.
chromtype	The type of chromatogram to create. "max" for the maximum value and "sum" for the sum of intensities.
logscale	A boolean to apply a log10 transformation of the intensities
interactive	A boolean indicating if the plot will be converted to a plotly

Value

A ggplot2 or plotly line plot of the chromatogram.

Author(s)

Jordi Rofes Herrera

jordirofes/OmniOmics documentation built on Nov. 22, 2022, 5:46 a.m.