ggTicQuality: Total ion count plot

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

Total ion count plot

Description

Creates a violin/boxplot TIC plot from an XCMS object

Usage

ggTicQuality(
  object,
  filenum = NA,
  pheno_var = 2,
  pheno_filter,
  logscale = TRUE,
  violin = FALSE,
  interactive = TRUE,
  order = FALSE
)

Arguments

object	A OnDiskXCMSnExp or XCMSnExp object
filenum	An optional numeric vector indicating the files to plot
pheno_var	A numeric or string indicating the variable from the phenodata to use as file groups.
pheno_filter	An optiona string of a variable name in pheno_var to filter from plotting
logscale	A boolean to apply a log10 transformation of the intensities
interactive	A boolean indicating if the plot will be converted to a plotly
order	A boolean indicating if the file order should be used for the order of the samples
violing	A boolean indicating if a violin plot should be plot instead of a boxplot

Value

A ggplot2 or plotly violin/boxplot TIC plot

Author(s)

Jordi Rofes Herrera

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