featurebatchQc: Feature sum intensity plot

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

Feature sum intensity plot

Description

Creates a scatter plot with the sum of intensities of all features for each sample ordered by injection order to visualize batch effect

Usage

featurebatchQc(
  features,
  groupvar,
  injectionvar,
  logscale = FALSE,
  interactive = TRUE
)

Arguments

features	A SummarizedExperiment with features
groupvar	A numeric indicating the column to use as grouping factor or a character indicating it's name
injectionvar	An optional string or numeric indicating the variable in the phenodata used to indicate the injection order, no value will default to the file order
logscale	log10 intensity transformation
interactive	A boolean indicating if the plot will be converted to an interactive 'ggplotly()'

Value

Returns a ggplot object or a ggplotly

Author(s)

Jordi Rofes Herrera

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