plot_pca_experiment: Plot first 2 dimensions of PCA
In MassDynamics/MassExpression: MassExpression

plot_pca_experiment

R Documentation

Plot first 2 dimensions of PCA

Description

Plot first 2 dimensions of PCA

Usage

plot_pca_experiment(
  Experiment,
  assayName = "intensities",
  format = "pdf",
  log = FALSE,
  onlyDEProteins = FALSE,
  title = "PCA plot"
)

Arguments

`Experiment`	SummarizedExperiment object
`assayName`	name of assay to use
`format`	'pdf' or 'html'. Prepare image to be rendered for pdf or html Rmd output
`log`	logical. Whether data should be logged before plotting
`onlyDEProteins`	logical. TRUE if only DE proteins should be considered.

Format

"pdf" or "html". If html an interactive plot is returned using plotly.

Details

#' A protein is defined DE is the adjusted PValue is less than 0.05. When multiple comparisons are available, the adjusted PValues of the F-test is used.

MassDynamics/MassExpression documentation built on May 7, 2023, 11:29 a.m.