plot_chosen_pca_experiment: Plot principal components

In MassDynamics/MassExpression: MassExpression

Plot principal components

Description

Plot principal components

Usage

plot_chosen_pca_experiment(
  Experiment,
  assayName = "intensities",
  dimPlot = c(1, 2),
  log = FALSE,
  auto_select_features = NULL,
  title_pca = "PCA plot",
  title_screeplot = "Scree plot",
  format = "html"
)

Arguments

Experiment	SummarizedExperiment object
assayName	name of assay to use
dimPlot	vector of size 2 specifying the dimensions to plot.
log	logical. Whether data should be logged before plotting
auto_select_features	str. One of 'de' (differentially expressed features see Details), 'hvf' (highly variable features). If not provided all features are kept.
title_pca	str. title on PCA plot
title_screeplot	str. title on screeplot
format	'pdf' or 'html'. Prepare image to be rendered for pdf or html Rmd output

Details

#' A protein is defined DE if the adjusted PValue of the t-test or ANOVA (with multiple groups) is less than 0.05.

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