plot_sample_pca: placeholder title for reference, standard pca (does not cope...

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

placeholder title for reference, standard pca (does not cope with missing values); summary(stats::prcomp(t(matrix_sample_intensities), center = T, scale. = F))

Description

placeholder title for reference, standard pca (does not cope with missing values); summary(stats::prcomp(t(matrix_sample_intensities), center = T, scale. = F))

Usage

plot_sample_pca(
  matrix_sample_intensities,
  samples,
  samples_colors,
  sample_label_property = "auto",
  pch_as_exclude = TRUE,
  infer_continuous_scale = TRUE,
  pca_dims = list(1:2, c(1, 3), 2:3)
)

Arguments

matrix_sample_intensities	peptide or protein abundance matrix
samples	sample metadata table
samples_colors	sample colors in wide format tibble
sample_label_property	labels used to represent the samples. Set to "auto" to automatically select based on number of samples (default). possible values; auto, shortname, index, index_asis
pch_as_exclude	should exclude samples be represented with a distinct symbol shape? possible values; FALSE, TRUE (default)
infer_continuous_scale	should the legends infer continuous scale from the data? FALSE = all categorical, TRUE = automatic (default)
pca_dims	a list of integer pairs indicating PCA plots to make

ftwkoopmans/msdap documentation built on March 5, 2025, 12:15 a.m.