plot_sample_pca__sample_in_contrast: helper function for use-case beyond making a report using...

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

helper function for use-case beyond making a report using standard analysis_quickstart() workflow; PCA on the subset of samples-of-interest from some contrast

Description

helper function for use-case beyond making a report using standard analysis_quickstart() workflow; PCA on the subset of samples-of-interest from some contrast

Usage

plot_sample_pca__sample_in_contrast(
  dataset,
  contr,
  sample_label_property = "auto"
)

Arguments

dataset	your dataset after application of dea. eg; results from analysis_quickstart()
contr	the exact name of the contrast. Example; "contrast: ctrl1,ctrl2 vs phenotype1,phenotype2,phenotype3" This should be one of the columns in dataset$samples table (which are generated by the setup_contrasts() function)
sample_label_property	see plot_sample_pca() function for params

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