Plot QC Filtering Summary by Feature Class

This function provides a summary of feature QC filtering based on class, showing the number of features that passed or failed various quality control criteria. It visualizes the hierarchical filtering process for different feature classes. Features are classified as failing a given criterion (e.g., CV) only after passing all the hierarchically lower filters (e.g., S/B ratio and LOD).

Usage

plot_qc_summary_byclass(
  data = NULL,
  include_qualifier = FALSE,
  include_istd = FALSE,
  user_defined_keeper = FALSE,
  font_base_size = 8
)

Arguments

data

MidarExperiment object

include_qualifier

Whether to include qualifier features in the plot. Default is FALSE. Qualifier features are those that may not be included in the final analysis but are still retained for reference.

include_istd

Whether to include internal standard features in the plot. Default is FALSE. Internal standards are used for calibration purposes in mass spectrometry experiments.

user_defined_keeper

Whether to retain user-specified features that were not selected by the QC filters. Default is FALSE. If TRUE, the user-defined features are kept even if they fail QC.

font_base_size

The base font size for the plot. Default is 8.

Value

A ggplot2 object showing the feature QC filtering summary by class.

See also

plot_qc_summary_overall for an overall summary plot