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Bar plot showing mean filtering efficiency by treatment group

Source: R/plot.R
plot_filter_means.Rd

Visualizes filtering efficiency as bar plots showing mean feature and abundance retention across sources within each treatment group. Shows three categories:

  • Unlabeled (blue): Features that passed filters in unlabeled samples

  • Labeled (red): Features that passed filters in labeled samples

  • Retained (purple): Features in the intersection (passed BOTH labeled and unlabeled)

Usage

plot_filter_means(qsip_data_object, use_counts = FALSE)

Arguments

qsip_data_object

A filtered qsip_data object (or list)

use_counts

If TRUE, plot absolute feature counts; if FALSE (default), plot percentages

Value

A ggplot2 object

Details

Interpreting the bars:

  • Taller bars = Higher retention (more features/abundance retained)

  • Retained (purple) bars are always at or below both labeled and unlabeled bars because the intersection cannot exceed either individual set

  • Error bars show standard deviation across sources within the treatment group

  • Large gap between labeled/unlabeled and retained = Poor filtering consistency (many features unique to one isotope)

  • Small gap = Good filtering consistency (most features that passed one isotope also passed the other)

  • Asymmetric bars: If unlabeled bar is much taller than labeled (or vice versa), one isotope had less stringent filtering and passed more features

See plot_filter_efficiency for per-source detail and arrow-based visualization of filtering consistency.