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Plot missingness statistics

Source: R/plots.R
plot_missingness.Rd

Creates a visualization of missing data patterns with two panels:

Usage

plot_missingness(fits)

Arguments

fits

A peppwr_fits object

Value

A ggplot object or gtable (combined panels)

Details

  • Panel 1: Distribution of NA rates across peptides

  • Panel 2: Mean abundance vs NA rate scatter plot showing the dataset-level MNAR correlation. The subtitle displays the Spearman correlation coefficient and p-value. A negative correlation indicates that low-abundance peptides have more missing values - the hallmark of detection-limit-driven MNAR.

MNAR Detection

MNAR (Missing Not At Random) in mass spectrometry typically manifests as low-abundance peptides having higher rates of missing values due to detection limits. Panel 2 visualizes this relationship and reports the correlation coefficient.

See also

compute_dataset_mnar() for the underlying correlation calculation