Pick the best available abundance measure, and say what it means

WHY THIS IS A FUNCTION AND NOT A HARDCODED COLUMN: three quantities in the frequency table look interchangeable and are not.

Usage

abundance_measure(freq, prefer = c("auto", "absolute", "frequency"))

Arguments

freq

Population frequency table, one row per sample x population.

prefer

Preferred choice; auto picks the best available. Default c("auto", "absolute", "frequency").

Details

count EVENT count. Depends on how long the operator ran the tube and on –max-events-per-file. NEVER comparable between samples; never a valid y-axis for a group comparison. pct_of_cd45_pos Comparable, but COMPOSITIONAL: populations are constrained to sum to 100%, so one lineage expanding mathematically forces the others down. A significant fall in "% NK" is equally consistent with NK loss and with granulocyte gain. cells_per_ul Absolute. Independent per population, so a change in one says nothing about the others. Requires wbc_per_ul.

Prefer absolute when available and fall back to frequency otherwise, carrying the axis label and the compositional caveat with the choice so the figure cannot silently misrepresent which of the two it is showing.