Assess Within-Fluorophore Spectral Variability

Summarises how much a fluorophore's spectral variants (rows 2+ of its variant matrix, as produced by get.spectral.variants()) disagree with its reference spectrum (row 1) and with each other, returning several complementary summary metrics per fluorophore.

Usage

assess.variability(variant.list, peak.height = 0.1)

Arguments

variant.list

Named list of spectral variant matrices (one per fluorophore), as returned in the variants element of get.spectral.variants(). Row 1 of each matrix is treated as the reference spectrum; rows 2+ are treated as variants.

peak.height

Numeric in [0, 1], default 0.1. Detectors where the reference spectrum falls below this fraction of that fluorophore's own peak value (peak.height * max(reference.spectrum)) are excluded from the denoised variability metric (Denoised_rSD). Relative to the peak rather than an absolute cutoff, so behavior is unchanged whether variant.list is L-infinity or L2 normalized.

Value

A numeric matrix with one row per fluorophore and four columns:

rSD

Sum, across detectors, of the robust SD (MAD) of the variant spectra.

Scaled

rSD weighted by the reference spectrum, summed across detectors, to downweight low-signal channels.

Sim_rSD

Robust SD of the pairwise cosine similarities among all variants (including the reference).

Denoised_rSD

As rSD, but restricted to detectors where the reference spectrum exceeds peak.height.

Returns NULL (with a message) if no fluorophore has usable variability data.