Assess Spectral Mismatch Between Reference and Test Spectra

For each fluorophore common to both reference.variants and test.variants, computes the cosine similarity between the reference spectrum (row 1 of each fluorophore's variant matrix) and the corresponding test spectrum. Typically used to compare a spectral reference library built from one particle type (e.g. Cells) against one built from another (e.g. a bead type), by passing the reference particle type as reference.variants.

reference.variants and test.variants are expected to come from independent get.spectral.variants() calls and are not guaranteed to share the same detector set or column order, so the comparison is aligned explicitly by detector name rather than position. A warning is issued if the two detector sets differ.

Usage

assess.mismatch(reference.variants, test.variants)

Arguments

reference.variants

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.

test.variants

Named list of spectral variant matrices in the same format as reference.variants, to be compared against it.

Value

A one-column numeric matrix of cosine similarity values, one row per fluorophore common to both lists.