Spectral Mismatch Plot

Produces a two-panel diagnostic figure comparing two fluorophore spectra. The upper panel overlays the normalised spectral traces for a reference and a test spectrum across all detectors. The lower panel shows the per-detector spectral difference (reference minus test) as a bar chart, making it easy to identify channels where the spectra diverge.

The combined figure is saved as a JPEG to plot.dir and returned invisibly as a ggplot / cowplot object so it can be embedded in downstream reports or further modified.

Usage

spectral.mismatch.plot(
  ref.spectrum,
  test.spectrum,
  ref.label = NULL,
  test.label = NULL,
  title = "Spectral comparison",
  bar.color = "lightblue",
  fluorophore.colors = c("black", "red"),
  plot.dir = NULL,
  line.width = 1,
  point.size = 1,
  color.palette = NULL,
  show.legend = TRUE,
  plot.width = NULL,
  plot.height = NULL
)

Arguments

ref.spectrum

A named numeric vector (or single-row matrix) of normalised spectral intensities for the reference spectrum. Names must correspond to detector channel names.

test.spectrum

A named numeric vector (or single-row matrix) of normalised spectral intensities for the test spectrum. Must have the same names as ref.spectrum.

ref.label

Character string used as the legend label for the reference spectrum. If NULL (default), the rownames() of ref.spectrum is used.

test.label

Character string used as the legend label for the test spectrum. If NULL (default), the rownames() of test.spectrum is used.

title

Character string used as both the plot title and the JPEG filename stem. Default is "Spectral comparison".

bar.color

Fill color for the spectral-difference bar chart. Default is "lightblue".

fluorophore.colors

Character vector of length 2 giving the line colors for the reference and test spectra respectively. Overrides color.palette when non-NULL. Default is c("black", "red").

plot.dir

Directory to save the JPEG file. If NULL (default), the current working directory is used. Created automatically if absent.

line.width

Numeric. Line width for the spectral traces. Default 1.

point.size

Numeric. Point size for the spectral traces. Default 1.

color.palette

Optional viridis palette name (e.g., "viridis", "plasma") used when fluorophore.colors is NULL. Ignored when fluorophore.colors is set. Default is NULL.

show.legend

Logical. Whether to display the color legend on the upper panel. Default is TRUE.

plot.width

Numeric. Width of the saved figure in inches. If NULL (default), an automatic width is derived from the number of detectors (approximately 12 inches per 64 channels, minimum 3 inches).

plot.height

Numeric. Height of the saved figure in inches. If NULL (default), an automatic height is derived from the number of spectra rows.

Value

The combined cowplot object is returned invisibly. The figure is always saved to disk as <plot.dir>/<title>.jpg.