Spectral Variant Plot — spectral.variant.plot • AutoSpectral

This function plots a spectral ribbon showing the optimized fluorophore signature with the range of variation from the spectral variants.

spectral.variant.plot(
  spectra.variants,
  median.spectrum,
  title = "Spectral_variants",
  save = FALSE,
  plot.width = NULL,
  plot.height = 5,
  plot.dir = "./figure_spectral_variants",
  variant.fill.color = "red",
  variant.fill.alpha = 0.7,
  median.line.color = "black",
  median.linewidth = 1
)

Arguments

spectra.variants: A matrix of variations in the normalized spectra signature for a fluorophore, rows being the variants, columns being the detectors.
median.spectrum: The optimized reference spectrum for the fluorophore, usually obtained from spectra prepared using AutoSpectral via get.fluorophore.spectra on cleaned control data.
title: Optional title to pass to the plot and output filename. Default is Spectral_variants.
save: Logical, controls whether the plot is displayed to the Viewer (FALSE) or also saved to disk (TRUE).
plot.width: Optional numeric to control saved plot width. Default is NULL, in which case the plot width will be calculated based on the number of detectors in the data.
plot.height: Optional numeric to control saved plot width. Default is 5.
plot.dir: Directory where the files will be saved if save = TRUE. Default is ./figure_spectral_variants.
variant.fill.color: Color for the shaded region indicating the range of variation in the spectra. Feeds to fill in geom_ribbon. Default is "red".
variant.fill.alpha: Transparency (alpha) for the color in variant.fill.color. How intense the color of the variant spectra will be. Default is 0.7
median.line.color: Color for the line representing the median or optimized single spectrum. Default is "black".
median.linewidth: Width of the line for the single optimized spectrum. Default is 1.

Value

Plots are displayed to the Viewer. Files are saved if saving enabled.