Spectral Variant Density Plot

Creates a static visualization showing multiple spectral variants overlaid against a median spectral signature to illustrate consistency and variance. Each variant is plotted as a semi-transparent line, and the median spectrum is drawn on top as a solid reference trace.

Usage

spectral.variant.plot.dens(
  spectra.variants,
  median.spectrum,
  title = "Spectral_variants_density",
  save = FALSE,
  plot.width = NULL,
  plot.height = 5,
  plot.dir = "./figure_spectral_variants",
  variant.color = "red",
  variant.alpha = 0.05,
  variant.linewidth = 1.5,
  median.line.color = "black",
  median.linewidth = 1
)

Arguments

spectra.variants

Matrix of spectral variants; rows are variants, columns are detectors. Column names are used as x-axis labels.

median.spectrum

Numeric vector of the median signal intensity across detectors. Must have the same length as ncol(spectra.variants).

title

Plot title and output filename prefix. Default is "Spectral_variants_density".

save

Logical. If TRUE, saves the plot to plot.dir. Default is FALSE.

plot.width

Width of the saved plot in inches. Default is NULL, which auto-scales based on the number of detectors.

plot.height

Height of the saved plot in inches. Default is 5.

plot.dir

Output directory for the saved plot. Default is "./figure_spectral_variants".

variant.color

Line color for the individual variant traces. Default is "red".

variant.alpha

Alpha transparency for the variant lines. Default is 0.05.

variant.linewidth

Thickness of the variant lines. Default is 1.5.

median.line.color

Color of the median reference line. Default is "black".

median.linewidth

Thickness of the median reference line. Default is 1.

Value

The ggplot object representing the variant density plot. When save = TRUE, a JPEG is also written to plot.dir.