Plot Fluorophore Spectra Traces — spectral.trace • AutoSpectral

This function plots the fluorophore spectra as normalized traces, optionally splitting by excitation lasers, and saves the plots as JPEG files.

Usage

spectral.trace(
  spectral.matrix,
  asp,
  title = "Fluorophore_Spectra",
  plot.dir = NULL,
  split.lasers = TRUE,
  figure.spectra.line.size = 1,
  figure.spectra.point.size = 1,
  color.palette = NULL,
  show.legend = TRUE,
  plot.width = NULL,
  plot.height = NULL,
  save = TRUE
)

Arguments

spectral.matrix: Matrix or dataframe containing spectral data. This should be in format fluorophores x detectors. Row names will be used as the fluorophore names. Column names will be used as the detectors (channels).
asp: The AutoSpectral parameter list defined using get.autospectral.param.
title: Title for the plot. Default is Fluorophore_Spectra
plot.dir: Directory to save the plot files. Default is NULL, in which case the current working directory will be used.
split.lasers: Logical indicating whether to create a second plot split by excitation lasers. Default is TRUE.
figure.spectra.line.size: Numeric. Defines the width of the trace lines on the plot. Default is 1.
figure.spectra.point.size: Numeric. Defines the size of the points on the plot (one per detector). Default is 1.
color.palette: Optional character string defining the viridis color palette to be used for the fluorophore traces. Default is NULL, in which case default R Brewer colors will be assigned automatically. Options are the viridis color options: magma, inferno, plasma, viridis, cividis, rocket, mako and turbo.
show.legend: Logical. If TRUE, figure legend will be included.
plot.width: Optional numeric to manually set the plot width. Default is NULL.
plot.height: Optional numeric to manually set the plot width. Default is NULL.
save: Logical, if TRUE, saves a JPEG file to the plot.dir. Otherwise, the plot will simply be created in the Viewer.

Value

Saves the plot(s) as JPEG files in the specified directory.