Cosine Similarity Plot — cosine.similarity.plot • AutoSpectral

This function plots the matrix of cosine similarities (AKA "Similarity Matrix") as a heatmap and saves it as a JPEG file. It also calculates and displays the mixing matrix condition number (AKA "Complexity Index") of the matrix.

Usage

cosine.similarity.plot(
  spectra,
  filename = "autospectral_similarity_matrix",
  title = NULL,
  output.dir = "figure_similarity_heatmap",
  figure.width = 8,
  figure.height = 6,
  color.palette = "viridis",
  show.legend = TRUE,
  save = TRUE
)

Arguments

spectra: Data frame or matrix containing spectral data.
filename: Character string for the output file. Default is autospectral_similarity_matrix.
title: Optional prefix for the plot filename. Default is NULL
output.dir: File path where the plot will be created. Default is figure_similarity_heatmap. The directory will be created if it does not already exist.
figure.width: Numeric. Width of output plot. Default is 8.
figure.height: Numeric. Height of output plot. Default is 6.
color.palette: Optional character string defining the viridis color palette to be used for the fluorophore traces. Default is viridis. 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.
save: Logical, if TRUE, saves a JPEG file to the output.dir. Otherwise, the plot will simply be created in the Viewer.

Value

Saves the heatmap plot as a JPEG file in the similarity directory.