Visualize Scaled Spectra and Median Profiles for Clustered IFU Data

This function creates a faceted plot that displays the individual pixel spectra (after scaling) and the corresponding median spectrum for each segmented cluster obtained from an IFU data cube. Each facet corresponds to a unique cluster, allowing for easy comparison of spectral profiles across different spatial regions.

Usage

plot_cluster_spectra(
  cluster_result,
  scale_fn = median_scale,
  palette = "magma"
)

Arguments

cluster_result

A list produced by a segmentation function (e.g. segment) containing at least the following elements:

cluster_map: A matrix mapping each spatial pixel to a cluster.
original_cube: The original data cube (typically a FITS object).
axDat: Axis metadata (including wavelength information).

scale_fn

A function that scales each individual spectrum (a numeric vector). The default is median_scale which should be defined elsewhere in your package.

palette

Either a single viridis palette name or a vector of colors used to color the per-cluster median spectra.

Value

A ggplot2 object representing a faceted plot of the median profile for each cluster.

Details

The function performs the following steps:

Extracts the spatial cluster map, original data cube, and wavelength information from cluster_result.
Converts the cube to a 2D matrix (assuming cube_to_matrix is available).
Creates a data frame mapping each valid spatial pixel to its cluster.
Extracts each pixel's spectrum and applies the scaling function scale_fn to it.
Computes the median spectrum for each cluster at every wavelength.
Constructs a faceted ggplot of the median spectrum for each cluster.

Examples

if (FALSE) { # \dontrun{
  # Assuming 'input_cube' is a FITS cube and 'segment' clusters the data:
  cluster_result <- segment(input_cube, Ncomp = 5)

  # Generate the spectra plot
  spectra_plot <- plot_cluster_spectra(cluster_result, scale_fn = median_scale, palette = "magma")
  print(spectra_plot)
} # }