as.data.frame.feem: Transform a FEEM object into a data.frame

Description

Transform a FEEM object from its matrix form accompanied by vectors of wavelengths into a three-column form consisting of \( (\lambda_\mathrm{em}, \lambda_\mathrm{ex}, I) \) tuples, which could be useful for export or plotting with lattice or ggplot2.

Usage

# S3 method for feem
as.data.frame(x, row.names = NULL, optional = FALSE, ...)
  # S3 method for feemcube
as.data.frame(x, ...)

Value

A data.frame containing three numeric columns:

emission: Emission wavelength, nm.
excitation: Excitation wavelength, nm.
intensity: Fluorescence intensity at \( (\lambda_\mathrm{em}, \lambda_\mathrm{ex}) \)
sample: For FEEM cube objects, the unique name of the sample possessing this tuple of values, a factor. If the original object didn't have any names, sequential integers are used instead. If the original object had non-unique names, sequence numbers are appended to them using make.unique.

Arguments

x: A FEEM object, or a FEEM cube object.
row.names: Passed to data.frame. If default of NULL is used, data.frame will generate sequential integer row.names.
optional: This option is required for compatibility with as.data.frame generic, but is ignored, since column names are already syntactic and row names are generated by data.frame automatically by default.
...: Passed as-is to data.frame.

Details

Rows where intensity is NA are omitted from the output.

Examples

Run this code

  z <- feem(matrix(1:42, nrow = 7), 1:7, 1:6)
  head(as.data.frame(z))