Plot absorbance spectrum — plot_absorbance

Processes parsed absorbance spectrum data, collected as a dilution series measured with an A200-1000 absorbance spectrum. Corrects raw data to path length of 1cm by a user-defined method, and normalises to the blanks. Plots spectra and returns processed data.

plot_absorbance_spectrum(
  spectrum_csv,
  subset_rows = FALSE,
  rows_to_keep = c("C", "D"),
  columns_to_keep = c(1, 12),
  xrange = c(200, 1000),
  pl_method = "calc_blanks",
  buffer_used = "water",
  concentration_used = 0,
  temperature_used = 25,
  outfolder = "."
)

Arguments

spectrum_csv	path of a .csv file of your spectrum data
subset_rows	logical. should script take a subset of the rows (or whole table)? Defaults to FALSE.
rows_to_keep	character array. If `subset_rows` is TRUE, script will choose rows to keep from this list. Defaults to `c("C","D")`.
columns_to_keep	numeric array. If `subset_rows` is TRUE, script will choose rows to keep from this list. Defaults to `c(1,12)`. Note that blanks are required for normalisation, so if blanks are in column12, it is necessary to include 12 in this list.
xrange	numerical lower and upper bounds of wavelengths, between which the is subset for plotting. This can be useful for clear plates, which have high background <300nm, so can set the xrange as c(300,800) or similar.
pl_method	string denoting which method of path length normalisation to use. Options are `calc_each`, `calc_blanks` and `volume`. All three are always calculated (and compared in one of the output plots), but only the chosen method is used. The `calc_each` method uses the path length calculated from each well separately using the A900 and A975 measurements and the k-factor of the buffer used. The `calc_blanks` method uses the path length calculated from the blanks for all wells. Finally, the `volume` method uses the path length expected from the given volume, using internal path length data measured with water via the internal `fpcountR::get_pathlength()` function. Defaults to `calc_blanks`.
buffer_used	string corresponding to buffer used for assay, for use in path length determination. Must be in table used by `fpcountR::get_kfactor()`. To look at table, use `fpcountR::view_kfactors()`. Defaults to "water".
concentration_used	numeric value corresponding to concentration of buffer, for use in path length determination. Must be in the same units as used by table in `fpcountR::get_kfactor()`. To look at table, use `fpcountR::view_kfactors()`. Defaults to 0, which effectively means water. Needs changing if using different buffer!
temperature_used	numeric value corresponding to temperature of assay, for use in path length determination. Defaults to 25.
outfolder	path to folder where output files should be saved. Defaults to current working directory.

Examples

spectrum <- plot_absorbance_spectrum(spectrum_csv = "spectrum_parsed.csv", subset_rows = TRUE, rows_to_keep = c("C","D"), columns_to_keep = c(1:12), pl_method = "calc_blanks", buffer_used = "TBS", concentration_used = 0.005, temperature_used = 30, xrange = c(250,1000), outfolder = "spectrum")