LBE_fluo3D_process_all: Applies 3D Fluoresce processing and plotting to every...
In guilayn/lbe3df: 3D Fluorescence spectra processing

Description Usage Arguments Details Examples

IMPORTANT:

LBE_fluo3D_process_all(plot_all = TRUE, exci_spec = FALSE,
  emi_spec = FALSE, indic = TRUE, zones_calc = TRUE,
  zones_polygons = "Default", args_process = list(increase_resolution =
  FALSE, remove_difdif = TRUE), args_volume = list(zones_polygons_ =
  zones_polygons), args_plot = list(zones_polygons_ = zones_polygons,
  plot_zones_polygons = TRUE, export_html = TRUE, export_png = TRUE, export_pdf
  = TRUE), args_exci = list(), args_emi = list(), args_indic = list(),
  all_directory = getwd())

`plot_all`	Default = TRUE. Use FALSE to avoid plotting.
`exci_spec`	Default = FALSE. Use TRUE to include this function and specify emission as in excitation_spectrum()
`emi_spec`	Default = FALSE. Use TRUE to include this function and specify excitation as in emission_spectrum()
`indic`	Default = TRUE. Will include calculation of indicators to every spectrum.
`zones_calc`	Default = TRUE. Will include calculation of volumes and barycenters of each zone to every spectrum.
`args_process`	List containing the conditions for the function LBE_fluo3D_processing. See individual help files for details (?LBE_fluo3D_processing)
`args_volume`	List containing the conditions for the function LBE_fluo3D_zones_volume. See individual help files for details (?LBE_fluo3D_zones_volume)
`args_plot`	List containing the conditions for the function LBE_fluo3D_levelplot. See individual help files for details (?LBE_fluo3D_levelplot)
`args_exci`	List containing the conditions for the function excitation_spectrum. See individual help files for details (?excitation_spectrum)
`args_emi`	List containing the conditions for the function emission_spectrum. See individual help files for details (?emission_spectrum)
`args_indic`	List containing the conditions for the function LBE_fluo3D_indicators. See individual help files for details (?LBE_fluo3D_indicators)
`all_directory`	Directory containing subfolders with .sp 3D fluorescence files. Default is the directory used by the user. Might be useful to manually specify another.

1) EVERY SUBFOLDER MUST PRESENT THE SAME CONFIGURATION OF SPECTRA (ANALYSIS METHOD), FOR A SINGLE SPECTRA Reminder: The default internal method results in 40 .sp files called XXX#01, XXX#02, ..., XXX#40 where XXX is the label defined by the user.

2) THE CODE WILL DETECT AND STOP IF THERE IS ANY SUBFOLDER THAT DOESN'T SATISTIFY THE CONDITION ABOVE

# (!!!) First of all, verify the conditions hilighted in "IMPORTANT". (!!!)
> setwd("C:\\XXXX")  #where XXXX is your directory (don't forget to replace \ by / or \\)
> LBE_fluo3D_process_all(exci_spec = T, emi_spec = T,
                         args_process = list(remove_difdif=F),
                         args_plot = list(plot_zones_polygons=F,color_palette=2),
                         args_exci = list(select_emission=327,export_png=T,export_pdf=F),
                         args_emi = list(select_excitation=328,export_png=F,export_pdf=T),
                         args_indic = list())
# The code above will plot the gray spectrum (color_pallette=2, see ?LBE_fluo3D_levelplot for details), for all subfolders of XXXX.
# It will not remove diffusion and diffraction peaks and outside areas (remove_difdif=F, see ?LBE_fluo3D_processing for details)
# It will also plot excitation and emission 2D spectras for 327 and 328 emission and excitation wavelenghts, respectively.
# Observe that emission 2D spectra will be exported as png while excitation will be exported as pdf (just as example).
# By default, all the available indicators will be exported into each subfolder and a summary in the master folder.