plot.EEM.go: Subtract and plot fluorescence Excitation-Emission Matrix...

In RichardLaBrie/paRafac_correction: Corrects EEM all at once before using Matlab for PARAFAC

Subtract and plot fluorescence Excitation-Emission Matrix (EEM)

Description

A simple function to visualize EEMs obtained using a Varian Cary Eclipse fluorometer in csv format (could evolved to include other instrument). The user is prompted to select one or many files

Usage

## S3 method for class 'EEM.go'
plot(
  path,
  zlim = c(0, 10),
  SUBTRACT.BLANK = TRUE,
  PLOT.RAMAN = TRUE,
  PLOT.BLANK = TRUE,
  excitation = c(220, 450, 5),
  emission = c(230, 600, 2),
  EMCOL = FALSE,
  samplepercsv = 1,
  RU = T
)

Arguments

path	Full path of the working directory (can be called using getwd())
zlim	is the limits of the fluoresence scale (z axis) in raw units. Default is c(0, 10) for clear oceanic waters.
SUBTRACT.BLANK	is a logical parameter to indicate if a blank EMM is to be subtract from the sample EEM. Default is TRUE and the user is prompted to first select the blank file.
PLOT.RAMAN	is a logical parameter indicating whether or not the raman peak is ploted. Default is TRUE.
PLOT.BLANK	is a logical parameter indicating whether the blank EEMs is ploted or not. Default is TRUE.
excitation	is a vector of three variables of the scanning setup (min, max, interval). Default is c(220, 450, 5)
emission	is a vector of three variables of the scanning setup (min, max, interval). Default is c(230, 600, 2)
EMCOL	is a logical parameter indicating whether or not the emission are stored as column in the csv file. Default is FALSE.
samplepercsv	is a parameter which indicates the number of sample in the csv file coming from the fluorometer.
RU	is a logical parameter to transform fluorescence intensities into Raman Unit at Ex = 350 nm. Default is TRUE

Value

Returns the EEM from the sample

Author(s)

Simon Bélanger & Richard LaBrie

See Also

read.EEM

Examples

plot.EEM.go(getwd(), zlim = c(0, 20), SUBTRACT.BLANK = FALSE)

RichardLaBrie/paRafac_correction documentation built on March 13, 2023, 2:11 p.m.