Analyses class and methods for handling Raman spectroscopy data

The RamanAnalyses class is used to store a list of Raman spectra.

Usage

RamanAnalyses(files = NULL)

# S3 method for class 'RamanAnalyses'
validate_object(x)

# S3 method for class 'RamanAnalyses'
get_analysis_names(x)

# S3 method for class 'RamanAnalyses'
get_replicate_names(x)

# S3 method for class 'RamanAnalyses'
set_replicate_names(x, value)

# S3 method for class 'RamanAnalyses'
get_blank_names(x)

# S3 method for class 'RamanAnalyses'
set_blank_names(x, value)

# S3 method for class 'RamanAnalyses'
get_concentrations(x)

# S3 method for class 'RamanAnalyses'
set_concentrations(x, value)

# S3 method for class 'RamanAnalyses'
info(x)

# S3 method for class 'RamanAnalyses'
add(x, value)

# S3 method for class 'RamanAnalyses'
remove(x, value)

# S3 method for class 'RamanAnalyses'
x[i]

# S3 method for class 'RamanAnalyses'
get_spectra(
  x,
  analyses = NULL,
  targets = NULL,
  rt = NULL,
  shift = NULL,
  minIntensity = NULL,
  useRawData = FALSE
)

# S3 method for class 'RamanAnalyses'
get_spectra_matrix(
  x,
  analyses = NULL,
  targets = NULL,
  rt = NULL,
  shift = NULL,
  minIntensity = NULL,
  useRawData = FALSE
)

# S3 method for class 'RamanAnalyses'
plot_spectra(
  x,
  analyses = NULL,
  targets = NULL,
  rt = NULL,
  shift = NULL,
  minIntensity = NULL,
  useRawData = FALSE,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "analyses",
  interactive = TRUE,
  renderEngine = "webgl"
)

# S3 method for class 'RamanAnalyses'
plot_spectra_3d(
  x,
  analyses = NULL,
  targets = NULL,
  rt = NULL,
  shift = NULL,
  minIntensity = NULL,
  useRawData = FALSE,
  legendNames = TRUE,
  colorBy = "analyses",
  xLab = NULL,
  yLab = NULL,
  zLab = NULL,
  renderEngine = "webgl"
)

# S3 method for class 'RamanAnalyses'
plot_spectra_baseline(
  x,
  analyses = NULL,
  targets = NULL,
  rt = NULL,
  shift = NULL,
  minIntensity = NULL,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "analyses",
  interactive = TRUE,
  renderEngine = "webgl"
)

# S3 method for class 'RamanAnalyses'
plot_chromatograms(
  x,
  analyses = NULL,
  targets = NULL,
  rt = NULL,
  shift = NULL,
  minIntensity = NULL,
  useRawData = FALSE,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "analyses",
  interactive = TRUE,
  renderEngine = "webgl"
)

# S3 method for class 'RamanAnalyses'
get_chromatograms_peaks(x, analyses = NULL, targets = NULL, rt = NULL)

# S3 method for class 'RamanAnalyses'
plot_chromatograms_peaks(
  x,
  analyses = NULL,
  targets = NULL,
  rt = NULL,
  title = NULL,
  legendNames = TRUE,
  colorBy = "targets",
  xlim = NULL,
  ylim = NULL,
  xLab = NULL,
  yLab = NULL,
  interactive = TRUE,
  renderEngine = "webgl"
)

Arguments

files: A character vector with full file paths to "asc", "sif", "json", "wdf", "sdf", "csv" and/or "txt" raman files or a data.frame with colnames file, replicate and blank. The "replicate" column is used to group the analyses and the "blank" column is used to identify the blank samples. The "file" column is the full to the raman files.
x: A RamanAnalyses object to validate.
value: An object that highly depends on the method. Check the specific method documentation for details.
i: A character or numeric vector to perform subsetting. Check the specific method for details.
analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.
targets: A character vector with the names of the targets (i.e., group or id) to filter the spectra by.
rt: Numeric of length two with the minimum and maximum retention time, in seconds.
shift: Numeric of length two with the minimum and maximum shift, in cm^-1.
minIntensity: Numeric (length 1) with the minimum intensity.
useRawData: Logical of length one. Set to TRUE for parsing raw data not data in results/processed.
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
title: A string with the title.
colorBy: A string defining how to legend the plot. Possible values are analyses, targets (the default) or replicates.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.
renderEngine: The engine to render the data. The default is "webgl".
legendNames: A character vector with the same length as the targets or TRUE or FALSE for using the name in the added targets as legend of the plot.
zLab: A string with the title for the z axis.
xlim: A length one or two numeric vector for setting the x limits of the plot.
ylim: A length one or two numeric vector for setting the y limits of the plot.

Value

A RamanAnalyses object which is fundamentally a list with each element representing a Raman analysis. Each analysis is a list with the following elements:

name: The name of the analysis.
replicate: The replicate identifier for the analysis.
blank: The blank sample identifier for the analysis.
concentration: The concentration of the sample in the analysis.
reference: The reference sample identifier for the analysis.
file: The file path to the Raman data file.
type: The type of analysis, which is "Raman".
metadata: A list containing metadata for the analysis.
spectra: A data.table containing the Raman spectra data, with columns for shift, intensity, and optionally other parameters like rt and id. The results element is a list that can hold results. Possible results is currently only RamanResults_Spectra.

Methods (by generic)

validate_object(RamanAnalyses): Validate the RamanAnalyses object, returning NULL if valid.
get_analysis_names(RamanAnalyses): Get the names of the analyses in the RamanAnalyses object.
get_replicate_names(RamanAnalyses): Get the replicates of the analyses in the RamanAnalyses object.
set_replicate_names(RamanAnalyses): Set the replicates of the analyses in the RamanAnalyses object. The argument value must be a character vector with the same length as the number of analyses in the object.
get_blank_names(RamanAnalyses): Get the blanks of the analyses in the RamanAnalyses object.
set_blank_names(RamanAnalyses): Set the blanks of the analyses in the RamanAnalyses object. The argument value must be a character vector with the same length as the number of analyses in the object.
get_concentrations(RamanAnalyses): Get the concentrations of the analyses in the RamanAnalyses object.
set_concentrations(RamanAnalyses): Set the concentrations of the analyses in the RamanAnalyses object. The argument value must be a numeric vector with the same length as the number of analyses in the object.
info(RamanAnalyses): Get a summary data.table of the RamanAnalyses object.
add(RamanAnalyses): Add Raman analyses to the RamanAnalyses object. The argument value can be a character vector with full file paths to "asc", "sif", "json", "wdf", "sdf", "csv" and/or "txt" raman files or a list of RamanAnalysis objects.
remove(RamanAnalyses): Remove Raman analyses from the RamanAnalyses object. The argument value can be a character vector with the names of the analyses or a numeric vector with the indices of the analyses to remove.
[: Subset the RamanAnalyses object by analyses. The argument i can be a character vector with the names of the analyses or a numeric vector with the indices of the analyses to keep.
get_spectra(RamanAnalyses): Get the spectra from the RamanAnalyses object.
get_spectra_matrix(RamanAnalyses): Get the spectra matrix from the RamanAnalyses object.
plot_spectra(RamanAnalyses): Plot the spectra from the RamanAnalyses object.
plot_spectra_3d(RamanAnalyses): Plot the spectra in 3D from the RamanAnalyses object.
plot_spectra_baseline(RamanAnalyses): Plot the baseline-corrected spectra from the RamanAnalyses object.
plot_chromatograms(RamanAnalyses): Plot the chromatograms from the RamanAnalyses object when the spectra have a time dimension.
get_chromatograms_peaks(RamanAnalyses): Get the chromatograms peaks from the RamanAnalyses object.
plot_chromatograms_peaks(RamanAnalyses): Plot the chromatograms peaks from the RamanAnalyses object.