Engine dedicated to Raman spectroscopic data processing

The RamanEngine R6 class is a framework for parsing, processing, inspecting and storing Raman spectroscopic data. The engine has Raman as data type. The Analyses active field has class RamanAnalyses, where Raman data can be loaded from "asc", "sif", "json", "wdf", "sdf", "csv" and "txt" files. The results active field is a list that can hold the class RamanResults_Spectra. Note that the RamanEngine is a subclass of Engine and inherits all methods from the parent class.

References

Sheehy G, Picot F, Dallaire F, Ember K, Nguyen T, Petrecca K, Trudel D, Leblond F (2023). “Open-sourced Raman spectroscopy data processing package implementing a baseline removal algorithm validated from multiple datasets acquired in human tissue and biofluids.” Journal of Biomedical Optics, 28(2), 025002. doi:10.1117/1.JBO.28.2.025002 .

Super class

StreamFind::Engine -> RamanEngine

Active bindings

RamanResults_Spectra: RamanResults_Spectra results object for each analysis or replicate.

Methods

Inherited methods

Method `new()`

Creates an R6 class RamanEngine. Child of Engine R6 class.

Usage

RamanEngine$new(metadata = NULL, workflow = NULL, analyses = NULL)

Arguments

metadata: A named list or a Metadata object. Each list element must have length one. There is no type restrictions except for name (must be type character), author (must be type character) and date (must be class POSIXct or POSIXt). A file entry must be a character string with a full path to a file.
workflow: A Workflow object, a list of ProcessingStep objects or a character string with a full path to a rds or json file containing a Workflow.
analyses: A RamanAnalyses class object or 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.

Method `get_analysis_names()`

Gets the analysis replicate names.

Usage

RamanEngine$get_analysis_names(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_replicate_names()`

Gets the analysis replicate names.

Usage

RamanEngine$get_replicate_names(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_blank_names()`

Gets the analysis blank replicate names.

Usage

RamanEngine$get_blank_names(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_files()`

Gets the full file paths of each analysis.

Usage

RamanEngine$get_files(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `get_overview()`

Gets an overview data.frame of all the analyses.

Usage

RamanEngine$get_overview()

Method `get_spectra()`

Gets a list of spectra data.table objects for each analysis/replicate.

Usage

RamanEngine$get_spectra(
  analyses = NULL,
  targets = NULL,
  rt = NULL,
  shift = NULL,
  minIntensity = NULL,
  useRawData = FALSE
)

Arguments

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.

Method `get_spectra_matrix()`

Gets a matrix with spectra.

Usage

RamanEngine$get_spectra_matrix(
  analyses = NULL,
  targets = NULL,
  rt = NULL,
  shift = NULL,
  minIntensity = NULL,
  useRawData = FALSE
)

Arguments

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.

Method `get_chromatograms_peaks()`

Gets a data.table with chromatographic peaks.

Usage

RamanEngine$get_chromatograms_peaks(analyses = NULL, targets = NULL, rt = NULL)

Arguments

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.

Method `add_analyses()`

Adds analyses to the engine from Raman files. Note that when adding new files, any existing results are removed.

Usage

RamanEngine$add_analyses(analyses = NULL)

Arguments

analyses: A character vector with full file paths to "asc", "sif", "json", "wdf", "sdf", "csv" and/or "txt" raman files.

Method `remove_analyses()`

Removes analyses.

Usage

RamanEngine$remove_analyses(analyses = NULL)

Arguments

analyses: Character or numeric vector with names or indexes of analyses in the Analyses object.

Method `add_replicate_names()`

Adds replicate names to the analysis.

Usage

RamanEngine$add_replicate_names(value)

Arguments

value: Character vector with the replicate names. Must have the same length as the number of analyses.

Method `add_blank_names()`

Adds blank names to the analysis.

Usage

RamanEngine$add_blank_names(value)

Arguments

value: Character vector with the replicate names. Must have the same length as the number of analyses and must be one of replicate names.

Method `has_spectra()`

Checks if there are spectra, returning TRUE or FALSE.

Usage

RamanEngine$has_spectra()

Method `plot_spectra()`

Plots spectra.

Usage

RamanEngine$plot_spectra(
  analyses = NULL,
  targets = NULL,
  rt = NULL,
  shift = NULL,
  minIntensity = NULL,
  useRawData = FALSE,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "analyses",
  interactive = TRUE,
  renderEngine = "webgl"
)

Arguments

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".

Method `plot_spectra_3d()`

Plots spectra in 3D, when a time dimension is available.

Usage

RamanEngine$plot_spectra_3d(
  analyses = NULL,
  targets = NULL,
  rt = NULL,
  shift = NULL,
  minIntensity = NULL,
  useRawData = FALSE,
  legendNames = TRUE,
  colorBy = "analyses",
  xLab = NULL,
  yLab = NULL,
  zLab = NULL,
  renderEngine = "webgl"
)

Arguments

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.
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.
colorBy: A string defining how to legend the plot. Possible values are analyses, targets (the default) or replicates.
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
zLab: Character (length 1). The label for the z-axis.
renderEngine: The engine to render the data. The default is "webgl".

Method `plot_spectra_baseline()`

Plots the spectra baseline correction.

Usage

RamanEngine$plot_spectra_baseline(
  analyses = NULL,
  targets = NULL,
  rt = NULL,
  shift = NULL,
  minIntensity = NULL,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "analyses",
  interactive = TRUE,
  renderEngine = "webgl"
)

Arguments

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.
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".

Method `plot_chromatograms()`

Plots chromatograms from each analysis/replicates by applying a cumulative sum of the spectrum signals for each time unit.

Usage

RamanEngine$plot_chromatograms(
  analyses = NULL,
  targets = NULL,
  rt = NULL,
  shift = NULL,
  minIntensity = NULL,
  useRawData = FALSE,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  colorBy = "analyses",
  interactive = TRUE,
  renderEngine = "webgl"
)

Arguments

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".

Method `plot_chromatograms_peaks()`

Plots peaks from chromatograms.

Usage

RamanEngine$plot_chromatograms_peaks(
  analyses = NULL,
  targets = NULL,
  rt = NULL,
  title = NULL,
  legendNames = TRUE,
  colorBy = "targets",
  xLab = NULL,
  yLab = NULL,
  interactive = TRUE,
  renderEngine = "webgl"
)

Arguments

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.
title: A string with the title.
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.
colorBy: A string defining how to legend the plot. Possible values are analyses, targets (the default) or replicates.
xLab: A string with the title for the x axis.
yLab: A string with the title for the y axis.
interactive: Logical (length 1). When TRUE, the data is plotted interactively using plotly.
renderEngine: The engine to render the data. The default is "webgl".

Method `clone()`

The objects of this class are cloneable with this method.

Usage

RamanEngine$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Engine dedicated to Raman spectroscopic data processing

References

See also

Super class

Active bindings

Methods

Public methods

Method new()

Usage

Arguments

Method get_analysis_names()

Usage

Arguments

Method get_replicate_names()

Usage

Arguments

Method get_blank_names()

Usage

Arguments

Method get_files()

Usage

Arguments

Method get_overview()

Usage

Method get_spectra()

Usage

Arguments

Method get_spectra_matrix()

Usage

Arguments

Method get_chromatograms_peaks()

Usage

Arguments

Method add_analyses()

Usage

Arguments

Method remove_analyses()

Usage

Arguments

Method add_replicate_names()

Usage

Arguments

Method add_blank_names()

Usage

Arguments

Method has_spectra()

Usage

Method plot_spectra()

Usage

Arguments

Method plot_spectra_3d()

Usage

Arguments

Method plot_spectra_baseline()

Usage

Arguments

Method plot_chromatograms()

Usage

Arguments

Method plot_chromatograms_peaks()

Usage

Arguments

Method clone()

Usage

Arguments

Method `new()`

Method `get_analysis_names()`

Method `get_replicate_names()`

Method `get_blank_names()`

Method `get_files()`

Method `get_overview()`

Method `get_spectra()`

Method `get_spectra_matrix()`

Method `get_chromatograms_peaks()`

Method `add_analyses()`

Method `remove_analyses()`

Method `add_replicate_names()`

Method `add_blank_names()`

Method `has_spectra()`

Method `plot_spectra()`

Method `plot_spectra_3d()`

Method `plot_spectra_baseline()`

Method `plot_chromatograms()`

Method `plot_chromatograms_peaks()`

Method `clone()`