RamanEngine R6 class and methods

The RamanEngine R6 class is a framework for parsing, processing, inspecting and storing Raman spectroscopic data.

Super class

StreamFind::CoreEngine -> RamanEngine

Active bindings

raw_spectra

List of raw spectra data.table objects for each analysis.

spectra

List of spectra data.table objects for each analysis.

Methods

Public methods

• RamanEngine$new()

• RamanEngine$get_overview()

• RamanEngine$get_spectra()

• RamanEngine$get_spectra_matrix()

• RamanEngine$subset_analyses()

• RamanEngine$add_files()

• RamanEngine$remove_analyses()

• RamanEngine$has_spectra()

• RamanEngine$plot_spectra()

• RamanEngine$plot_spectra_baseline()

• RamanEngine$plot_spectra_peaks()

• RamanEngine$plot_chromatograms()

• RamanEngine$plot_chromatograms_peaks()

• RamanEngine$processing_methods()

• RamanEngine$clone()

Inherited methods

• StreamFind::CoreEngine$add_analyses()
• StreamFind::CoreEngine$add_blank_names()
• StreamFind::CoreEngine$add_headers()
• StreamFind::CoreEngine$add_metadata()
• StreamFind::CoreEngine$add_replicate_names()
• StreamFind::CoreEngine$add_results()
• StreamFind::CoreEngine$add_settings()
• StreamFind::CoreEngine$export()
• StreamFind::CoreEngine$export_analyses()
• StreamFind::CoreEngine$export_headers()
• StreamFind::CoreEngine$export_settings()
• StreamFind::CoreEngine$get_analyses()
• StreamFind::CoreEngine$get_analysis_names()
• StreamFind::CoreEngine$get_blank_names()
• StreamFind::CoreEngine$get_files()
• StreamFind::CoreEngine$get_formats()
• StreamFind::CoreEngine$get_headers()
• StreamFind::CoreEngine$get_history()
• StreamFind::CoreEngine$get_number_analyses()
• StreamFind::CoreEngine$get_replicate_names()
• StreamFind::CoreEngine$get_results()
• StreamFind::CoreEngine$get_results_names()
• StreamFind::CoreEngine$get_settings()
• StreamFind::CoreEngine$get_settings_names()
• StreamFind::CoreEngine$get_types()
• StreamFind::CoreEngine$get_workflow_overview()
• StreamFind::CoreEngine$has_analyses()
• StreamFind::CoreEngine$has_results()
• StreamFind::CoreEngine$has_settings()
• StreamFind::CoreEngine$import()
• StreamFind::CoreEngine$import_analyses()
• StreamFind::CoreEngine$import_headers()
• StreamFind::CoreEngine$import_settings()
• StreamFind::CoreEngine$load()
• StreamFind::CoreEngine$print()
• StreamFind::CoreEngine$print_analyses()
• StreamFind::CoreEngine$print_headers()
• StreamFind::CoreEngine$print_results()
• StreamFind::CoreEngine$print_workflow()
• StreamFind::CoreEngine$process()
• StreamFind::CoreEngine$remove_headers()
• StreamFind::CoreEngine$remove_results()
• StreamFind::CoreEngine$remove_settings()
• StreamFind::CoreEngine$run_app()
• StreamFind::CoreEngine$run_workflow()
• StreamFind::CoreEngine$save()

---

Method new()

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

Usage

RamanEngine$new(
  files = NULL,
  headers = NULL,
  settings = NULL,
  analyses = NULL,
  results = NULL
)

Arguments

files

Vector with full paths of .asc files from Raman analyses.

headers

A named list with headers or a ProjectHeaders S3 class object. Each list element must have length one. There is no type restrictions except for name (must be type character length 1), author (must be type character length 1), file (must be type character length 1) and date (must be class POSIXct or class POSIXt length 1). See more information in ?ProjectHeaders.

settings

A named list of ProcessingSettings objects or a single ProcessingSettings object. The list names should match the call name of each ProcessingSettings object. Alternatively, a named list with call name, algorithm and parameters to be transformed and added as ProcessingSettings object.

settings

A ProcessingSettings S3 class object with the call name applicable to the processing method. Alternatively, a named list with call, algorithm and parameters to be transformed and used as ProcessingSettings S3 class object. When not given, settings for the processing method will be searched within the engine object.

analyses

A numeric/character vector with the number/name of the analyses.

results

A named list of objects from processing methods.

---

Method get_overview()

Gets an overview data.frame of all the analyses.

Usage

RamanEngine$get_overview()

---

Method get_spectra()

Gets a data.table with spectra from analyses.

Usage

RamanEngine$get_spectra(
  analyses = NULL,
  rt = NULL,
  shift = NULL,
  minIntensity = 0,
  raw_spectra = FALSE
)

Arguments

analyses

A numeric/character vector with the number/name of the analyses.

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.

raw_spectra

Logical of length one. Set to TRUE for parsing raw spectra not spectra results/processed.

---

Method get_spectra_matrix()

Gets a matrix with spectra from analyses.

Usage

RamanEngine$get_spectra_matrix(analyses = NULL)

Arguments

analyses

A numeric/character vector with the number/name of the analyses.

---

Method subset_analyses()

Subsets on analyses.

Usage

RamanEngine$subset_analyses(analyses = NULL)

Arguments

analyses

A numeric/character vector with the number/name of the analyses.

Returns

A new cloned engine with only the analyses as defined by the analyses argument.

---

Method add_files()

Adds analyses based on asc files. Note that when adding new files, any existing results are removed.

Usage

RamanEngine$add_files(files = NULL)

Arguments

files

Vector with full paths of .asc files from Raman analyses.

Returns

Invisible.

---

Method remove_analyses()

Removes analyses.

Usage

RamanEngine$remove_analyses(analyses = NULL)

Arguments

analyses

A numeric/character vector with the number/name of the analyses.

Returns

Invisible.

---

Method has_spectra()

Checks if there are spectra, returning TRUE or FALSE.

Usage

RamanEngine$has_spectra()

---

Method plot_spectra()

Plots spectra for given RamanAnalyses.

Usage

RamanEngine$plot_spectra(
  analyses = NULL,
  rt = NULL,
  shift = NULL,
  minIntensity = 0,
  raw_spectra = FALSE,
  xVal = "shift",
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  cex = 0.6,
  showLegend = TRUE,
  colorBy = "analyses",
  interactive = TRUE
)

Arguments

analyses

A numeric/character vector with the number/name of the analyses.

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.

raw_spectra

Logical of length one. Set to TRUE for parsing raw spectra not spectra results/processed.

xVal

Character of length one. Possible are "rt" or "shift" for using the retention time or the shift as x axis, respectively.

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.

cex

Numeric (length 1) defining the scale of the legend for non interactive plotting.

showLegend

Logical (length 1). Set to TRUE to show legend.

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.

Returns

A plot.

---

Method plot_spectra_baseline()

Plots spectra corrected for given RamanAnalyses.

Usage

RamanEngine$plot_spectra_baseline(
  analyses = NULL,
  rt = NULL,
  shift = NULL,
  minIntensity = 0,
  xVal = "shift",
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  cex = 0.6,
  showLegend = TRUE,
  colorBy = "analyses",
  interactive = TRUE
)

Arguments

analyses

A numeric/character vector with the number/name of the analyses.

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.

xVal

Character of length one. Possible are "rt" or "shift" for using the retention time or the shift as x axis, respectively.

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.

cex

Numeric (length 1) defining the scale of the legend for non interactive plotting.

showLegend

Logical (length 1). Set to TRUE to show legend.

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.

Returns

A plot.

---

Method plot_spectra_peaks()

Plots peaks from spectra from analyses.

Usage

RamanEngine$plot_spectra_peaks(
  analyses = NULL,
  legendNames = NULL,
  title = NULL,
  colorBy = "analyses",
  showLegend = TRUE,
  xlim = NULL,
  ylim = NULL,
  cex = 0.6,
  xLab = NULL,
  yLab = NULL,
  interactive = TRUE
)

Arguments

analyses

A numeric/character vector with the number/name of the analyses.

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.

title

A string with the title.

colorBy

A string defining how to legend the plot. Possible values are analyses, targets (the default) or replicates.

showLegend

Logical (length 1). Set to TRUE to show legend.

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.

cex

Numeric (length 1) defining the scale of the legend for non interactive plotting.

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.

---

Method plot_chromatograms()

Plots chromatograms from analyses with spectra coupled to LC.

Usage

RamanEngine$plot_chromatograms(
  analyses = NULL,
  rt = NULL,
  shift = NULL,
  minIntensity = 0,
  raw_spectra = FALSE,
  xLab = NULL,
  yLab = NULL,
  title = NULL,
  cex = 0.6,
  showLegend = TRUE,
  colorBy = "analyses",
  interactive = TRUE
)

Arguments

analyses

A numeric/character vector with the number/name of the analyses.

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.

raw_spectra

Logical of length one. Set to TRUE for parsing raw spectra not spectra 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.

cex

Numeric (length 1) defining the scale of the legend for non interactive plotting.

showLegend

Logical (length 1). Set to TRUE to show legend.

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.

Returns

A plot.

---

Method plot_chromatograms_peaks()

Plots peaks from chromatograms from analyses.

Usage

RamanEngine$plot_chromatograms_peaks(
  analyses = NULL,
  chromatograms = NULL,
  legendNames = NULL,
  title = NULL,
  colorBy = "targets",
  showLegend = TRUE,
  xlim = NULL,
  ylim = NULL,
  cex = 0.6,
  xLab = NULL,
  yLab = NULL,
  interactive = TRUE
)

Arguments

analyses

A numeric/character vector with the number/name of the analyses.

chromatograms

A character or integer vector with the ID (i.e. name) or the index of the chromatograms.

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.

title

A string with the title.

colorBy

A string defining how to legend the plot. Possible values are analyses, targets (the default) or replicates.

showLegend

Logical (length 1). Set to TRUE to show legend.

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.

cex

Numeric (length 1) defining the scale of the legend for non interactive plotting.

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.

---

Method processing_methods()

A data.table with available data processing methods.

Usage

RamanEngine$processing_methods()

---

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.