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Report workflow data

Source: R/generics.R, R/report.R
reporting.Rd

Functionality to report data produced by most workflow steps such as features, feature groups, formula and compound annotations, and TPs.

Usage

report(
  fGroups,
  MSPeakLists = NULL,
  formulas = NULL,
  compounds = NULL,
  compsCluster = NULL,
  components = NULL,
  TPs = NULL,
  settingsFile = system.file("report", "settings.yml", package = "patRoon"),
  path = NULL,
  EICParams = getDefEICParams(topMost = 1, topMostByReplicate = TRUE),
  EIMParams = getDefEIMParams(topMost = 1, topMostByReplicate = TRUE),
  specSimParams = getDefSpecSimParams(),
  clearPath = FALSE,
  openReport = TRUE,
  parallel = FALSE,
  overrideSettings = list()
)

# S4 method for class 'featureGroups'
report(
  fGroups,
  MSPeakLists = NULL,
  formulas = NULL,
  compounds = NULL,
  compsCluster = NULL,
  components = NULL,
  TPs = NULL,
  settingsFile = system.file("report", "settings.yml", package = "patRoon"),
  path = NULL,
  EICParams = getDefEICParams(topMost = 1, topMostByReplicate = TRUE),
  EIMParams = getDefEIMParams(topMost = 1, topMostByReplicate = TRUE),
  specSimParams = getDefSpecSimParams(),
  clearPath = FALSE,
  openReport = TRUE,
  parallel = FALSE,
  overrideSettings = list()
)

genReportSettingsFile(out = "report.yml", baseFrom = NULL)

Arguments

fGroups

The featureGroups object that should be used for reporting data.

MSPeakLists, formulas, compounds, compsCluster, components, TPs

Further objects (MSPeakLists, formulas, compounds, compoundsCluster, components, transformationProducts) that should be reported. Specify NULL to skip reporting a particular object. Note that MSPeakLists must be set if either formulas or compounds is set.

settingsFile

The path to the report settings file used for report configuration (see Report settings).

path

The destination file path for files generated during reporting. Will be generated if needed. If path=NULL then the destination path is taken from the report settings (see below).

EICParams

A named list with parameters used for extracted ion chromatogram (EIC) creation. See the EIC parameters documentation for more details.

EIMParams

A named list with parameters used for extracted ion mobilogram (EIM) creation. See the EIM parameters documentation for more details.

specSimParams

A named list with parameters that influence the calculation of MS spectra similarities. See the spectral similarity parameters documentation for more details.

clearPath

If TRUE then the report destination path will be (recursively) removed prior to reporting.

openReport

If set to TRUE then the output report file will be opened with the system browser.

parallel

If set to TRUE then code is executed in parallel through the future package. Please see the parallelization section in the handbook for more details.

NOTE: parallelization is disabled by default, as it may slow down reporting on some systems (e.g. Windows) and under some circumstances. It is best to experiment with this setting to see if it speeds up report generation for your system and data.

overrideSettings

A list with settings that override those from the report settings file. Example: overrideSettings=list(compounds=list(topMost=25)).

out

The output file path.

baseFrom

An existing report file to which the report settings should be based from. This is primarily used to update old settings files: the output settings file will be based on the old settings and amended with any missing.

Details

The reporting functionality is typically used at the very end of the workflow. It is used to overview the data generated during the workflow, such as features, their annotations and TP screening results.

report reports all workflow data in an interactive HTML file. The reports include both tabular data (e.g. retention times, annotation properties, screening results) and various plots (e.g. chromatograms, (annotated) mass spectra and many more). This function uses functionality from other R packages, such as rmarkdown, knitr and bslib.

The genReportSettingsFile function generates a new template YAML file to configure report settings (see the next section).

Note

No data will be reported for feature groups in any of the reported objects (formulas, compounds etc) which are not present in the input featureGroups object (fGroups).

The topMost, topMostByReplicate and onlyPresent EIC parameters may be ignored, e.g., when generating overview plots.

Report settings

The report generation can be customized with a variety of settings that are read from a YAML file. This is especially useful if you want to change more advanced settings or want to add or remove the parts that are reported. The report settings file is specified through the settingsFile argument. If not specified then default settings will be used. To ease creation of a new template settings file, the genReportSettingsFile function can be used.

The following settings are currently available:

  • General

    • version: version of the settings file.

    • format: the report format. Currently this can only be "html".

    • path: the destination path (ignored if the path argument is specified).

    • keepUnusedPlots: the number of days that unused plot files are kept (see Plot file caching).

    • selfContained: If true then the output report.html embeds all graphics and script dependencies. Otherwise these files are read from the report_files/ directory. Self-contained reports are generally smaller and easily shared, since only the report.html needs to be copied. However, they are slower to generate and plots cannot be cached.

    • noDate: Set to true to omit the date from the report. Mainly used for internal purposes.

  • summary: defines the plots on the summary page: chord, venn and/or upset.

  • features

    • retMin: if true then retention times are reported in minutes.

    • chromatograms

      • large: inclusion of large chromatograms (used in feature group table and TP parent chromatogram view).

      • small: inclusion of small chromatograms (feature group table).

      • features: inclusion of chromatograms for individual features (features view). Set to all to also include plots for analyses in which a feature was not found (or removed afterwards).

      • intMax: Method to determine the maximum intensity plot range: eic or feature. Sets the intMax argument to plotChroms.

    • mobilograms

      • large, small, features: inclusion of mobilogram plots, see chromatograms above.

    • intensityPlots: inclusion of intensity trend plots.

    • aggregateConcs, aggregateTox: function name used for concentration and toxicity aggregation, e.g. mean.

  • MSPeakLists

    • spectra: inclusion of MS and MS/MS spectra (not annotated).

  • formulas

    • include: whether formula results are reported (formula view). If false then the input formulas object is still used to amend e.g. compound annotated spectra.

    • normalizeScores, exclNormScores: controls score normalization and which score fields to exclude from normalization; these are forwarded to e.g. plotScores.

    • topMost: only report this number of top ranked candidates. This number can be lowered to speed-up report generation.

  • compounds

    • normalizeScores, exclNormScores, topMost: same as formulas, see above.

    • onlyUsedScorings: if true only scorings used by the current dataset are considered when normalizing or reporting compound scores.

  • TPs

    • graphs: inclusion of TP hierarchy graphs (generated with plotGraph).

    • graphStructuresMax: maximum number of structures to plot in hierarchy graphs (sets structuresMax argument of plotGraph).

  • internalStandards

    • graph: inclusion of internal standard network plot (plotGraph).

Plot file caching

When a new report is generated the plot files are stored inside the report_files sub-directory inside the destination path of the report. The plot files are kept so they can be reused to speed-up re-creation of reports (e.g. with different report settings). After the report is generated, any unused plot files are removed unless they were recently created (controlled by the keepUnusedPlots setting, see previous section). The clearPath argument can be used to completely remove any old files.

Use of raw HRMS data

The raw data interface of patRoon is used by report to process HRMS (or IMS-HRMS) data. Please see its documentation for more information on the supported formats and available configuration options.

References

Creating MetFrag landing page URLs based on code from MetFamily R package.

Xie Y (2014). “knitr: A Comprehensive Tool for Reproducible Research in R.” In Stodden V, Leisch F, Peng RD (eds.), Implementing Reproducible Computational Research. Chapman and Hall/CRC. ISBN 978-1466561595.

Xie Y (2015). Dynamic Documents with R and knitr, 2nd edition. Chapman and Hall/CRC, Boca Raton, Florida. ISBN 978-1498716963, https://yihui.org/knitr/.

Xie Y (2025). knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.51, https://yihui.org/knitr/.