_pkgdown.yml

template:
  params:
    bootswatch: cosmo
#title: FT-MS Data Analysis in R
home:
#  strip_header: true
  links:
  - text: Learn more
    href: https://msc-viz.emsl.pnnl.gov
navbar:
  structure:
    left:  [home, intro, reference, articles, news]
    right: github
reference:
- title: ftmsData object construction
  desc: Functions to construct an ftmsData object
  contents:
  - '`as.compoundData`'
  - '`as.moduleData`'
  - '`as.peakData`'
  - '`as.reactionData`'
  - '`subset.peakData`'
  - '`summary.ftmsData`'
- title: Meta data calculation
  desc: Functions to calculate meta-data fields
  contents:
  - '`compound_calcs`'
  - '`assign_class`'
  - '`assign_elemental_composition`'
  - '`assign_mf`'
- title: Filtering
  desc: Functions to filter
  contents:
  - '`applyFilt`'
  - '`mass_filter`'
  - '`molecule_filter`'
  - '`formula_filter`'
  - '`emeta_filter`'
  - '`plot.formulaFilt`'
  - '`plot.massFilt`'
  - '`plot.moleculeFilt`'
  - '`plot.emetaFilt`'
  - '`summary.formulaFilt`'
  - '`summary.massFilt`'
  - '`summary.moleculeFilt`'
  - '`summary.emetaFilt`'
- title: Data transformation
  desc: Functions to transform data (e.g. scale)
  contents:
  - '`edata_replace`'
  - '`edata_transform`'
- title: Treatment groups and group comparisons
  desc: Defining experimental groups and comparisons
  contents:
  - '`group_designation`'
  - '`comparisonMatrix`'
  - '`concat`'
  - '`divideByGroup`'
  - '`summarizeGroups`'
  - '`divideByGroupComparisons`'
  - '`divideBySample`'
  - '`summarizeGroupComparisons`'
  - '`uniqueness_gtest`'
  - '`uniqueness_nsamps`'
  - '`uniqueness_prop`'
- title: Visualization
  desc: Visualization methods
  contents:
  - '`plot.peakData`'
  - '`classesPlot`'
  - '`densityPlot`'
  - '`kendrickPlot`'
  - '`vanKrevelenPlot`'
  - '`scatterPlot`'
  - '`plotPrincipalCoordinates`'
  - '`vignette_interactivity_between_plots`'
  - '`panelFunctionGenerator`'
  - '`densityCognostics`'
  - '`kendrickCognostics`'
  - '`vanKrevelenCognostics`'
- title: Database mapping
  desc: Functions to map to biological databases
  contents:
  - '`mapPeaksToCompounds`'
  - '`mapCompoundsToReactions`'
  - '`mapCompoundsToModules`'
  - '`parseModuleReaction`'
  - '`combinePeaksWithSameFormula`' 
#  - '`plotReactionGraph`'
#  - '`plotlyHeatmap`'
- title: Convenience methods
  desc: ~
  contents:
  - '`getDataScale`'
  - '`getDatabase`'
  - '`getGroupDF`'
  - '`getGroupSummaryFunctionNames`'
  - '`getInstrumentType`'
  - '`getModuleName`'
  - '`getVanKrevelenCategoryBounds`'
- title: CoreMS to ftmsRanalysis conversion
  contents:
  - 'coreMSDataToFtmsData'
  - 'as.CoreMSData'
- title: Column name methods
  desc: Methods to get the column name used to store various meta data values
  contents:
  - '`getAromaColName`'
  - '`getBS1ColName`'
  - '`getBS2ColName`'
  - '`getBS3ColName`'
  - '`getCarbonColName`'
  - '`getCompoundColName`'
  - '`getDBEAIColName`'
  - '`getDBEColName`'
  - '`getDBEoColName`'
  - '`getEDataColName`'
  - '`getElCompColName`'
  - '`getElementColName`'
  - '`getExtractionColName`'
  - '`getFDataColName`'
  - '`getGibbsColName`'
  - '`getHCRatioColName`'
  - '`getHydrogenColName`'
  - '`getIsotopicColName`'
  - '`getKendrickDefectColName`'
  - '`getKendrickMassColName`'
  - '`getMFColName`'
  - '`getMFNameColName`'
  - '`getMassColName`'
  - '`getModAromaColName`'
  - '`getModuleColName`'
  - '`getModuleNodeColName`'
  - '`getNCRatioColName`'
  - '`getNOSCColName`'
  - '`getNPRatioColName`'
  - '`getNitrogenColName`'
  - '`getOCRatioColName`'
  - '`getOxygenColName`'
  - '`getPCRatioColName`'
  - '`getPhosphorusColName`'
  - '`getRatioColName`'
  - '`getReactionColName`'
  - '`getSulfurColName`'
- title: Example data objects
  desc: Example data included in the `ftmsRanalysis` package
  contents:
  - '`examplePeakData`'
  - '`exampleProcessedPeakData`'
  - '`ftms12T_edata`'
  - '`ftms12T_emeta`'
  - '`ftms12T_fdata`'
- title: internal
  desc: Other functions
  contents:
  - calc_aroma
  - calc_dbe
  - calc_element_ratios
  - calc_gibbs
  - calc_kendrick
  - calc_nosc
  - conf_filter
  - conf_filter_dt
  - filter_worker
  - getGroupComparisonSummaryFunctionNames
  - getPrincipalCoordinates
  - gtest.standard
  - heatmap
  - mass_error_plot
  - numPeaksPlot
  - one_factor_change
  - parse_mf
  - plot.CoreMSData
  - plot.confFilt
  - plotlyHeatmap
  - read_CoreMS_data
  - setAromaColName
  - setBS1ColName
  - setBS2ColName
  - setBS3ColName
  - setCarbonColName
  - setCompoundColName
  - setDBEAIColName
  - setDBEColName
  - setDBEValenceDF
  - setDBEoColName
  - setEDataColName
  - setElCompColName
  - setElementColName
  - setExtractionColName
  - setFDataColName
  - setGibbsColName
  - setHCRatioColName
  - setHydrogenColName
  - setIsotopicColName
  - setKendrickDefectColName
  - setKendrickMassColName
  - setMFColName
  - setMFNameColName
  - setMassColName
  - setModAromaColName
  - setModuleColName
  - setModuleNodeColName
  - setNCRatioColName
  - setNOSCColName
  - setNPRatioColName
  - setNitrogenColName
  - setOCRatioColName
  - setOxygenColName
  - setPCRatioColName
  - setPhosphorusColName
  - setRatioColName
  - setReactionColName
  - setSulfurColName
  - transformation_counts
  - unique_mf_assignment
  - vector_replace

github:
  - icon: fa-github
    href: https://github.com/EMSL-Computing