abundanceHeatmap        Abundance Heatmap module - server
abundanceHeatmapUI      Abundance Heatmap module - UI
add_plotly_config       Adds a config call based on plotly::config
add_plotly_layout       Adds a layout call based on plotly::layout
addFeatData             Add feature data to MRobj.
addPhenoData            Add phenotype data to object.
aggFeatures             Aggregates counts by level
aggregationTab          Aggregation module server function
aggregationTabUI        Aggregation module ui function
alphaDiversity          Alpha Diversity module - server
alphaDiversityUI        Alpha Diversity module - UI
avgAbundance            Relative abundance plot module - server
avgAbundanceUI          Relative abundance plot module - UI
betaDiversity           Beta Diversity module - server
betaDiversityUI         Beta Diversity module - UI
betaInput               Server side for the analysis input module
                        handling analysis control
betaInputUI             Main beta analysis input module. Set up to
                        handle all analysis tabs in the app depending
                        on given parameters
buildEmptyPlotlyPlot    Creates an empty plotly plot using the given
                        labels on the x and y axis
buildPlottingDF         Sets up a dataframe used by several plotting
                        functions by joining the required data with
                        relevant phenotype data
calculatePCAs           Function to compute the PCAs for a given
                        distance matrix
computeCI_Interval      Helper function to calculate the confidence
                        interval for a cor.test
computeDistMat          Function to compute the distance matrix using
                        vegdist from the vegan package
corrAnalysis            corr Analysis Module - server
corrAnalysisUI          corr Analysis Module - UI
corrFeature             Scatterplot of two features
corrInput               Server side for the analysis input module
                        handling analysis control
corrInputUI             Main correlation analysis input module. Handles
                        correlation analysis tab in the app
corrPhenotype           Scatterplot of a feature and a phenotype
createHeader            Makes header for R script
dataInput               Main Data input server where the user selects
                        files to upload to the app or connects to
                        database
dataInputUI             Main Data input UI where the user selects files
                        to upload to the app or connects to database
designPairs             Produce design matrix of pairwise comparisons
diffAnalysis            diff Analysis Module - server
diffAnalysisUI          Diff Analysis Module - UI
diffInput               Server side for the analysis input module
                        handling analysis control
diffInputUI             Main diffanalysis input module. Set up to
                        handle diff analysis tabs in the app depending
                        on given parameters
diffTable               Differential analysis module server code
diffTableUI             Differential Analysis module UI
extendPhenoData         Extends existing phenodata for an object
featAbundance           Feature plot module - server
featAbundanceUI         Feature plot module - UI
featureAnalysis         feature Analysis Module - server
featureAnalysisUI       feature Analysis Module - UI
featureCorr             Feature correlation analysis server module
featureCorrUI           Feature correlation analysis module UI
featureInput            Server side for the feature analysis input
                        module
featureInputUI          Main feature analysis input module. Set up to
                        handle all analysis tabs in the app depending
                        on given parameters
featureTable            Feature table module server code
featureTableUI          Feature table UI module
fileUpload              Module handling file upload for the
                        application: server
fileUploadUI            Module handling file upload for the
                        application: UI In a deployed version this
                        module should be replaced with database access
filterByPheno           Function to filter the MRexperiment by certain
                        phenotype values
filterMEData            Function to filter the MRexperiment data by
                        numerical parameters
generateReport          Generates report
getFeatModCode          Helper function returning the fData
                        modifications as strings for report generation
getFeatSplitCode        Helper function returning the fData
                        modifications as strings for report generation
getFileType             Helper function assigning different file
                        extensions to specific short texts identifying
                        the types
getFilterChoices        Helper function to filter phenodata for
                        interesting phenotypes to be used for filtering
                        or subsetting
getLegendLevel          Function to find a non-empty facet in the last
                        row. This will be the one to be connected to
                        the plot legend to avoid duplicates within
getPhenoChanges         Helper function returning the code used to
                        modify the data types of the pheno table
getPhenoModCode         Helper function returning the code used to
                        modify the phenotable as a string
getWidths               Helper function to account for issues plotly
                        has with very small widths (these end up being
                        1 and cover the entire plotting area)
heatmapInput            Server side for the analysis input module
                        handling analysis control
heatmapInputUI          Heatmap analysis input module. Set up to handle
                        all analysis tabs in the app depending on given
                        parameters
interAnalysis           inter Analysis Module - server
interAnalysisUI         inter Analysis Module - UI
intraAnalysis           Intra Analysis Module - server
intraAnalysisUI         Intra Analysis Module - UI
intraInput              Server side for the intra analysis input module
intraInputUI            Main intra analysis input module. Set up to
                        handle all analysis tabs in the app depending
                        on given parameters
longAnalysis            long Analysis Module - server
longAnalysisUI          Long Analysis Module - UI
longInput               Server side for the analysis input module
                        handling analysis control
longInputUI             Main diffanalysis input module. Set up to
                        handle diff analysis tabs in the app depending
                        on given parameters
longResults             Longitudinal analysis module server code
longResultsUI           Longitudinal Analysis module UI
makeQCPlot              Plots sequencing statistics scatterplot
normalizeData           Calls appropriate normalization functions
                        depending on input parameter The two available
                        methods included in the package are based on
                        either calculating proportions or by using
                        cumulative sum scaling (CSS), Paulson, et al.
                        Nat Meth 2013.
parseInteractionName    Helper function used to build a correct
                        interactionName based on the chosen columns
phenotypeCorr           Phenotype correlation analysis server module
phenotypeCorrUI         Phenotype correlation analysis module
phenotypeTable          Phenotype table server module
phenotypeTableUI        Phenotype table UI module
plotAbundance           Plot relative abundance
plotAlpha               Plot alpha diversity
plotAvgAbundance        Plot average relative abundance
plotBeta                Plot beta diversity
plotHeatmap             Plot heatmap
plotLongFeature         Plot longitudinal features
plotlyHistogram         Function plotting a plotly histogram on the
                        given histvalue
plotlySampleBarplot     Function plotting a barplot showing number of
                        OTUs per samples
plotSingleFeature       Plot features
readData                Reads in data
relAbundance            Relative abundance plot module - server
relAbundanceUI          Relative abundance plot module - UI
replaceWithUnknown      Helper function to replace any un-annotated
                        features with the term unknown
reportList              Report tab module server
reportListUI            report tab ui
reportRow               Report Row
reportRowUI             Report row module consisting of a checkbox,
                        image and description/R code area
rollDownFeatures        Helper function which rolls down annotated from
                        closest higher order with annotation
runDiffTest             Performs differential abundance testing
runMicrobiomeExplorer   Main function to start the Microbiome Explorer
                        Shiny app via a command line call
