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| abundanceHeatmap | Abundance Heatmap module - server |
| abundanceHeatmapUI | Abundance Heatmap module - UI |
| addFeatData | Add feature data to MRobj. |
| addPhenoData | Add phenotype data to object. |
| add_plotly_config | Adds a config call based on plotly::config |
| add_plotly_layout | Adds a layout call based on plotly::layout |
| 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 |
| 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 |