Man pages for microbiomeExplorer
Microbiome Exploration App
| 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... |
| betaInputUI | Main beta analysis input module. Set up to handle all... |
| buildEmptyPlotlyPlot | Creates an empty plotly plot using the given labels on the x... |
| buildPlottingDF | Sets up a dataframe used by several plotting functions by... |
| calculatePCAs | Function to compute the PCAs for a given distance matrix |
| computeCI_Interval | Helper function to calculate the confidence interval for a... |
| computeDistMat | Function to compute the distance matrix using vegdist from... |
| 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... |
| corrInputUI | Main correlation analysis input module. Handles correlation... |
| 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... |
| dataInputUI | Main Data input UI where the user selects files to upload to... |
| 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... |
| diffInputUI | Main diffanalysis input module. Set up to handle diff... |
| 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... |
| 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... |
| filterByPheno | Function to filter the MRexperiment by certain phenotype... |
| filterMEData | Function to filter the MRexperiment data by numerical... |
| generateReport | Generates report |
| getFeatModCode | Helper function returning the fData modifications as strings... |
| getFileType | Helper function assigning different file extensions to... |
| getFilterChoices | Helper function to filter phenodata for interesting... |
| getLegendLevel | Function to find a non-empty facet in the last row. This will... |
| getPhenoChanges | Helper function returning the code used to modify the data... |
| getPhenoModCode | Helper function returning the code used to modify the... |
| getWidths | Helper function to account for issues plotly has with very... |
| heatmapInput | Server side for the analysis input module handling analysis... |
| heatmapInputUI | Heatmap analysis input module. Set up to handle all analysis... |
| 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... |
| longAnalysis | long Analysis Module - server |
| longAnalysisUI | Long Analysis Module - UI |
| longInput | Server side for the analysis input module handling analysis... |
| longInputUI | Main diffanalysis input module. Set up to handle diff... |
| longResults | Longitudinal analysis module server code |
| longResultsUI | Longitudinal Analysis module UI |
| makeQCPlot | Plots sequencing statistics scatterplot |
| normalizeData | Calls appropriate normalization functions depending on input... |
| parseInteractionName | Helper function used to build a correct interactionName based... |
| 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... |
| 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... |
| reportList | Report tab module server |
| reportListUI | report tab ui |
| reportRow | Report Row |
| reportRowUI | Report row module consisting of a checkbox, image and... |
| rollDownFeatures | Helper function which rolls down annotated from closest... |
| runDiffTest | Performs differential abundance testing |
| runMicrobiomeExplorer | Main function to start the Microbiome Explorer Shiny app via... |
