# Microbiome Exploration App

## Documentation for package ‘microbiomeExplorer’ version 1.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I L M N P R

## -- A --

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

## -- B --

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

## -- C --

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

## -- D --

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

## -- E --

extendPhenoData | Extends existing phenodata for an object

## -- F --

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

## -- G --

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)

## -- H --

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

## -- I --

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

## -- L --

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

## -- M --

makeQCPlot | Plots sequencing statistics scatterplot

## -- N --

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.

## -- P --

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

## -- R --

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