Microbiome Exploration App

Documentation for package ‘microbiomeExplorer’ version 1.10.0

Help Pages

-- 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
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)

-- 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

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