R/app-metatranscriptomeAnalysis.R

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

###################################################################
# Functional Genomics Center Zurich
# This code is distributed under the terms of the GNU General
# Public License Version 3, June 2007.
# The terms are available here: http://www.gnu.org/licenses/gpl.html
# www.fgcz.ch

ezMethodMetatranscriptomeAnalysis = function(input=NA, output=NA, param=NA, 
                                             htmlFile="00index.html"){
    
    library(purrr)
    library(rtracklayer)
    library(RColorBrewer)
    library(GO.db)
    library(stringi)
    library(DESeq2)
    library(plyr)
    library(pheatmap)
    library(ggpubr)
    library(gridExtra)
    
    dataset = input$meta
    sampleNames = input$getNames() 
    numberOfTopNCategories = param$numberOfTopNCategories
    isGroupThere = param$grouping != ""
    group = param$grouping
    sampleGroup = param$sampleGroup
    refGroup = param$refGroup
    
    colnames(dataset) <-  gsub(" \\[File\\]","",colnames(dataset))
    annotationFiles <- input$getFullPaths("annotationFileRefSeq")
    sampleNames <- input$getNames()
    
    ## Merge annotation files 
    names(annotationFiles) <- sampleNames
    listOfAnnotatedAbundTable <- lapply(annotationFiles,convertDiamondAnnotationToAbund)
    listOfAnnotatedAbundTableOrg <- lapply(listOfAnnotatedAbundTable,
                                           function(x) x[["orgAbundDF"]])
    listOfAnnotatedAbundTableFunc <-lapply(listOfAnnotatedAbundTable,
                                           function(x) x[["funcAbundDF"]])
    orgDFforHeatmap <- listOfAbundMerge(listOfAnnotatedAbundTableOrg,sampleNames)
    funcDFforHeatmap <- listOfAbundMerge(listOfAnnotatedAbundTableFunc,sampleNames)
    
    ##
    setwdNew(basename(output$getColumn("Report")))
    ## Copy the style files and templates
    styleFiles <- file.path(system.file("templates", package="ezRun"),
                            c("fgcz.css", "metatranscriptomicsAnalysis.Rmd", 
                              "fgcz_header.html", "banner.png"))
    file.copy(from=styleFiles, to=".", overwrite=TRUE)
    rmarkdown::render(input="metatranscriptomicsAnalysis.Rmd", envir = new.env(),
                      output_dir=".", output_file=htmlFile, quiet=TRUE)
    
}
##' @template app-template
##' @templateVar method ezMethodMetatranscriptomeAnalysis()
##' @templateVar htmlArg )
##' @description Use this reference class to run 
EzAppMetatranscriptomeAnalysis<-
    setRefClass("EzAppMetatranscriptomeAnalysis",
                contains = "EzApp",
                methods = list(
                    initialize = function()
                    {
                        "Initializes the application using its specific defaults."
                        runMethod <<- ezMethodMetatranscriptomeAnalysis
                        name <<- "EzAppMetatranscriptomeAnalysis"
                        appDefaults <<- rbind(numberOfTopNCategories = ezFrame(Type="integer",  DefaultValue="20",
                                                                               Description="How many top N GO and 
                                                                         prot families.")
                        )
                    }
                )
    )