R/mareGUI.R

In katrikorpela/mare: Microbiota Analysis in R Easily

mareGUI <- function(){
library(fgui)
  
helpfunction <- function(function.name){
h <- help(function.name)
print(h)
}

guidefunction <- function(guide.name){
browseURL(system.file(paste(guide.name,".pdf",sep=""), package = "mare"))
}

wdfunction <- function(dir){
  setwd(dir)
}

fguiWindow(title="mare", text="Welcome to mare! 
Start by reading the help files and guides.
To analyse your data, first do the pre-processing
(functions ProcessReads and TaxonomicTables),
copy the files to a new folder (optional) for analysis and organise the data
(functions CopyFiles and Organise),
then explore the results by plotting
(functions PCoA, GroupPlot, CovariatePlot, Clusters, CorrelationMap), 
and finally conduct sigficance testing
(functions GroupTest, CovariateTest, ChangeTest, PathModel),
and carbohydrate utilization prediction
(function CAZy).")
fguiNewMenu(c("Help", "SEPARATOR"))
mgui(helpfunction, title = c("Help","Help files"), modal=F, output=NULL,
    argText = list(function.name="Write the name of the function in quotations"))
mgui(guidefunction, title = c("Help","Guides"), 
     argOption=list(guide.name=c("mareGuide","mareBackground")), modal=F, output=NULL)
fguiNewMenu(c("Preprocess","SEPARATOR"))
mgui(wdfunction, title = c("Preprocess", "Set working directory"), output=NULL, 
     argText = list(dir = "Write the full path to the working directory"))
mgui(ProcessReads, title = c("Preprocess", "ProcessReads"), output=NULL, 
     argFilename=list(usearch.path=NULL))
mgui(TaxonomicTable, title = c("Preprocess", "TaxonomicTable"), output=NULL,
     argFilename=list(usearch.path=NULL,refDB=NULL))
     #argList=list(refDB=c("RDP.fasta","RDP_Gut.fasta","silva_full.fasta",            
 #"silva_full_Gut.fasta", "silva_full_Gut_namedSP.fasta", "silva_full_namedSP.fasta",   
 ##"silva_v3v4.fasta","silva_v3v4_Gut.fasta","silva_v3v4_Gut_namedSP.fasta","silva_v3v4_namedSP.fasta",
# "RDP.udb","RDP_Gut.udb","silva_full.udb","silva_full_Gut_namedSP.udb",
#"silva_full_namedSP.udb","silva_v3v4_Gut.udb","silva_v3v4_Gut_namedSP.udb","silva_v3v4_namedSP.udb")))
mgui(CopyFiles, title = c("Preprocess", "CopyFiles"), output=NULL)
mgui(Organise, title = c("Preprocess", "Organise"), output=NULL)
fguiNewMenu(c("Plot","SEPARATOR"))
mgui(PCoA, title = c("Plot", "PCoA"),argFilename=list(taxonomic.table=NULL, meta=NULL,output="m"))
mgui(Clusters, title = c("Plot", "Clusters"),argFilename=list(taxonomic.table=NULL, meta=NULL,output="m"))
mgui(CorrelationMap, title = c("Plot", "CorrelationMap"),argFilename=list(taxonomic.table=NULL, meta=NULL,output="m"))
mgui(GroupPlot, title = c("Plot", "GroupPlot"),argFilename=list(taxonomic.table=NULL, meta=NULL), output="m")
mgui(CovariatePlot, title = c("Plot", "CovariatePlot"),
     argFilename=list(taxonomic.table=NULL, meta=NULL), output="m")
fguiNewMenu(c("Test","SEPARATOR"))
mgui(GroupTest, title = c("Test", "GroupTest"),argFilename=list(species.table=NULL,genus.table=NULL,family.table=NULL,class.table=NULL,order.table=NULL, phylum.table=NULL,meta=NULL), output="m")
mgui(CovariateTest, title = c("Test", "CovariateTest"),argFilename=list(species.table=NULL,genus.table=NULL,family.table=NULL,class.table=NULL,order.table=NULL, phylum.table=NULL, meta=NULL), output="m")
mgui(ChangeTest, title = c("Test", "ChangeTest"),argFilename=list(species.table=NULL,genus.table=NULL,family.table=NULL,class.table=NULL,order.table=NULL, phylum.table=NULL, meta=NULL), output="m")
mgui(PathModel, title = c("Test", "PathModel"),argFilename=list(taxonomic.table=NULL, meta=NULL), output="m")
fguiNewMenu(c("CAZy prediction","SEPARATOR"))
mgui(CAZy, title = c("CAZy prediction","CAZy"), argFilename=list(species=NULL),output=NULL)
}