Commit 49d292d0 authored by Amine  GHOZLANE's avatar Amine GHOZLANE
Browse files

Remove expanded mode with R 3.2, otherwise activate. And remove some useless print

parent 72223423
......@@ -292,7 +292,11 @@ CheckCountsTable <- function(counts)
dds <- DESeqDataSetFromMatrix(countData=counts, colData=target, design=design)
sizeFactors(dds) = normFactorsOTU
dds <- estimateDispersions(dds, fitType=input$fitType)
dds <- nbinomWaldTest(dds,modelMatrixType = "expanded")
if(as.numeric(R.Version()$major)+as.numeric(R.Version()$minor) >= 4.3){
dds <- nbinomWaldTest(dds)
}else{
dds <- nbinomWaldTest(dds,modelMatrixType = "expanded")
}
countsNorm = counts(dds, normalized = TRUE)
return(list(dds = dds,raw_counts=counts,countsNorm=countsNorm,target=target,design=design,normFactors = normFactorsOTU,CT_noNorm=CT_noNorm))
}
......
......@@ -384,7 +384,7 @@ shinyServer(function(input, output,session) {
taxo = rbind(taxo,rep(NA,ncol(taxo)))
tmpPercent = round(apply(is.na(taxo),2,table)["FALSE",]/nrow(counts)*100,2)
print(tmpPercent)
#print(tmpPercent)
df <- data.frame(Label = colnames(taxo),Value = tmpPercent)
res = gvisGauge(df,options=list(min=0, max=100, greenFrom=80,
......@@ -440,9 +440,9 @@ shinyServer(function(input, output,session) {
#rownames(data) <- colnames(counts)
# Percent annotated
print(ind)
print(colnames(counts))
print(rownames(data))
# print(ind)
# print(colnames(counts))
# print(rownames(data))
labeled = length(ind)/length(colnames(counts))*100.0
return(list(target=data[ind,], labeled=labeled))
......@@ -899,7 +899,7 @@ output$InfoContrast <- renderInfoBox({
normFactors = dataMergeCounts()$normFactors
## HEEEERRREE
target = dataInputTarget()$target
print(target)
#print(target)
design = GetDesign(input)
Get_dds_object(input,counts,target,design,normFactors,CT_noNorm)
......@@ -1565,7 +1565,7 @@ output$RunButton <- renderUI({
taxo = input$TaxoSelect
if(!is.null(data$counts) && !is.null(data$taxo) && nrow(data$counts)>0 && nrow(data$taxo)>0 && !is.null(taxo) && taxo!="...")
{
print(data$counts)
#print(data$counts)
krona_table=tempfile(pattern = "krona", tmpdir = tempdir(), fileext = "")
url=paste(krona_table, ".html", sep="")
#system(paste("export PERL5LIB=/home/aghozlan/workspace/SHAMAN_App/KronaTools-2.6/lib:$PERL5LIB; /home/aghozlan/workspace/META10S_App/krona_bin/bin/ktImportText", krona_table))
......
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