Skip to content
GitLab
Commit 1341b3fc authored by Amine GHOZLANE's avatar Amine GHOZLANE
Browse files

Include Stevenn modification for project number from upload your data section

parent 12721cab
Expand all Hide whitespace changes
Inline Side-by-side
Rfunctions/Data_Management.R
View file @ 1341b3fc
......@@ -574,6 +574,7 @@ GetCountsMerge <- function(input,dataInput,taxoSelect,target,design)
normFactors = NULL
FeatureSize = NULL
CT_Norm = NULL
Error = NULL
## Counts and taxo tables
CT = dataInput$counts
......@@ -607,13 +608,15 @@ GetCountsMerge <- function(input,dataInput,taxoSelect,target,design)
CT=CT_int
} else CT = CT[,ind]
print("start order")
## Order CT according to the target
CT = OrderCounts(counts=CT,labels=labels)$CountsOrder
CT_noNorm = CT
RowProd = sum(apply(CT_noNorm,1,prod))
print("end order")
merged_table = merge(CT, taxo, by="row.names")
save(merged_table, file = "/tmp/wtf.rdata")
print("end merged")
CT = as.data.frame(merged_table[,2: (dim(CT)[2]+1)])
taxo = as.data.frame(merged_table[,(dim(CT)[2]+2):dim(merged_table)[2]])
......@@ -622,96 +625,99 @@ GetCountsMerge <- function(input,dataInput,taxoSelect,target,design)
colnames(taxo) = namesTaxo
#ordOTU = order(rownames(taxo))
counts_annot = CT
## Create the dds object
dds <- DESeqDataSetFromMatrix(countData=CT, colData=target, design=design,ignoreRank=TRUE)
#save(dds,file="testdds.RData")
if(is.null(VarNorm)){
## Counts normalisation
## Normalisation with or without 0
if(input$AccountForNA=="NonNull" || RowProd==0) dds = estimateSizeFactors(dds,locfunc=eval(as.name(input$locfunc)),geoMeans=GeoMeansCT(CT))
if(input$AccountForNA=="All" && RowProd!=0) dds = estimateSizeFactors(dds,locfunc=eval(as.name(input$locfunc)))
if(input$AccountForNA=="Weighted" && input$AccountForNA!="NonNull" ) {dds = estimateSizeFactors(dds,locfunc=eval(as.name(input$locfunc)),geoMeans=GeoMeansCT(CT)); sizeFactors(dds) = w.sizefactor(CT)}
if(input$AccountForNA=="Total counts") { sizeFactors(dds) = colSums(CT)/mean(colSums(CT))}
normFactors = sizeFactors(dds)
} else{
group = as.data.frame(target[,VarNorm])
group = apply(group,1,paste, collapse = "-")
normFactors = c()
mod = unique(group)
## At least 2 samples are needed for the normalization
if(min(table(group))>1){
for(i in unique(group))
{
indgrp = which(group==i)
CT_tmp = CT[,indgrp]
CT_tmp = removeNulCounts(CT_tmp)
target_tmp = data.frame(labels = rownames(target)[indgrp])
dds_tmp <- DESeqDataSetFromMatrix(countData=CT_tmp, colData=target_tmp, design=~labels,ignoreRank=TRUE)
if(input$AccountForNA=="NonNull") {dds_tmp = estimateSizeFactors(dds_tmp,locfunc=eval(as.name(input$locfunc)),geoMeans=GeoMeansCT(CT_tmp)); normFactors[indgrp] = sizeFactors(dds_tmp)}
if(input$AccountForNA=="All") {dds_tmp = estimateSizeFactors(dds_tmp,locfunc=eval(as.name(input$locfunc))); normFactors[indgrp] = sizeFactors(dds_tmp)}
if(input$AccountForNA=="Weighted" && input$AccountForNA!="NonNull" ) {dds_tmp = estimateSizeFactors(dds_tmp,locfunc=eval(as.name(input$locfunc)),geoMeans=GeoMeansCT(CT_tmp)); normFactors[indgrp] = w.sizefactor(CT_tmp)}
if(input$AccountForNA=="Total counts") { normFactors[indgrp] = colSums(CT_tmp)/mean(colSums(CT_tmp))}
}
} else{
if(0%in%colSums(counts_annot)){Error = "At least one of the column of the counts table is 0" }
else{
print("DDS start")
## Create the dds object
dds <- DESeqDataSetFromMatrix(countData=CT, colData=target, design=design,ignoreRank=TRUE)
print("DDS end")
#save(dds,file="testdds.RData")
if(is.null(VarNorm)){
## Counts normalisation
## Normalisation with or without 0
if(input$AccountForNA=="NonNull" || RowProd==0) dds = estimateSizeFactors(dds,locfunc=eval(as.name(input$locfunc)),geoMeans=GeoMeansCT(CT))
if(input$AccountForNA=="All" && RowProd!=0) dds = estimateSizeFactors(dds,locfunc=eval(as.name(input$locfunc)))
if(input$AccountForNA=="Weighted" && input$AccountForNA!="NonNull" ) {dds = estimateSizeFactors(dds,locfunc=eval(as.name(input$locfunc)),geoMeans=GeoMeansCT(CT)); sizeFactors(dds) = w.sizefactor(CT)}
if(input$AccountForNA=="Total counts") { sizeFactors(dds) = colSums(CT)/mean(colSums(CT))}
normFactors = sizeFactors(dds)
} else{
group = as.data.frame(target[,VarNorm])
group = apply(group,1,paste, collapse = "-")
normFactors = c()
mod = unique(group)
## At least 2 samples are needed for the normalization
if(min(table(group))>1){
for(i in unique(group))
{
indgrp = which(group==i)
CT_tmp = CT[,indgrp]
CT_tmp = removeNulCounts(CT_tmp)
target_tmp = data.frame(labels = rownames(target)[indgrp])
dds_tmp <- DESeqDataSetFromMatrix(countData=CT_tmp, colData=target_tmp, design=~labels,ignoreRank=TRUE)
if(input$AccountForNA=="NonNull") {dds_tmp = estimateSizeFactors(dds_tmp,locfunc=eval(as.name(input$locfunc)),geoMeans=GeoMeansCT(CT_tmp)); normFactors[indgrp] = sizeFactors(dds_tmp)}
if(input$AccountForNA=="All") {dds_tmp = estimateSizeFactors(dds_tmp,locfunc=eval(as.name(input$locfunc))); normFactors[indgrp] = sizeFactors(dds_tmp)}
if(input$AccountForNA=="Weighted" && input$AccountForNA!="NonNull" ) {dds_tmp = estimateSizeFactors(dds_tmp,locfunc=eval(as.name(input$locfunc)),geoMeans=GeoMeansCT(CT_tmp)); normFactors[indgrp] = w.sizefactor(CT_tmp)}
if(input$AccountForNA=="Total counts") { normFactors[indgrp] = colSums(CT_tmp)/mean(colSums(CT_tmp))}
}
} else{
if(input$AccountForNA=="NonNull" || RowProd==0) dds = estimateSizeFactors(dds,locfunc=eval(as.name(input$locfunc)),geoMeans=GeoMeansCT(CT))
if(input$AccountForNA=="All" && RowProd!=0) dds = estimateSizeFactors(dds,locfunc=eval(as.name(input$locfunc)))
if(input$AccountForNA=="Weighted" && input$AccountForNA!="NonNull" ) {dds = estimateSizeFactors(dds,locfunc=eval(as.name(input$locfunc)),geoMeans=GeoMeansCT(CT)); sizeFactors(dds) = w.sizefactor(CT)}
if(input$AccountForNA=="Total counts") { sizeFactors(dds) = colSums(CT)/mean(colSums(CT))}
normFactors = sizeFactors(dds)
}
sizeFactors(dds) = normFactors
}
sizeFactors(dds) = normFactors
}
## Keep normalized OTU table
CT_Norm = counts(dds, normalized=TRUE)
# Only interesting OTU
# merged_table = merge(CT, taxo[order(rownames(CT)),], by="row.names")
# merged_table = merge(CT, taxo, by="row.names")
# CT = as.data.frame(merged_table[,2: (dim(CT)[2]+1)])
# taxo = as.data.frame(merged_table[,(dim(CT)[2]+2):dim(merged_table)[2]])
#
# rownames(CT) = merged_table[,1]
# rownames(taxo) = merged_table[,1]
# #ordOTU = order(rownames(taxo))
# counts_annot = CT
# ordOTU = order(rownames(taxo))
# indOTU_annot = which(rownames(CT)%in%rownames(taxo))
# counts_annot = CT[indOTU_annot[ordOTU],]
## Aggregate matrix
if(taxoSelect=="OTU/Gene") counts = counts_annot
else{
if(input$TypeTable == "MGS" && input$FileFormat!="fileBiom"){
MGS_taxocol = which(toupper(colnames(taxo))%in%"MGS")
taxoS = taxo[,MGS_taxocol]
counts = aggregate(counts_annot,by=list(Taxonomy = taxoS),mean)
rownames(counts)=counts[,1]
counts=counts[,-1]
counts_int=t(apply(counts,1,as.integer))
rownames(counts_int)=rownames(counts)
colnames(counts_int)=colnames(counts)
counts=counts_int
}
if(taxoSelect != "MGS" || input$FileFormat=="fileBiom"){
#taxoS = taxo[ordOTU,taxoSelect]
taxoS = taxo[,taxoSelect]
counts = aggregate(counts_annot,by=list(Taxonomy = taxoS),sum)
rownames(counts)=counts[,1];counts=counts[,-1]
## Keep normalized OTU table
CT_Norm = counts(dds, normalized=TRUE)
# Only interesting OTU
# merged_table = merge(CT, taxo[order(rownames(CT)),], by="row.names")
# merged_table = merge(CT, taxo, by="row.names")
# CT = as.data.frame(merged_table[,2: (dim(CT)[2]+1)])
# taxo = as.data.frame(merged_table[,(dim(CT)[2]+2):dim(merged_table)[2]])
#
# rownames(CT) = merged_table[,1]
# rownames(taxo) = merged_table[,1]
# #ordOTU = order(rownames(taxo))
# counts_annot = CT
# ordOTU = order(rownames(taxo))
# indOTU_annot = which(rownames(CT)%in%rownames(taxo))
# counts_annot = CT[indOTU_annot[ordOTU],]
## Aggregate matrix
if(taxoSelect=="OTU/Gene") counts = counts_annot
else{
if(input$TypeTable == "MGS" && input$FileFormat!="fileBiom"){
MGS_taxocol = which(toupper(colnames(taxo))%in%"MGS")
taxoS = taxo[,MGS_taxocol]
counts = aggregate(counts_annot,by=list(Taxonomy = taxoS),mean)
rownames(counts)=counts[,1]
counts=counts[,-1]
counts_int=t(apply(counts,1,as.integer))
rownames(counts_int)=rownames(counts)
colnames(counts_int)=colnames(counts)
counts=counts_int
}
if(taxoSelect != "MGS" || input$FileFormat=="fileBiom"){
#taxoS = taxo[ordOTU,taxoSelect]
taxoS = taxo[,taxoSelect]
counts = aggregate(counts_annot,by=list(Taxonomy = taxoS),sum)
rownames(counts)=counts[,1];counts=counts[,-1]
}
}
## Ordering the counts table according to the target labels
tmpOrder = OrderCounts(counts,normFactors,labels)
counts = tmpOrder$CountsOrder
normFactors = tmpOrder$normFactorsOrder
CheckTarget = TRUE
}
## Ordering the counts table according to the target labels
tmpOrder = OrderCounts(counts,normFactors,labels)
counts = tmpOrder$CountsOrder
normFactors = tmpOrder$normFactorsOrder
CheckTarget = TRUE
}
return(list(counts=counts,CheckTarget=CheckTarget,normFactors=normFactors, CT_noNorm=CT_noNorm, CT_Norm =CT_Norm))
return(list(counts=counts,CheckTarget=CheckTarget,normFactors=normFactors, CT_noNorm=CT_noNorm, CT_Norm =CT_Norm, Error = Error))
#return(list(counts=counts,target=target[ind,],labeled=labeled,normFactors=normFactors, CT_noNorm=CT_noNorm))
}
......
server.R
View file @ 1341b3fc
This diff is collapsed.
ui.R
View file @ 1341b3fc
......@@ -109,8 +109,8 @@ body <- dashboardBody(
tabPanel("Introduction",
p("First check out our user guide:"),
tags$ul(
tags$li(a("User's guide", href="Userguide.pdf")),
tags$li(a("Writing a target file for the experimental design", href="experimental_design_guide.pdf"))
tags$li(a("User's guide",target="_blank", href="Userguide.pdf")),
tags$li(a("Writing a target file for the experimental design",target="_blank", href="experimental_design_guide.pdf"))
),
p(" You can test SHAMAN with the dataset from", a("[Tap et al. 2015]",href="http://www.ncbi.nlm.nih.gov/pubmed/26235304"),
", which is available", a("here",target="_blank",href="Alimintest.zip"),"."),
......@@ -487,10 +487,20 @@ body <- dashboardBody(
fluidRow(
box(title="Select your file format",width = 3,status = "success", solidHeader = TRUE,collapsible = FALSE,
# selectInput("FileFormat","",c("Count table & taxonomy (*.csv or *.tsv)"="fileCounts","BIOM file"="fileBiom","Saved project"="fileRData"),selected="fileCounts"),
selectInput("FileFormat","",c("Count table & taxonomy (*.csv or *.tsv)"="fileCounts","BIOM file"="fileBiom"),selected="fileCounts"),
selectInput("FileFormat","",c("Count table & taxonomy (*.csv or *.tsv)"="fileCounts","BIOM file"="fileBiom","Project number"="projnum"),selected="fileCounts"),
conditionalPanel(condition="input.FileFormat=='fileCounts'",
checkboxInput("NoTaxoFile","No taxonomy table",value=FALSE)
),
conditionalPanel(condition="input.FileFormat=='projnum'",
inlineCSS(list(.pwdGREEN = "background-color: #DDF0B3",.pwdRED = "background-color: #F0B2AD")),
textInput("password_home","Enter the key",value = NULL),
div(style = "text-align:right;",
actionButton("Check_project_home", "Check project number",icon=icon("check-circle")),
tags$style(type='text/css', "#Check_project_home {margin-top: 15px;}")
)
)
),
conditionalPanel(condition="input.FileFormat=='fileCounts'",
......@@ -527,18 +537,24 @@ body <- dashboardBody(
)
),
box(title="Load phylogenetic tree (optional)",width = 3, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = TRUE,
fileInput('fileTree', h6(strong('Select your file (tree)')),width="100%"),
tags$script('$( "#fileTree" ).on( "click", function() { this.value = null; });')
conditionalPanel(condition="input.FileFormat=='projnum'",
uiOutput("Project_box_home")
),
conditionalPanel(condition="input.FileFormat!='projnum'",
box(title="Load phylogenetic tree (optional)",width = 3, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = TRUE,
fileInput('fileTree', h6(strong('Select your file (tree)')),width="100%"),
tags$script('$( "#fileTree" ).on( "click", function() { this.value = null; });')
)
),
fluidRow(column(width=3,
uiOutput("InfoCountsFile"),
uiOutput("InfoTaxoFile"),
uiOutput("InfoBIOM")
)
)
)
),
column(id="tabboxdata_col",width=12,uiOutput("TabBoxData")),
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment