bug dataset 1 & sampleAnnot loading

server_function/SERVER_Data_Upload.R

@@ -9,7 +9,7 @@
 
 # Data Upload
 
-sampleAnnot <- reactive({
+sampleAnnot <- eventReactive(input$goPrevalence, {
   if (input$LoadExample == "Example1"){
     sampleMetadata<-"data/data_breast/clinical.csv" #sample sheet path
     sampleAnnot <- read.csv(sampleMetadata, sep = ",", header = TRUE, row.names = 1)
@@ -88,7 +88,7 @@ sampleAnnot <- reactive({
   sampleAnnot <- sampleAnnot[order(rownames(sampleAnnot)),]
   
   sampleAnnot
-})
+}, ignoreNULL = FALSE, ignoreInit = FALSE)
 
 
 sampleName <- reactive({
@@ -103,7 +103,7 @@ sampleAnnot1 <- reactive({
 
 # Data Upload
 
-exprDat <- reactive({
+exprDat <- eventReactive(input$goPrevalence, {
   if (input$LoadExample == "Example1"){
     expressionData<-"data/data_breast/mirna.csv" #expression file path
     exprDat <- read.csv(expressionData, sep = ",", header = TRUE, row.names = 1)
@@ -165,12 +165,6 @@ exprDat <- reactive({
   }
   rownames(exprDat) <- sampleID
   
-  exprDat
-})
-
-### ExprDat after filtration, normalization and transformation
-exprDat_advanced <- eventReactive(input$goPrevalence, {
-  exprDat <- exprDat()
   ### SELECTED FILTRATION
   if (input$Filtration == "Yes"){
     if (input$TypeFiltration == "prevalence"){
@@ -270,14 +264,18 @@ exprDat_advanced <- eventReactive(input$goPrevalence, {
   
   
   exprDat <- exprDat[order(rownames(exprDat)),]
+  
   exprDat
-}, ignoreNULL = FALSE)
+}, ignoreNULL = FALSE, ignoreInit = FALSE)
+
+
+
 
 exprDat_present <- reactive({
   if (input$LoadExample == "Example1" || input$LoadExample == "Example2"){
-    exprDat_present <- exprDat_advanced()
+    exprDat_present <- exprDat()
   }else{
-    exprDat_present <- exprDat_advanced()     
+    exprDat_present <- exprDat()     
   }
   # if (nchar(colnames(exprDat_present)[1]) > 20 ){
   #   for (i in 1:ncol(exprDat_present)){
@@ -288,7 +286,7 @@ exprDat_present <- reactive({
 })
 
 
-exprDatSec <- eventReactive(input$goPrevalence1,{
+exprDatSec <- eventReactive(input$goPrevalence1, {
   if (input$TypeAnalysis == "multivariate"){
     if (input$LoadExample == "Example1"){
       expressionData<-"data/data_breast/mrna.csv" #expression file path
@@ -804,8 +802,8 @@ taxTable_rownames <- reactive({
 
 
 exprDat_2 <- reactive({
-  expr <- exprDat_advanced()
-  annot <- sampleAnnot1()
+  expr <- exprDat()
+  annot <- sampleAnnot()
   exprDat1 <- expr
   
   if (any(rownames(annot) %!in% rownames(expr)) == TRUE ){
@@ -824,7 +822,7 @@ exprDat_2 <- reactive({
 
 
 sampleAnnot_2 <- reactive({
-  annot <- sampleAnnot1()
+  annot <- sampleAnnot()
   if (any(rownames(exprDat_2()) %!in% rownames(annot)) == TRUE ){
     exprDat1 <- exprDat2()[which(rownames(exprDat_2() ) %in% rownames(annot ) ),]
   }else{
@@ -839,7 +837,7 @@ sampleAnnot_2 <- reactive({
 })
 
 sampleAnnot_WGCNA <- reactive({
-  sampleAnnot <- sampleAnnot1()[which(rownames(sampleAnnot1()) %in% rownames(exprDat_2())),]
+  sampleAnnot <- sampleAnnot()[which(rownames(sampleAnnot()) %in% rownames(exprDat_2())),]
   sampleAnnot <- sampleAnnot[match(rownames(sampleAnnot), rownames(exprDat_2())),]
   sampleAnnot
 })