added download data for per cell expressions

vizapp/shinyapp/server.R

@@ -9,7 +9,7 @@ library(data.table)
 source("./functions/SeuratObjectFunctions.R")
 source("./functions/my_ui.R")
 
-astrocyte_flag<-T #Set to true if running on Astrocyte, else, set to false
+astrocyte_flag<-F #Set to true if running on Astrocyte, else, set to false
 # Determines the location where data gets read from
 # If it is set to FALSE, then data is read from the ./data/ folder
 # If it is set to TRUE, then data is read from the rootdir provided by Astrocyte 
@@ -1001,6 +1001,63 @@ server <- function(input, output, session) {
     list(out, all_out)
     })
 
+  single_cell_data <- reactive({
+
+    if (length(input$clusters)==0){my_clust="none"}
+    else {my_clust=input$clusters}
+    
+    if(length(input$samples)==0){my_samp="none"}
+    else{my_samp=input$samples}
+    
+    if (input$subset==c("csv")){
+        seuratObject=subsetSeuratObject(seuratObject=samples.integrated,
+            cellFile=input$subset_csv$datapath)
+    }
+    if (input$subset==c("manual")){
+        seuratObject=subsetSeuratObject(seuratObject=samples.integrated,
+            selectedClusters=my_clust,
+            selectedSamples=my_samp)
+    }
+    if (input$subset==c("none")) 
+    {seuratObject = subsetSeuratObject(seuratObject=samples.integrated,
+        selectedClusters = 'none',
+        selectedSamples = 'none')}
+
+        if (input$score_genes == T) {
+            seuratObject=seuratObject$seuratObject
+            if (input$log==F) {
+              seuratObject=NormalizeData(seuratObject,verbose=F,normalization.method='RC')
+            }
+            infoList=getInfo(seuratObject,T)
+            signatures<-read.csv(input$g_score$datapath,sep=',',header=T)
+            temp=AddModuleScore(seuratObject,signatures,search=F)
+            g=dim(signatures)[2]
+            n=dim(temp@meta.data)[2]
+            colnames(temp@meta.data)[(n-g+1):n]=colnames(signatures)
+            gene_list=input$signature
+            if (input$phasing == T){
+              temp@meta.data[,c('orig.ident','idents','Phase',gene_list)]
+            }
+            else {
+              temp@meta.data[,c('orig.ident','idents',gene_list)]
+            }
+        }
+        else {
+            seuratObject=seuratObject$seuratObject
+            if (input$log==F) {
+              seuratObject=NormalizeData(seuratObject,verbose=F,normalization.method='RC')
+            }
+            gene_list=input$features
+            temp<-seuratObject@assays$RNA$data[gene_list,] %>% as.matrix() %>% t()
+            if (input$phasing == T){
+              data.frame(seuratObject@meta.data[,c('orig.ident','idents','Phase')],temp,check.rows=F)
+            }
+            else {
+              data.frame(seuratObject@meta.data[,c('orig.ident','idents')],temp,check.rows=F)
+            }
+        }
+    })
+
   percent_expression_table <- reactive({ 
     phasing=input$phasing
     group.by=input$group
@@ -1669,6 +1726,13 @@ server <- function(input, output, session) {
         }
       )
 
+    output$download_single_cell_data <- downloadHandler(
+    filename = function() { paste('Single_Cell_Data', '.csv', sep='') },
+    content = function(file) {
+        write.csv(single_cell_data(),file=file)
+    }
+    )
+
   output$download_DE <- downloadHandler(
       filename = function() { paste0(runDE()[[4]],"_vs_",runDE()[[5]],'_DE_Genes.zip', sep='') },
       content = function(file) {

vizapp/shinyapp/ui.R

@@ -149,7 +149,10 @@ ui <- fluidPage(
 								column(12, 
 									downloadButton("download_data_table",
 										"Download Expression Data")
-									)
+									),
+								column(12, 
+								downloadButton("download_single_cell_data",
+									"Download Single Cell Data"))
 								# column(12, 
 								# 	downloadButton("download_percent_expression",
 								# 		"Download Percent Expression Data"))