From 0ab9d7478ae97a879226d157f85416a4ad74104e Mon Sep 17 00:00:00 2001
From: erzakiev <e.r.zakiev@gmail.com>
Date: Thu, 2 Nov 2023 11:20:14 +0100
Subject: [PATCH] Adding the cerebro exporting functionality

---
 src/Shiva/Export_module.R | 48 +++++++++++++++++++++++++++++++++++++--
 src/Shiva/global.R        |  1 +
 src/dockerfile            |  1 +
 3 files changed, 48 insertions(+), 2 deletions(-)

diff --git a/src/Shiva/Export_module.R b/src/Shiva/Export_module.R
index 9b19fee..07d66b3 100644
--- a/src/Shiva/Export_module.R
+++ b/src/Shiva/Export_module.R
@@ -12,7 +12,7 @@ ExportUI <- function(id) {
             width = 6, height = NULL,  
             solidHeader = TRUE, status = "primary", 
             radioButtons(ns("type_export"), label = "Choose the Type of Data to Export",
-                         c("Seurat Object RDS File" = "seurat", "List of Genes" = "genes", "List of Cells" = "cells"), inline = T),
+                         c("Seurat Object RDS File" = "seurat", "Cerebro .crb file" = "Cerebro", "List of Genes" = "genes", "List of Cells" = "cells"), inline = T),
             uiOutput(ns("select_export")),
             uiOutput(ns("button_export"))
             #Asif
@@ -64,6 +64,18 @@ Export <- function(input, output, session, rval) {
     
   })
   
+  getCerebro <- reactive({
+    
+    if(length(rval$seurat_list) > 0){
+      
+      seu <- rval$seurat_list
+      
+      return(seu)
+      
+    }
+    
+  })
+  
   
   
   
@@ -131,6 +143,11 @@ Export <- function(input, output, session, rval) {
         selectInput(ns("select"), "Select", getCellsList(), selected = tail(getCellsList(),1), 
                     multiple = F, selectize = T)
         
+        }else if(input$type_export == "Cerebro"){
+          
+          selectInput(ns("select"), "Select", getCerebro(), selected = tail(getCerebro(),1), 
+                      multiple = F, selectize = T)
+          
         }
       }
       
@@ -164,7 +181,9 @@ Export <- function(input, output, session, rval) {
       
       if(input$type_export == "seurat"){
         paste(input$select, ".rds", sep = "")
-      }else{
+      } else if (input$type_export == "Cerebro") {
+        paste(input$select, ".crb", sep = "")
+      } else{
         paste(input$select, ".csv", sep = "")
       }
       
@@ -239,6 +258,31 @@ Export <- function(input, output, session, rval) {
         # Close modal progress when csv is saved
         remove_modal_spinner()
         
+      } else if(input$type_export == "Cerebro"){
+        
+        # Create modal progress during csv creation and saving
+        show_modal_spinner(text = 'Creating a Cerebro file... Please wait...', spin = 'circle')
+        
+        if(input$select == rval$seurat_selected){
+          
+          exportFromSeurat(object = rval$seurat, groups = c('orig.ident', 'seurat_clusters'), nUMI = "nCount_RNA", nGene = "nFeature_RNA", experiment_name = "exportFromShIVA", organism = "mouse", file = "CerebroExportFromShiva.crb")
+          
+        }else{
+          
+          for(seu in rval$seurat_list){
+            
+            if(seu == input$select){
+              
+              saveRDS(readRDS(paste0(rval$output,"/",seu,".rds")), file)
+              
+            }
+            
+          }
+          
+        }
+        
+        # Close modal progress when csv is saved
+        
       }
     }
   )
diff --git a/src/Shiva/global.R b/src/Shiva/global.R
index 854dbf2..d2f6614 100644
--- a/src/Shiva/global.R
+++ b/src/Shiva/global.R
@@ -26,6 +26,7 @@ library(kableExtra)
 library(org.Mm.eg.db)
 library(clusterProfiler)
 library(org.Hs.eg.db)
+library(cerebroApp)
 
 options(shiny.maxRequestSize = 1000 * 1024^10)
 
diff --git a/src/dockerfile b/src/dockerfile
index 39fe37f..4205201 100644
--- a/src/dockerfile
+++ b/src/dockerfile
@@ -67,6 +67,7 @@ RUN R -e 'install.packages( "viridis")'
 
 RUN R -e 'library(devtools);devtools::install_github("JinmiaoChenLab/Rphenograph")'
 RUN R -e 'library(devtools);devtools::install_github("JinmiaoChenLab/ClusterX")'
+RUN R -e 'library(devtools);devtools::install_github("romanhaa/cerebroApp")'
 
 RUN R -e 'BiocManager::install("flowCore")'
 RUN R -e 'BiocManager::install("openCyto")'