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scMonitor/app.R

@@ -26,18 +26,20 @@ ui <- fluidPage(
 
         mainPanel(
            plotOutput("umapPlot"),
-           uiOutput("featPlotUI"),
-           uiOutput("mod_featPlotUI"),
+           uiOutput("featPlotUI")
         )
     )
 )
 
-# Define server logic required to draw a histogram
+# Define server logic
 server <- function(input, output) {
+  
+  ## Defining reactive values
   dades<-reactiveValues()
   dades$seu<-NULL
   dades$mods<-NULL
   
+  ## Conecting with file location and entering Seurat object
   volumes <- c(Home = fs::path_home(), "R Installation" = R.home(), getVolumes()())
   shinyFileChoose(input, 'file', roots=volumes)
   
@@ -47,6 +49,7 @@ server <- function(input, output) {
     }
   })
   
+  ## Rendering UI depending on seu meta.data
   output$groupby<-renderUI({
     if (!is.null(dades$seu)){
       selectInput("groupby", "GroupBy", c("Default", colnames(dades$seu@meta.data)))
@@ -59,6 +62,7 @@ server <- function(input, output) {
     }
   })
   
+  ## Render DimPlot
   output$umapPlot <- renderPlot({
     observeEvent(dades$seu, {})
     if (!is.null(dades$seu)){
@@ -70,11 +74,31 @@ server <- function(input, output) {
     plot
     }
   })
-
+  
+  ## Signature - Module Definition
+  observeEvent(input$modButton, {
+    if (input$modButton > 0){
+      mod_list<-strsplit(input$mod_feat, " ")[[1]]
+      mod_list<-mod_list[mod_list %in% rownames(dades$seu)]
+      dades$seu<-AddModuleScore(dades$seu,list(mod_list),
+                                name=input$mod_name)
+    }
+  })
+  
+  ## FeaturePlot construction
   query<-eventReactive(input$goButton,{
     dades$fet_query<-strsplit(input$features, " ")[[1]]
   })
   
+  output$featPlotUI<- renderUI({
+    observeEvent(dades$fet_query, {})
+    if (!is.null(dades$seu)){
+      plotOutput("featPlot", 
+                 height = paste0(input$height/10,"px"))
+    }
+  })
+
+  ## ModulePlot/SigPlot construction
   query_mod<-eventReactive(input$goButton,{
     if (length(strsplit(input$mods, " ")[[1]]) > 0){
       dades$mods<-paste(strsplit(input$mods, " ")[[1]], "1", sep="")
@@ -83,14 +107,15 @@ server <- function(input, output) {
     }
   })
   
-  output$featPlotUI<- renderUI({
-    observeEvent(dades$fet_query, {})
-    if (!is.null(dades$seu)){
-      plotOutput("featPlot", 
+  output$modPlotUI<- renderUI({
+    observeEvent(dades$mod_name, {})
+    if (!is.null(dades$mod_name)){
+      plotOutput("modPlot",
                  height = paste0(input$height/10,"px"))
     }
   })
   
+  ## Feature/Mod plot rendering
   output$featPlot<-renderPlot({
     observeEvent(input$goButton, {})
     if (!is.null(dades$seu)){
@@ -112,41 +137,7 @@ server <- function(input, output) {
       do.call(ggarrange, c(plot, ncol=1))
     }
   })
-  
-  observeEvent(input$modButton, {
-    if (input$modButton > 0){
-      mod_list<-strsplit(input$mod_feat, " ")[[1]]
-      mod_list<-mod_list[mod_list %in% rownames(dades$seu)]
-      dades$seu<-AddModuleScore(dades$seu,list(mod_list),
-                                name=input$mod_name)
-    }
-  })
-  
-  # query_mod<-eventReactive(input$modButton,{
-  #   dades$seu<-AddModuleScore(dades$seu,strsplit(input$mod_feat, " ")[[1]],
-  #                             name=input$mod_name)
-  #   dades$mods<-if(is.null(dades$mods)){input$mod_name}else{c(dades$mods, input$mod_name)}
-  #   print(input$mod_name)
-  # })
-  
-  output$modPlotUI<- renderUI({
-    observeEvent(dades$mod_name, {})
-    if (!is.null(dades$mod_name)){
-      plotOutput("modPlot",
-                 height = paste0(input$height/10,"px"))
-    }
-  })
 
-  output$modPlot<-renderPlot({
-    # observeEvent(dades$seu, {})
-    input$goButton
-    if (input$mods){
-      print(dades$mods)
-      FeaturePlot(dades$seu,
-                  split.by=if(input$facetby != "None"){input$facetby}else{NULL},
-                  features = dades$mods)&theme(aspect.ratio = 1)
-    }
-  })
   
 }