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scMonitor/app.R

@@ -2,6 +2,8 @@ library(shiny)
 library(Seurat)
 library(shinyFiles)
 library(ggplot2)
+library(ggpubr)
+
 
 # Define UI for application
 ui <- fluidPage(
@@ -15,8 +17,13 @@ ui <- fluidPage(
           uiOutput('groupby'),
           uiOutput('facetby'),
           textInput('features', label = "Genes"),
+          textInput('mods', label = "Signatures"),
           actionButton("goButton", "Query"),
-          sliderInput("height", "Altura", min=1000, max=20000, step=1000, value=6000)
+          sliderInput("height", "Altura", min=1000, max=20000, step=1000, value=6000),
+          h3("Add Signature"),
+          textInput('mod_name', label = "Name"),
+          textInput('mod_feat', label = "Genes"),
+          actionButton("modButton", "Add Signature")
         ),
 
         mainPanel(
@@ -26,11 +33,15 @@ ui <- fluidPage(
     )
 )
 
-# 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)
   
@@ -40,6 +51,7 @@ 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)))
@@ -52,10 +64,7 @@ server <- function(input, output) {
     }
   })
   
-  query<-eventReactive(input$goButton,{
-    dades$fet_query<-strsplit(input$features, " ")[[1]]
-  })
-  
+  ## Render DimPlot
   output$umapPlot <- renderPlot({
     observeEvent(dades$seu, {})
     if (!is.null(dades$seu)){
@@ -67,7 +76,22 @@ 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$seu)){
@@ -75,17 +99,48 @@ server <- function(input, output) {
                  height = paste0(input$height/10,"px"))
     }
   })
-  
-  output$featPlot<-renderPlot({
-    observeEvent(dades$seu, {})
-    if (!is.null(dades$seu)){
-      query()
-      
-      FeaturePlot(dades$seu,
-                  split.by=if(input$facetby != "None"){input$facetby}else{NULL},
-                  features = dades$fet_query)&theme(aspect.ratio = 1)
+
+  ## ModulePlot/SigPlot construction
+  query_mod<-eventReactive(input$goButton,{
+    if (length(strsplit(input$mods, " ")[[1]]) > 0){
+      dades$mods<-paste(strsplit(input$mods, " ")[[1]], "1", sep="")
+    }else{
+      dades$mods<-NULL
     }
   })
+  
+  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$seu)){
+      query()
+      plot<-list()
+      print(dades$fet_query)
+      if (length(dades$fet_query) > 0){
+        plot[["Genes"]]<-FeaturePlot(dades$seu,
+                    split.by=if(input$facetby != "None"){input$facetby}else{NULL},
+                    features = dades$fet_query)&theme(aspect.ratio = 1)
+      }
+      query_mod()
+      print(dades$mods)
+      if (length(dades$mods) > 0){
+        plot[["Mods"]]<-FeaturePlot(dades$seu,
+                    split.by=if(input$facetby != "None"){input$facetby}else{NULL},
+                    features = dades$mods)&theme(aspect.ratio = 1)&scale_color_viridis_c()
+      }
+      do.call(ggarrange, c(plot, ncol=1))
+    }
+  })
+
+  
 }
 
 # Run the application