From e185aa2935aed9df88c8263c9938b8cc649aa3d0 Mon Sep 17 00:00:00 2001
From: marcelcosta <marcelcosta@mcosta.cat>
Date: Wed, 4 Oct 2023 15:25:28 +0200
Subject: [PATCH] Soporte para Modulos (Signaturas).

---
 scMonitor/app.R | 80 +++++++++++++++++++++++++++++++++++++++++++------
 1 file changed, 71 insertions(+), 9 deletions(-)

diff --git a/scMonitor/app.R b/scMonitor/app.R
index eb905b3..c0a776e 100644
--- a/scMonitor/app.R
+++ b/scMonitor/app.R
@@ -15,13 +15,19 @@ 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(
            plotOutput("umapPlot"),
-           uiOutput("featPlotUI")
+           uiOutput("featPlotUI"),
+           uiOutput("mod_featPlotUI"),
         )
     )
 )
@@ -30,6 +36,7 @@ ui <- fluidPage(
 server <- function(input, output) {
   dades<-reactiveValues()
   dades$seu<-NULL
+  dades$mods<-NULL
   
   volumes <- c(Home = fs::path_home(), "R Installation" = R.home(), getVolumes()())
   shinyFileChoose(input, 'file', roots=volumes)
@@ -52,10 +59,6 @@ server <- function(input, output) {
     }
   })
   
-  query<-eventReactive(input$goButton,{
-    dades$fet_query<-strsplit(input$features, " ")[[1]]
-  })
-  
   output$umapPlot <- renderPlot({
     observeEvent(dades$seu, {})
     if (!is.null(dades$seu)){
@@ -68,6 +71,18 @@ server <- function(input, output) {
     }
   })
 
+  query<-eventReactive(input$goButton,{
+    dades$fet_query<-strsplit(input$features, " ")[[1]]
+  })
+  
+  query_mod<-eventReactive(input$goButton,{
+    if (length(strsplit(input$mods, " ")[[1]]) > 0){
+      dades$mods<-paste(strsplit(input$mods, " ")[[1]], "1", sep="")
+    }else{
+      dades$mods<-NULL
+    }
+  })
+  
   output$featPlotUI<- renderUI({
     observeEvent(dades$fet_query, {})
     if (!is.null(dades$seu)){
@@ -77,15 +92,62 @@ server <- function(input, output) {
   })
   
   output$featPlot<-renderPlot({
-    observeEvent(dades$seu, {})
+    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))
+    }
+  })
+  
+  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$fet_query)&theme(aspect.ratio = 1)
+                  features = dades$mods)&theme(aspect.ratio = 1)
     }
   })
+  
 }
 
 # Run the application