- Possibilité de calculer les marqueurs s'ils n'ont pas déjà été pré-calculés...

- Possibilité de calculer les marqueurs s'ils n'ont pas déjà été pré-calculés (pour Heatmap et Genes)
- Ebauche de l'onglet Grid

app.R

@@ -10,7 +10,7 @@ library(plotly)
 library(BiocManager)
 library(shinydashboard)
 library(shinyjs)
-library(DT)          
+library(DT)              
 library(RColorBrewer) 
 library(MAST)     
 library(data.table)
@@ -36,6 +36,8 @@ header <- dashboardHeader(tags$li(class="dropdown",
                                                    tags$p(style="color:white;font-size:25px;margin-right:20px","- Compare -")),
                                   conditionalPanel(condition="input.tabs == 'pipeline_item'",
                                                    tags$p(style="color:white;font-size:25px;margin-right:20px","- Pipeline -")),
+                                  conditionalPanel(condition="input.tabs == 'grid_item'",
+                                                   tags$p(style="color:white;font-size:25px;margin-right:20px","- Grid -")),
                                   tags$head(HTML("<link rel='icon' href='min.png'>"))
 ))
 anchor <- tags$a(tags$img(src='logo.png', height='30', width='20'),'Shiny SChnurR', style="color: white")
@@ -55,6 +57,7 @@ sidebar <- dashboardSidebar(
               menuItem("Heatmap", tabName = "heatmap_item", icon=icon("fas fa-align-justify")),
               menuItem("Genes", tabName = "genes_item", icon=icon("dna")),
               menuItem("Compare", tabName="compare_item", icon = icon("table")),
+              menuItem("Grid", tabName="grid_item", icon = icon("fas fa-th")),
               menuItem("Pipeline", tabName="pipeline_item", icon = icon("fas fa-bezier-curve")),
               menuItem("About", tabName = "about_item", icon = icon("far fa-id-card"))
   ),
@@ -136,11 +139,27 @@ sidebar <- dashboardSidebar(
                             conditionalPanel(condition= "output.fileUploaded", align="center",
                                              radioButtons(inputId="graph", label= "Choose the graph mode :", c("t-SNE" = "tsne", "UMAP" = "umap")),
                                              checkboxInput(inputId="show_clusters", label="Clusters information", value=FALSE),
-                                             # checkboxInput(inputId="show_gene", label="Gene information", value=FALSE),
                                              sliderInput(inputId="ptsize", label="Point size :", min=0.1, max=2, step=0.1, value = 0.6, ticks = FALSE)
                             )
                      )
                    )
+  ),
+
+  # Grid Panel --------
+  conditionalPanel(condition="input.tabs=='grid_item'", align="center",
+                   fluidRow(
+                     column(1),
+                     column(10, h4(align="center", "Control Panel"),
+                            div(actionLink("help5", "", icon = icon("far fa-question-circle")), align="center"),
+                            verbatimTextOutput(outputId = "no_file5"),
+                            conditionalPanel(condition= "output.fileUploaded",align="center",
+                                             radioButtons(inputId="graph_grid", label= "Choose the graph mode :", c("t-SNE" = "tsne", "UMAP" = "umap")),
+                                             sliderInput(inputId="ptsize_grid", label="Point size :", min=0.1, max=2, step=0.1, value = 0.6, ticks = FALSE),
+                                             hr(),
+                                             selectizeInput(inputId="listminigenes", label="Choose a gene :", choices ="", multiple = TRUE)
+                            )
+                     )
+                   )
   )
 )
 
@@ -215,6 +234,14 @@ body <- dashboardBody(
                                       column(align="center",width=6, column(align="center", width=10, br(), dataTableOutput("onto_compare2")), column(align="align", width=2, uiOutput("topgenes2"),br(), uiOutput(align="align","dlontobutton_compare2") )))
             )
     ),
+    # Grid Item --------
+    tabItem(tabName="grid_item", align="left",
+            conditionalPanel(condition= "output.fileUploaded",
+                             br(), br(),
+                             plotOutput(outputId="minigenes", width="1400px", height="1400px")
+            )
+    ),
+    
     # Pipeline Item --------
     tabItem(tabName="pipeline_item", align="center", 
             br(),
@@ -274,6 +301,7 @@ server <- function(input, output, session) {
     genesList <- filedata$data@assays$SCT@data@Dimnames[1]
     updateSelectizeInput(session, "genes", choices = genesList[[1]], selected = "IGKC")
     updateSelectizeInput(session, "genes2", choices = genesList[[1]], selected = "IGKC")
+    updateSelectizeInput(session, "listminigenes", choices = genesList[[1]], selected = "IGKC")
     return(filedata$data)
     return(filedata$name)
   })
@@ -334,7 +362,6 @@ server <- function(input, output, session) {
     }
   })
   
-  
   miniplot_compareData <- reactive ({ # Mini Graph 1 Compare page
     withProgress(DimPlot(object = wrfile(), label=TRUE, pt.size = input$ptsize_compare, legend="none", reduction=input$graph_compare, group.by = input$fsel2, cols = as.character(eval(parse(text=paste0("alldf()$",input$fsel2,"$color"))) )), message = "Plot Generation", value=1)  + theme_bw() + theme(panel.grid.major=element_blank(),plot.title = element_text(size=12),panel.grid.minor=element_blank(),plot.background=element_blank()) + NoAxes() + NoLegend()
   })
@@ -443,6 +470,18 @@ server <- function(input, output, session) {
     }
   })
   
+  ## 9 Grid Genes Miniplots Generation & Outputs --------
+  
+  output$minigenes <- renderPlot({
+    req(wrfile())
+    plot(gridData())
+  })
+
+  gridData <- reactive ({ # Grid MiniGraph
+    withProgress(FeaturePlot(object = wrfile(),  cols=c("lightgrey",plasma(200)), pt.size = input$ptsize_grid, features = c(input$listminigenes), reduction = input$graph_grid), message = "Plot Generation", value=1) + theme_bw()+ NoLegend() + NoAxes() + theme(panel.grid.major=element_blank(),plot.title = element_text(size=12),panel.grid.minor=element_blank(),plot.background=element_blank())
+  })
+
+  
   ## Heatmap Generation & Output --------
   output$heat_numb <- renderUI ({
     sliderInput("top_number", label="Choose the number of top genes :", min=1, max=10, step=1, value=3)
@@ -450,7 +489,13 @@ server <- function(input, output, session) {
   heatmapData <- reactive ({
     req(input$goheatmap)
     if (is.null(wrfile()@misc$markers[[input$fsel3]])) { 
-      showModal(modalDialog("The markers may have not been calculated for this factor yet.", title=strong("Warning !"), easyClose=TRUE, footer = NULL )) 
+      showModal(modalDialog("The markers may have not been calculated for this factor yet.", title=strong("Warning !"), easyClose=TRUE, footer = NULL ))
+      tempfile <- wrfile()
+      Idents(tempfile) <- as.factor(paste0(eval(parse(text=paste0("tempfile@meta.data$",input$fsel3)))))
+      tempmarkers <- withProgress(FindAllMarkers(tempfile, assay = 'SCT', test.use = "MAST", only.pos = TRUE, min.pct = 0.25, logfc.threshold = 0.25), message = "Calculating all markers. This may take a while...", value=1)
+      topgenesfam <- tempmarkers %>% group_by(cluster) %>% top_n(n = input$top_number, wt = avg_logFC)
+      datascalefam <- withProgress(ScaleData(object = wrfile(), features = topgenesfam$gene), message = "Scaling data...", value=1)
+      withProgress(DoHeatmap(object = datascalefam, features = topgenesfam$gene, group.by=input$fsel3), message = "Heatmap Generation", value=1) + NoLegend() + ggtitle(paste(file_path_sans_ext(filedata$name),"- Heatmap -", input$fsel3,"- top",input$top_number,"genes")) + theme(plot.title = element_text(size=20))
     } else {
       topgenes <- wrfile()@misc$markers[[input$fsel3]] %>% group_by(cluster) %>% top_n(n = input$top_number, wt = avg_logFC)
       datascale <- withProgress(ScaleData(object = wrfile(), features = topgenes$gene), message = "Scaling data...", value=1)
@@ -469,8 +514,17 @@ server <- function(input, output, session) {
     }
   })
   egot <- reactive({
+    if (is.null(wrfile()@misc$markers[[input$fsel4]])) { 
+      showModal(modalDialog("The markers may have not been calculated for this factor yet.", title=strong("Warning !"), easyClose=TRUE, footer = NULL )) 
+      tempfile <- wrfile()
+      Idents(tempfile) <- as.factor(paste0(eval(parse(text=paste0("tempfile@meta.data$",input$fsel4)))))
+      tempmarkers <- withProgress(FindAllMarkers(tempfile, assay = 'SCT', test.use = "MAST", only.pos = TRUE, min.pct = 0.25, logfc.threshold = 0.25), message = "Calculating all markers. This may take a while...", value=1)
+      genes <- tempmarkers$cluster == input$group_genepage
+      genes <- tempmarkers$gene[genes]
+    } else {
     genes <- wrfile()@misc$markers[[input$fsel4]]$cluster == input$group_genepage
     genes <- wrfile()@misc$markers[[input$fsel4]]$gene[genes]
+    }
     genes <- bitr(genes, fromType = "SYMBOL",toType = "ENTREZID",OrgDb = org.Hs.eg.db,drop = TRUE)
     ego <- withProgress(enrichGO(gene = genes$ENTREZID, OrgDb = "org.Hs.eg.db", keyType= "ENTREZID", ont = input$ontology, readable = TRUE), value = 1, message = "Ontology in progress...")
     return(ego)
@@ -479,16 +533,12 @@ server <- function(input, output, session) {
   goplotData <- reactive ({ # Ontology Graph
     req(input$gogo)
     req(!is.null(input$group_genepage))
-    if (is.null(wrfile()@misc$markers[[input$fsel4]])) { 
-      showModal(modalDialog("The markers may have not been calculated for this factor yet.", title=strong("Warning !"), easyClose=TRUE, footer = NULL )) 
-    } else {
       if (input$gographtype == "dplot") {
         dotplot(egot()) + ggtitle(paste(file_path_sans_ext(filedata$name),"-",input$ontology,"-",input$fsel4)) + theme(panel.grid.major=element_blank(),plot.title = element_text(size=18),panel.grid.minor=element_blank(),plot.background=element_blank())
       } else if (input$gographtype == "bplot") {
         barplot(egot(), drop=TRUE) + ggtitle(paste(file_path_sans_ext(filedata$name),"-",input$ontology,"-",input$fsel4)) + theme(panel.grid.major=element_blank(),plot.title = element_text(size=18),panel.grid.minor=element_blank(),plot.background=element_blank())
       } else {
         emapplot(egot()) + ggtitle(paste(file_path_sans_ext(filedata$name),"-",input$ontology,"-",input$fsel4)) + theme(panel.grid.major=element_blank(),plot.title = element_text(size=18),panel.grid.minor=element_blank(),plot.background=element_blank())
-      }
     }
   })
   
@@ -717,6 +767,11 @@ server <- function(input, output, session) {
     req(is.null(input$file1))
     print("Please upload or \n choose a file")
   })
+  output$no_file5  <- renderText({
+    req(input$file =="")
+    req(is.null(input$file1))
+    print("Please upload or \n choose a file")
+  })
   
   
   ## Clusters + selection information text in visualization page --------
@@ -892,7 +947,10 @@ server <- function(input, output, session) {
                           The Heatmap is exportable in .png.", title=strong("Heatmap page Help"), easyClose=TRUE, footer = NULL )
     )
   })
-  
+  observeEvent (input$help5, { 
+    showModal(modalDialog("The Grid !", title=strong("Grid page Help"), easyClose=TRUE, footer = NULL )
+    )
+  })
   ## Compare Page - Barcodes data --------
   
   cbar1Data <- reactive ({