Visor scRNAseq.

BDAccess/app.R

@@ -1,5 +1,9 @@
 library(shiny)
 library(rhandsontable)
+library(tidyverse)
+library(reshape2)
+library(Matrix)
+library(CitFuns)
 
 print(getwd())
 source("../sqlFunctions.R", encoding = "UTF-8")
@@ -59,6 +63,19 @@ ui <- fluidPage(
                 h3("Nitrogen"),
                 tableOutput("nitrogen")
             )
+        ),
+        tabPanel("scRNAseq",
+                 sidebarPanel(
+                     textInput("sqlquery", label = "sqlquery", value = ""),
+                     uiOutput("PATID"),
+                     checkboxInput("cd45_chk", "Purificación CD45")
+                 ),
+                 mainPanel(
+                     tabsetPanel(
+                         tabPanel("Table", tableOutput("sc_table")),
+                         tabPanel("Plots", plotOutput("sc_plot"))
+                     )
+                 )
         )
     )
 )
@@ -677,6 +694,56 @@ server <- function(input, output) {
     
     ## scRNAseq
     
+    output$PATID = renderUI({
+        observeEvent(input$goButton, {})
+        sc_cod<-sqlFetch(dta, "CNAG") %>% pull(CODIGO)
+        selectizeInput("sc_cod", "CÓDIGO", sc_cod, multiple = T)
+    })
+    
+    output$sc_table<-renderTable({
+        if (input$sqlquery != ""){
+            print(input$sqlquery)
+            sqlQuery(dta, input$sqlquery)
+        }else{
+            if (!is.null(input$sc_cod)){
+                sqlFetch(dta, "CNAG") %>% filter(CODIGO %in% input$sc_cod)
+            }else{
+                sqlFetch(dta, "CNAG")
+            }
+        }
+    })
+    
+    output$sc_plot <-renderPlot({
+        meta<-readRDS(paste0(scRNAseqRoute,"metadata_full_object.rds"))
+        
+        if (input$sqlquery != ""){
+            sc_codigos<-sqlQuery(dta, input$sqlquery) %>% pull(CNAG_NAME)
+        }else{
+            if (!is.null(input$sc_cod)){
+                sc_codigos<-sqlFetch(dta, "CNAG") %>% filter(CODIGO %in% input$sc_cod) %>% pull(CNAG_NAME)
+            }else{
+                sc_codigos<-sqlFetch(dta, "CNAG") %>% pull(CNAG_NAME)
+            }
+        }
+        sc_codigos<-gsub(" _","_", sc_codigos )
+        sc_codigos<-gsub("_ ","_", sc_codigos )
+        sc_codigos<-gsub(" ","_", sc_codigos )
+        
+        meta<-meta %>% mutate(sample2=gsub("_CD45", "", sample)) %>% filter(sample2 %in% sc_codigos)
+        if (isFALSE(input$cd45_chk)){ meta<-meta %>% filter(!grepl("_CD45", sample))}
+        
+        g1<-ggplot(meta, aes(coord_x, coord_y, color=predicted.id))+
+            geom_point(size=0.2)+
+            guides(colour = guide_legend(override.aes = list(size=2)))+
+            theme_bw()+
+            theme(aspect.ratio = 1)
+        
+        meta_perc<-meta %>% group_by(sample, predicted.id) %>% summarise(N=n()) %>% mutate(N=perc(N)) %>% 
+            spread(predicted.id, N) %>% gather("predicted.id","N",-sample) %>% mutate(N=case_when(is.na(N)~0,TRUE~N))
+        g2<-ggheatmap(meta_perc, "sample","predicted.id", "N", color = "grey50")
+        ggpubr::ggarrange(g1,g2, ncol=1, heights = c(0.3, 0.7))
+    }, height = 1000)
+
 }
 
 # Run the application