Add multiqc to vizapp

vizapp/global.R

@@ -11,6 +11,6 @@ setwd("../")
 source("./vizapp/functions.R")
   
 #load data
-dir.shared <- "/work/BICF/s189701/cellranger_count/workflow/output/count310/"
+dir.shared <- "workflow/output/count310/"
 samples <- list.dirs(dir.shared,full.names=FALSE,recursive=FALSE)
 results <- LoadData(dim=c("umap","tsne","pca"),dir=dir.shared,samp=samples[1])

vizapp/server.R

@@ -104,17 +104,8 @@ shinyServer(function(input,output,session){
   })
   output$nav.qc <- renderUI({
     req(values$results()$sample)
-    tabPanel("Output",
-      sidebarPanel(
-        h3(textOutput("lab.sample.qc")),
-        h4(textOutput("lab.cell.count")),
-        br(),
-        tableOutput("qc")
-      ),
-      mainPanel(
-        plotOutput("plot.cliffknee")
-      )
-    )
+    xml2::write_html(rvest::html_node(xml2::read_html(Sys.glob("workflow/output/multiqc/*/multiqc_report.html")), "body"), file = "workflow/output/multiqc/multiqc_report_vizapp.html")
+    includeHTML("workflow/output/multiqc/multiqc_report_vizapp.html")
   })
   
   #sidebar input/outputs