Remove input file, simplified table output and add some informations

shinyapps-virhostevol.io/helper.R

-
+#Modified msaplot function to deal with DGINN data formats
 dginn_msaplot <- function(p, fasta,dginn_position=NULL, offset=0, width=1, color=NULL, window=NULL, bg_line = TRUE, height = 0.8){
   if (missingArg(fasta)) {
     x <- NULL
@@ -87,12 +87,11 @@ dginn_msaplot <- function(p, fasta,dginn_position=NULL, offset=0, width=1, color
   })
   
   msa.df <- do.call("rbind", msa)
-  
   p <- p + geom_rect(aes(xmin=xmin, xmax=xmax,
                          ymin=ymin, ymax=ymax,
                          fill=seq),
                      data=msa.df, inherit.aes = FALSE) +
-    scale_fill_manual(values=c(NA,"lightgrey","red"))
+    scale_fill_manual(values=c("darkgrey","lightgrey","red"))
   
   breaks <- graphics::hist(seq_along(slice), breaks=10, plot=FALSE)$breaks
   pos <- start + breaks * width

shinyapps-virhostevol.io/server.R

@@ -7,19 +7,20 @@ shinyServer(
         # reactive function
         
         # 
-        # Taxonomy reactive
+        # DGINN reactive
         # 
         
         dginn_df_reactive <- reactive({
           
-            dginn_file <- input$dginn_file_tsv
+            dginn_file <- "../data/covid_comp_DGINNscreen.csv"
+            
             if (is.null(dginn_file)){
                 return(NULL)
             }
             else{
             colnames <- c("File","Name","Gene","Description","GeneSize","NbSpecies","omegaM0Bpp","omegaM0codeml","BUSTED","BUSTED_p-value","MEME_NbSites","MEME_PSS","BppM1M2","BppM1M2_p-value","BppM1M2_NbSites","BppM1M2_PSS","BppM7M8","BppM7M8_p-value","BppM7M8_NbSites","BppM7M8_PSS","codemlM1M2","codemlM1M2_p-value","codemlM1M2_NbSites","codemlM1M2_PSS","codemlM7M8","codemlM7M8_p-value","codemlM7M8_NbSites","codemlM7M8_PSS")
               
-            df <- read.csv2(dginn_file$datapath,sep=",")
+            df <- read.csv2(dginn_file,sep=",")
             
             #split primates and bat data
             df_primates <- df[,c(5,6,2,3,7:30)]
@@ -38,6 +39,10 @@ shinyServer(
             
         })
         
+        # 
+        # Tree data reactive
+        # 
+        
         tree_data_reactive <- reactive({
           
           selected <- input$dginn_data_rows_selected
@@ -52,19 +57,26 @@ shinyServer(
           
         })   
         
+        # 
+        # MSA data reactive
+        #    
+        
         msa_data_reactive <- reactive({
           selected <- input$dginn_data_rows_selected
           
           
           file=dginn_df_reactive()[selected,"File"]
+          species=dginn_df_reactive()[selected,"Name"]
           path="../data/"
           gene=dginn_df_reactive()[selected,"Gene"]
-          file_url=paste(path,file,sep="/")
-
-          read_file(paste(file_url,".fas",sep=""))
+          file_url=paste(path,species,file,sep="/")
+          
+          read_file(paste(file_url,".best.fas",sep=""))
           
         })
-
+        
+        # rendering functions
+        
         # renderDataTable -- DGINN data table 
         output$dginn_data <- DT::renderDataTable({
 
@@ -73,7 +85,10 @@ shinyServer(
 
             
         },
-        selection = 'single')
+        selection = 'single',        
+        rownames= FALSE,
+        options = list( columnDefs = list( list(targets = 0, visible = FALSE))),
+        )
         
         #renderPlotOutput -- ggTree + msa + summary 
         output$ggtree_plot <- renderPlot({
@@ -174,5 +189,6 @@ shinyServer(
           }
         )
         
-    })
+    }
+)
 

shinyapps-virhostevol.io/ui.R

 
 
 # Define UI for application that draws a histogram
-shinyUI(fluidPage(
+shinyUI(
+    fluidPage(
+        
     theme = shinytheme("cerulean"),
+    lang = "en",
     
     # Application title
-    titlePanel("VirHostEvol"),
+    titlePanel("VirHostEvol - Positive selection of the SARSCov-2 viral interaction proteins."),
     
     # Sidebar with a slider input for number of bins 
     sidebarLayout(
         sidebarPanel(
-            # Input: Select a file ----
-            fileInput("dginn_file_tsv", "Choose DGINN tab File",
-                      multiple = FALSE,
-                      accept = c("text/tsv",
-                                 "text/tabulated-separated-values,text/plain",
-                                 "tsv"))        
+            tags$div(class="header", checked=NA,
+                     HTML("Supplementary materials of the manuscript entitled <b>'Evolutionary history of SARS-CoV-2 interacting proteins in primates and bats reveals major host determinants, including TMPRSS2, FYCO1, RIPK1, and TBK1.'</b> by Cariou M. et <i>al.</i><br><br>Add other informatio stuff ..."),
+            )
             ),
         # Show a plot of the generated distribution
         mainPanel(
             tabsetPanel(type = "tabs",
                         
                         tabPanel("DGINN dataset",
+                                 tags$div(class="header", checked=NA,
+                                          HTML("This table highlights the sites under positive selection infered by BppM1M2, BppM7M8, codemlM1M2, codemlM7M8 models in either primates and bats lineages for SARSCov-2 Viral Interacting proteins<br><br><b>Please select a row</b> to visualise canidates sites on top of the phylogenetic tree and the simplified Multiple Sequence Alignment (lightgrey and darkgrey region of the MSA corresponds respectively to substitution and insertion) <br>At the bottom of the phylogenetic tree and msa you can download data by following the <b>.tree</b> and <b>.fas</b> hyperlinks. </br>Add other informatio stuff ...<br><br>"),
+                                 ),
                                  DT::dataTableOutput("dginn_data"),
                                  plotOutput("ggtree_plot",height = "800px")
 
@@ -30,5 +33,5 @@ shinyUI(fluidPage(
             )
         )
     )
-)
+    )
 )