From 568fef38ae98a941794dffaf705befa3587300f7 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Sun, 11 Dec 2022 19:26:29 +0000
Subject: [PATCH] aaaaaaa

---
 tb_host/app.R | 131 ++++++++++++++++++++++++++++++++++++++++++++------
 1 file changed, 115 insertions(+), 16 deletions(-)

diff --git a/tb_host/app.R b/tb_host/app.R
index 05d98b8..b114665 100644
--- a/tb_host/app.R
+++ b/tb_host/app.R
@@ -52,23 +52,34 @@ ui=dashboardPage(skin="purple",
                                 selected="alr" # "alr" is a value
                    ),
                    actionButton("clear_ngl",
-                                "Clear Structures")
-                   
+                                "Reset Structures"),
+                   actionButton("all_mutations",
+                                "All Mutations")
                  ),
                  dashboardBody(
                    useShinyjs(),
                    fluidRow(
                      box(
                        title="Crystallised Structure",
+                       width=5,
                        column(
                          NGLVieweROutput("structure"),
                          width=12
+                       ) 
+                     ),
+                     box(
+                       title="AlphaFold Structure",
+                       width=5,
+                       column(
+                         NGLVieweROutput("af_structure"),
+                         width=12
                        )
                      ),
                      box(
-                       title="AlphaFold Structure",
+                       title="Mutation Information",
+                       width=2,
                        column(
-                         NGLVieweROutput("af_structure"),
+                         htmlOutput("information"),
                          width=12
                        )
                      )
@@ -104,8 +115,8 @@ server <- function(input, output) {
     NGLVieweR(ngl_gene) %>%
       addRepresentation("cartoon",
                         param = list(name = "cartoon",
-                                     #color="tan"
-                                     colorScheme = "bfactor",
+                                     color="tan",
+                                     #colorScheme = "bfactor",
                                      opacity = 1
                         )
       ) %>%
@@ -155,6 +166,7 @@ server <- function(input, output) {
   observeEvent(input$table_rows_selected,{
     #req(length(input$table_row_selected) > 0)
     mutation = as.character(unique_missense_genes[input$table_rows_selected,"hgvd_p"])
+    chain = as.character(unique_missense_genes[input$table_rows_selected,"chain"])
     # what the absolute FUCK is this mess? I JUST WANT THE MATCH ASDLASJASDASHFKLJASDFK
     # coming down from the trees was a mistake, and abandoning Perl doubly so.
     clicked_position = regmatches(mutation, regexpr("[0-9]+", mutation, perl=TRUE))
@@ -163,22 +175,22 @@ server <- function(input, output) {
     
     NGLVieweR_proxy("structure") %>%
       #addSelection('ball+stick'
-      addSelection('ball+stick'
+      addSelection('spacefill'
                    , param = list(
                      name = "Pos"
-                     , sele = clicked_position
-                     , color = "green"
+                     , sele = trimws(paste0(clicked_position,':', chain))
+                     , color = "red"
                      #, colorValue="00ff00"
                      #, colorScheme="element"
                    )
       )
     NGLVieweR_proxy("af_structure") %>%
       #addSelection('ball+stick'
-      addSelection('ball+stick'
+      addSelection('spacefill'
                    , param = list(
                      name = "Pos"
                      , sele = clicked_position
-                     , color = "green"
+                     , color = "red"
                      #, colorValue="00ff00"
                      #, colorScheme="element"
                    )
@@ -191,12 +203,37 @@ server <- function(input, output) {
       z_offSet = -1
     )
     NGLVieweR_proxy("structure") %>% updateZoomMove(
-      center = clicked_position,
-      zoom = clicked_position,
+      center = trimws(paste0(clicked_position,':', chain)),
+      zoom = trimws(paste0(clicked_position,':', chain)),
       duration = 1000, # animation time in ms
       z_offSet = -1
     )
-    
+    output$information <- renderUI({
+      selected_gene=input$gene
+      HTML(paste0("<strong>Mutation: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"mutationinformation"]),"<br/>",
+                  "<strong>PDB ID: </strong>", as.character(genes[genes$Gene==selected_gene,"PDB"]),"<br/>",
+                  "<strong>AlphaFold ID: </strong>", as.character(genes[genes$Gene==selected_gene,"AF_PDB"]), "<br/>",
+                  "<strong>Ligand Distance: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"ligand_distance"]), "<br/>",
+                  "<strong>mCSM Lig: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"mcsm_lig"]), "<br/>",
+                  "<strong>mmCSM Lig: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"mmcsm_lig"]), "<br/>",
+                  "<strong>mCSM DUET: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"ddg_duet"]), "<br/>",
+                  "<strong>FoldX: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"ddg_foldx"]), "<br/>",
+                  "<strong>DeepDDG: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"ddg_deepddg"]), "<br/>",
+                  "<strong>Dynamut2: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"ddg_dynamut2"]), "<br/>",
+                  "<strong>mCSM PPI2: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"mcsm_ppi2_affinity"]), "<br/>",
+                  "<strong>Interface Distance: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"interface_dist"]), "<br/>",
+                  "<strong>mCSM NA: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"mcsm_na_affinity"]), "<br/>",
+                  "<strong>Consurf: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"consurf_score"]), "<br/>",
+                  #"<strong>SNAP2: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"snap2_score"]), "<br/>",
+                  "<strong>SNAP2 Outcome: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"snap2_outcome"]), "<br/>",
+                  #"<strong>PROVEAN: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"provean_score"]), "<br/>",
+                  "<strong>PROVEAN Outcome: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"provean_outcome"]), "<br/>",
+                  "<strong>RSA: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"rsa"]), "<br/>",
+                  "<strong>Residue Depth: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"rd_values"]), "<br/>"
+      )
+      )
+      
+    })
     
     # output$debug <- renderPrint({
     #   print(c(mutation, clicked_position))
@@ -207,9 +244,71 @@ server <- function(input, output) {
       input$clear_ngl
     }, {
       NGLVieweR_proxy("structure") %>%
-        removeSelection("Pos")
+        removeSelection("Pos") %>%
+        removeSelection("all_mutations_surface") %>%
+        updateVisibility("cartoon", TRUE) %>%
+        removeSelection("all_mutations")
       NGLVieweR_proxy("af_structure") %>%
-        removeSelection("Pos")
+        removeSelection("Pos") %>%
+        removeSelection("all_mutations_surface") %>%
+        updateVisibility("cartoon", TRUE) %>%
+        removeSelection("all_mutations")
+    })
+  # add a surface representation and highlight all mutations on it
+  observeEvent(
+    {
+      input$all_mutations
+    }, {
+      gene = input$gene
+      mutations = paste0(
+        apply(
+          unique_missense_genes[unique_missense_genes$gene_name == gene,c("position","chain")],
+          1,
+          function(x){
+            paste0(trimws(x[1]),
+                   ":",
+                   trimws(x[2])
+            )}
+        ),
+        collapse=","
+      )
+      print(mutations)
+      
+      
+      NGLVieweR_proxy("structure") %>%
+        updateVisibility("cartoon", FALSE) %>%
+        addSelection(type="surface",
+                     param = list(name = "all_mutations_surface",
+                                  sele = "all",
+                                  color="tan",
+                                  opacity = 0.2
+                     )
+        ) %>%
+        addSelection(type="surface",
+                     param = list(name = "all_mutations",
+                                  color="green",
+                                  sele = "20:A, 22:A, 157:A"
+                                  #colorScheme = "bfactor",
+                                  #opacity = 1
+                     )
+        )
+      # addSelection('spacefill',
+      #              param = list(
+      #                name = "Pos",
+      #                sele = "4:A,20:A,22:A,157:A,344:A",
+      #                color = "red",
+      #                opacity=0.1
+      #              )
+      # )
+      # NGLVieweR_proxy("af_structure") %>%
+      #   addSelection('ball+stick',
+      #                param = list(
+      #                  name = "Pos",
+      #                  sele = mutations,
+      #                  color = "red",
+      #                  opacity=0.1
+      #                )
+      #   )
     })
   
 }