From a0866a136ab812fee90bed4c65d0fd9b361e0582 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Sun, 11 Dec 2022 19:47:38 +0000
Subject: [PATCH] aaaaaaa

---
 tb_host/app.R | 63 ++++++++++++++++++++++++++-------------------------
 1 file changed, 32 insertions(+), 31 deletions(-)

diff --git a/tb_host/app.R b/tb_host/app.R
index b114665..53b954c 100644
--- a/tb_host/app.R
+++ b/tb_host/app.R
@@ -260,17 +260,19 @@ server <- function(input, output) {
       input$all_mutations
     }, {
       gene = input$gene
-      mutations = paste0(
-        apply(
-          unique_missense_genes[unique_missense_genes$gene_name == gene,c("position","chain")],
-          1,
-          function(x){
-            paste0(trimws(x[1]),
-                   ":",
-                   trimws(x[2])
-            )}
-        ),
-        collapse=","
+      mutations = paste0(":",
+                         as.matrix(unique_missense_genes[unique_missense_genes$gene_name == gene,c("chain")])[1],
+                         " and (",
+                         paste0(
+                           apply(
+                             unique_missense_genes[unique_missense_genes$gene_name == gene,c("position","chain")],
+                             1,
+                             function(x){
+                               paste0(trimws(x[1])
+                               )}
+                           ),
+                           collapse=", "
+                         ), ")"
       )
       print(mutations)
       
@@ -286,31 +288,30 @@ server <- function(input, output) {
         ) %>%
         addSelection(type="surface",
                      param = list(name = "all_mutations",
-                                  color="green",
-                                  sele = "20:A, 22:A, 157:A"
+                                  color="red",
+                                  sele = mutations
+                                  #colorScheme = "bfactor",
+                                  #opacity = 1
+                     )
+        )
+      NGLVieweR_proxy("af_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="red",
+                                  sele = mutations
                                   #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
-      #                )
-      #   )
     })
-  
 }
 
 # Run the application