shuffle everything

global.R

@@ -0,0 +1,29 @@
+library(dplyr)
+library(DT)
+library(ggplot2)
+library(grid) # for the info box
+library(plotly)
+library(NGLVieweR)
+library(httr)
+library(readr)
+library(RCurl)
+# make shiny non-stupid
+#options(shiny.launch.browser = FALSE) # i am a big girl and can tie my own laces
+#options(shiny.port = 8000) # don't change the port every time
+#options(shiny.host = '0.0.0.0') # This means "listen to all addresses on all interfaces"
+#options(DT.options = list(scrollX = TRUE))
+
+
+# An "application token" is required here. I generated this one like this:
+# curl -H "Content-Type: application/json" -d '{"name":"r-data"}' -u <username>:<password> https://git.tunstall.in/api/v1/users/sethp/tokens
+
+# Gitea access token
+access_token = read_lines("~/secret-token")
+
+gene_url = "https://git.tunstall.in/api/v1/repos/tanu/fellowship_dcdf/raw/tb_data_fc/data_dashboard/list_unique_missense_genes.csv"
+missense_gene_url = "https://git.tunstall.in/api/v1/repos/tanu/fellowship_dcdf/raw/tb_data_fc/data_dashboard/missense_genes_params.csv"
+alphafold_url = "https://alphafold.ebi.ac.uk/files/"
+
+genes=read_csv(paste0(gene_url,"?token=",access_token))
+unique_missense_genes = read_delim(paste0(missense_gene_url,"?token=",access_token))
+

server.R

@@ -13,7 +13,7 @@ library(httr)
 library(readr)
 library(RCurl)
 
-shinyServer(function(input, output) {
+shinyServer(function(input, output){
   
   output$distPlot <- renderPlot({
     # generate bins based on input$bins from ui.R
@@ -83,11 +83,13 @@ shinyServer(function(input, output) {
   
   observeEvent(input$table_rows_selected,{
     #req(length(input$table_row_selected) > 0)
+    mutation_pdb = as.character(unique_missense_genes[input$table_rows_selected,"position_pdb"])
+    mutation_af = as.character(unique_missense_genes[input$table_rows_selected,"position_af"])
     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))
+    #clicked_position = regmatches(mutation, regexpr("[0-9]+", mutation, perl=TRUE))
     
     # Now update the 3D structure to highlight the clicked thing and then zoom in.
     
@@ -96,7 +98,7 @@ shinyServer(function(input, output) {
       addSelection('spacefill'
                    , param = list(
                      name = "Pos"
-                     , sele = trimws(paste0(clicked_position,':', chain))
+                     , sele = trimws(paste0(mutation_pdb,':', chain))
                      , color = "red"
                      #, colorValue="00ff00"
                      #, colorScheme="element"
@@ -107,7 +109,7 @@ shinyServer(function(input, output) {
       addSelection('spacefill'
                    , param = list(
                      name = "Pos"
-                     , sele = clicked_position
+                     , sele = mutation_af
                      , color = "red"
                      #, colorValue="00ff00"
                      #, colorScheme="element"
@@ -115,20 +117,20 @@ shinyServer(function(input, output) {
       )
     
     NGLVieweR_proxy("af_structure") %>% updateZoomMove(
-      center = clicked_position,
+      center = mutation_af,
-      zoom = clicked_position,
+      zoom = mutation_af,
       duration = 1000, # animation time in ms
       z_offSet = -1
     )
     NGLVieweR_proxy("structure") %>% updateZoomMove(
-      center = trimws(paste0(clicked_position,':', chain)),
+      center = trimws(paste0(mutation_pdb,':', chain)),
-      zoom = trimws(paste0(clicked_position,':', chain)),
+      zoom = trimws(paste0(mutation_pdb,':', 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$table_rows_selected,"mutationinformation"]),"<br/>",
+      HTML(paste0("<strong>Mutation: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"mutationinformation_pdb"]),"<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$table_rows_selected,"ligand_distance"]), "<br/>",
@@ -186,7 +188,21 @@ shinyServer(function(input, output) {
                          " and (",
                          paste0(
                            apply(
-                             unique_missense_genes[unique_missense_genes$gene_name == gene,c("position","chain")],
+                             unique_missense_genes[unique_missense_genes$gene_name == gene,c("position_pdb","chain")],
+                             1,
+                             function(x){
+                               paste0(trimws(x[1])
+                               )}
+                           ),
+                           collapse=", "
+                         ), ")"
+      )
+      mutations_af = paste0(":",
+                         as.matrix(unique_missense_genes[unique_missense_genes$gene_name == gene,c("chain")])[1],
+                         " and (",
+                         paste0(
+                           apply(
+                             unique_missense_genes[unique_missense_genes$gene_name == gene,c("position_af","chain")],
                              1,
                              function(x){
                                paste0(trimws(x[1])
@@ -207,7 +223,7 @@ shinyServer(function(input, output) {
                                   opacity = 0.2
                      )
         ) %>%
-        addSelection(type="ball+stick", #spacefill
+        addSelection(type="spacefill", #spacefill
                      param = list(name = "all_mutations",
                                   color="orange",
                                   sele = mutations
@@ -225,14 +241,14 @@ shinyServer(function(input, output) {
                                   opacity = 0.2
                      )
         ) %>%
-        addSelection(type="ball+stick", #spacefill
+        addSelection(type="spacefill", #spacefill
                      param = list(name = "all_mutations",
                                   color="orange",
-                                  sele = mutations
+                                  sele = mutations_af
                                   #colorScheme = "bfactor",
                                   #opacity = 1
                      )
         )
     })
-}
+})
-)
+

ui.R

@@ -12,7 +12,6 @@ library(NGLVieweR)
 library(httr)
 library(readr)
 library(RCurl)
-
 dashboardPage(skin="purple",
                  dashboardHeader(title="Tuberculosis Host"),
                  dashboardSidebar(