feature complete dashboard

tb_host/app.R

@@ -18,13 +18,29 @@ library(grid) # for the info box
 library(plotly)
 library(shinycssloaders)
 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))
 
-genes = c("Gene 1", "Gene 2", "Gene 3", "Gene 4", "Gene 5")
+
+# 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/dashboard/list_unique_missense_genes.csv"
+missense_gene_url = "https://git.tunstall.in/api/v1/repos/tanu/fellowship_dcdf/raw/tb_data_fc/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))
+#genes = c("Gene 1", "Gene 2", "Gene 3", "Gene 4", "Gene 5")
 
 # Define UI for application that draws a histogram
 ui=dashboardPage(skin="purple",
@@ -32,9 +48,12 @@ ui=dashboardPage(skin="purple",
                  dashboardSidebar(
                    radioButtons("gene",
                                 label="Gene",
-                                choices = genes,
+                                choices = genes$Gene,
-                                selected="Gene 1" # "none" is a value
+                                selected="alr" # "alr" is a value
-                   )
+                   ),
+                   actionButton("clear_ngl",
+                                "Clear Structures")
+                   
                  ),
                  dashboardBody(
                    useShinyjs(),
@@ -80,47 +99,121 @@ server <- function(input, output) {
   ### NGLViewer ####
   # Structure Viewer WebGL/NGLViewR window
   output$structure <- renderNGLVieweR({
-    #ngl_gene=isolate(input$switch_target)
+    selected_gene=input$gene
-    #ngl_gene=input$switch_target
+    ngl_gene=as.character(genes[genes$Gene==selected_gene,"PDB"])
-    #ngl_drug=target_map[[ngl_gene]]
+    NGLVieweR(ngl_gene) %>%
-    #ngl_pdb_file=paste0(load_dir, "Data/", ngl_drug, '/output/depth/', ngl_gene, '_complex.pdb')
-    #print(ngl_pdb_file)
-    #NGLVieweR(ngl_pdb_file) %>%
-    NGLVieweR("3pl1") %>%
       addRepresentation("cartoon",
                         param = list(name = "cartoon",
-                                     color="tan"
+                                     #color="tan"
-                                     #, colorScheme = "chainid"
+                                     colorScheme = "bfactor",
+                                     opacity = 1
                         )
       ) %>%
-      stageParameters(backgroundColor = "lightgrey") %>%
+      stageParameters(backgroundColor = "white") %>%
       setQuality("high") %>%
       setFocus(0) %>%
       setSpin(FALSE)
   })
   output$af_structure <- renderNGLVieweR({
-    #ngl_gene=isolate(input$switch_target)
+    selected_af_gene=input$gene
-    #ngl_gene=input$switch_target
+    ngl_af_gene=as.character(genes[genes$Gene==selected_af_gene,"AF_PDB"])
-    #ngl_drug=target_map[[ngl_gene]]
+    
+    #af_pdb=cat(content(GET(paste0(alphafold_url,"AF-",ngl_af_gene,"-F1-model_v4.pdb")), as="text"), "\n")
+    af_pdb=content(GET(paste0(alphafold_url,"AF-",ngl_af_gene,"-F1-model_v4.pdb")), as="text")
+    #print(af_pdb)
     #ngl_pdb_file=paste0(load_dir, "Data/", ngl_drug, '/output/depth/', ngl_gene, '_complex.pdb')
-    #print(ngl_pdb_file)
+    NGLVieweR(af_pdb, format="pdb") %>%
-    #NGLVieweR(ngl_pdb_file) %>%
-    NGLVieweR("3pl1") %>%
       addRepresentation("cartoon",
                         param = list(name = "cartoon",
-                                     color="tan"
+                                     #color="tan"
-                                     #, colorScheme = "chainid"
+                                     colorScheme = "bfactor",
+                                     opacity = 1
                         )
       ) %>%
-      stageParameters(backgroundColor = "lightgrey") %>%
+      stageParameters(backgroundColor = "white") %>%
       setQuality("high") %>%
       setFocus(0) %>%
       setSpin(FALSE)
   })
-  output$table = DT::renderDataTable(mtcars)
   
+  # output$table <- DT::renderDataTable({
+  #   selected_gene=input$gene
+  #   gene=as.character(genes[genes$Gene==selected_gene,"Gene"])
+  #   #unique_missense_genes[unique_missense_genes$gene_name==gene,]
+  #   unique_missense_genes
+  # },
+  # selection = "single",
+  # search = list(search="alr"))
+  output$table <- DT::renderDataTable(
+    unique_missense_genes,
+    selection = "single",
+    options=list(
+      search = list(search=as.character(genes[genes$Gene==input$gene,"Gene"]))
+    )
+  )
+  
+  observeEvent(input$table_rows_selected,{
+    #req(length(input$table_row_selected) > 0)
+    mutation = as.character(unique_missense_genes[input$table_rows_selected,"hgvd_p"])
+    # 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))
+    
+    # Now update the 3D structure to highlight the clicked thing and then zoom in.
+    
+    NGLVieweR_proxy("structure") %>%
+      #addSelection('ball+stick'
+      addSelection('ball+stick'
+                   , param = list(
+                     name = "Pos"
+                     , sele = clicked_position
+                     , color = "green"
+                     #, colorValue="00ff00"
+                     #, colorScheme="element"
+                   )
+      )
+    NGLVieweR_proxy("af_structure") %>%
+      #addSelection('ball+stick'
+      addSelection('ball+stick'
+                   , param = list(
+                     name = "Pos"
+                     , sele = clicked_position
+                     , color = "green"
+                     #, colorValue="00ff00"
+                     #, colorScheme="element"
+                   )
+      )
+    
+    NGLVieweR_proxy("af_structure") %>% updateZoomMove(
+      center = clicked_position,
+      zoom = clicked_position,
+      duration = 1000, # animation time in ms
+      z_offSet = -1
+    )
+    NGLVieweR_proxy("structure") %>% updateZoomMove(
+      center = clicked_position,
+      zoom = clicked_position,
+      duration = 1000, # animation time in ms
+      z_offSet = -1
+    )
+    
+    
+    # output$debug <- renderPrint({
+    #   print(c(mutation, clicked_position))
+    # })
+  })
+  observeEvent(
+    {
+      input$clear_ngl
+    }, {
+      NGLVieweR_proxy("structure") %>%
+        removeSelection("Pos")
+      NGLVieweR_proxy("af_structure") %>%
+        removeSelection("Pos")
+    })
   
 }
 
 # Run the application 
 shinyApp(ui = ui, server = server)
+