Dev

kvfinder-web-portal/NAMESPACE

@@ -10,6 +10,7 @@ export(check_results)
 export(choose_input)
 export(choose_run_mode)
 export(color_cavity_deepth)
+export(color_cavity_hyd)
 export(create_init_scene)
 export(create_work_scene)
 export(deal_sele_nonstand)

kvfinder-web-portal/R/app_server.R

@@ -243,6 +243,10 @@ app_server <- function(input, output, session) {
         id = "cavity_deep",
         time = 0
       )
+      hideElement(
+        id = "cavity_hyd",
+        time = 0
+      )
     }
   })
   #----------------------------------------------------
@@ -353,6 +357,10 @@ app_server <- function(input, output, session) {
       id = "cavity_deep_pg2",
       time = 0
     )
+    hideElement(
+      id = "cavity_hyd_pg2",
+      time = 0
+    )
   })
   #----------------------------------------------------
 
@@ -427,6 +435,10 @@ app_server <- function(input, output, session) {
         id = "cavity_deep",
         time = 0
       )
+      showElement(
+        id = "cavity_hyd",
+        time = 0
+      )
       # disable view button to avoid user to click on it multiple times
       disable("view_str")
     },
@@ -519,7 +531,32 @@ app_server <- function(input, output, session) {
     color_cavity_deepth(input = input, output = output, is_pg2 = FALSE, cav_rep_list=cav_rep_list,result_pdb_list=result_pdb )
   })
 
-
+  observeEvent(input$input_cavity_hyd, {
+    color_cavity_hyd(input = input, output = output, is_pg2 = FALSE, cav_rep_list=cav_rep_list,result_pdb_list=result_pdb )
+    output$scale_plot <- renderPlot({
+      EisenbergWeiss_scale = c(-0.64, 2.6,0.8,0.92,-0.3,0.87,0.76,
+                               -0.49,0.41,-1.42,-1.09,1.54,-0.66,-1.22,
+                               -0.12,0.18,0.05, -0.83, -0.27, -1.11)
+      df <- data.frame(x = seq(1,length(EisenbergWeiss_scale)), y = EisenbergWeiss_scale)
+      p <- ggplot(data = df, aes(x = x, y = y, colour = y)) + 
+        geom_point() +
+        scale_colour_gradient2(name = "Hydropathy", low = "yellow", mid = "white", high = "blue", midpoint = 0.59,breaks = seq(-1,2.5,0.5))+
+        theme(plot.title = element_text(hjust = 0.5),
+              legend.position = "bottom",
+              legend.key.width= unit(0.2, 'npc'),
+              #legend.spacing = unit(0.25,"cm"),
+              legend.title = element_text(hjust = 0.5),
+              legend.justification = "center") +
+        guides(colour = guide_colourbar(title.position="top", title.hjust = 0.5),
+               size = guide_legend(title.position="top", title.hjust = 0.5))
+
+      # ggpubr does this for you
+      leg <- get_legend(p)
+      as_ggplot(leg)
+
+    }) #, height =50, width = '100%'
+  })
+
   ##### View in Get latest results page (pg2)
 
   # Click view in the secondary page to initialize the result visualization with the NGL engine
@@ -592,6 +629,10 @@ app_server <- function(input, output, session) {
       id = "cavity_deep_pg2",
       time = 0
     )
+    showElement(
+      id = "cavity_hyd_pg2",
+      time = 0
+    )
     disable("view_str_pg2")
   })
 
@@ -673,6 +714,10 @@ app_server <- function(input, output, session) {
   observeEvent(input$input_cavity_deep_pg2, {
     color_cavity_deepth(input = input, output = output, is_pg2 = TRUE, cav_rep_list=cav_rep_list,result_pdb_list=result_pdb )
   })
+
+  observeEvent(input$input_cavity_hyd_pg2, {
+    color_cavity_hyd(input = input, output = output, is_pg2 = TRUE, cav_rep_list=cav_rep_list,result_pdb_list=result_pdb )
+  })
 
   #----------------------------------------------------
 }

kvfinder-web-portal/R/app_ui.R

@@ -142,6 +142,7 @@ app_ui <- function(request) {
                 tags$br(),
                 uiOutput("results_table"),
                 tags$br(),
+                htmlOutput("table_footer")
               ),
               column(
                 7,
@@ -154,12 +155,20 @@ app_ui <- function(request) {
                       NGLVieweROutput("structure", width = "100%", height = "75vh")
                     )
                   ),
+                  conditionalPanel(
+                    condition="input.input_cavity_hyd==1",
+                  fluidRow(
+                    column(12, align='center',
+                           plotOutput("scale_plot", height = '50', width = '50%'))
+                  )
+                    ),
                   fluidRow(
                     column(2, uiOutput("selection_pdb")),
                     column(2, uiOutput("cavity_rep")),
                     column(2, uiOutput("cavity_color")),
                     column(2, div(style = "display: inline-block; vertical-align: -20px;", uiOutput("cavity_deep"))),
-                    column(4, div(style = "display: inline-block; vertical-align: -20px;", uiOutput("show_interface"))),
+                    column(2, div(style = "display: inline-block; vertical-align: -20px;", uiOutput("cavity_hyd"))),
+                    column(2, div(style = "display: inline-block; vertical-align: -20px;", uiOutput("show_interface"))),
                   ),
                   fluidRow(
                     column(2, uiOutput("protein_rep")),
@@ -243,7 +252,8 @@ app_ui <- function(request) {
                     column(2, uiOutput("cavity_rep_pg2")),
                     column(2, uiOutput("cavity_color_pg2")),
                     column(2, div(style = "display: inline-block; vertical-align: -20px;", uiOutput("cavity_deep_pg2"))),
-                    column(4, div(style = "display: inline-block; vertical-align: -20px;", uiOutput("show_interface_pg2"))),
+                    column(2, div(style = "display: inline-block; vertical-align: -20px;", uiOutput("cavity_hyd_pg2"))),
+                    column(2, div(style = "display: inline-block; vertical-align: -20px;", uiOutput("show_interface_pg2"))),
                   ),
                   fluidRow(
                     column(2, uiOutput("protein_rep_pg2")),

kvfinder-web-portal/R/mod_server_checkResults.R

@@ -86,18 +86,19 @@ check_results <- function(input, output, run_id, is_pg2, url_address, session) {
         })
         output[[table_out]] <- DT::renderDataTable(
           data.table(
-            `Cavity ID` = names(result_toml$AREA),
+            `ID` = names(result_toml$AREA),
             `Area (A²)` = unlist(result_toml$AREA),
-            `Volume (A³)` = unlist(result_toml$VOLUME),
-            `Avg Depth  (A)` = unlist(result_toml$AVG_DEPTH)
+            `Vol. (A³)` = unlist(result_toml$VOLUME),
+            `Dep. (A)` = unlist(result_toml$AVG_DEPTH),
+            `Hyd.` = unlist(result_toml$AVG_HYDROPATHY)
           ),
           filter = c("none"),
           style = "auto",
           options = list(dom = "lBfrtip", 
                          buttons = c("excel", "pdf"), 
                          autoWidth = TRUE,
                          scrollX = TRUE,
-                         columnDefs = list(list(targets=c(4), visible=TRUE, width='75'))
+                         columnDefs = list(list(targets=c(5), visible=TRUE, width='60'))
                          ),
           extensions = "Buttons"
         )
@@ -130,11 +131,16 @@ check_results <- function(input, output, run_id, is_pg2, url_address, session) {
             write_toml(param_list, output = filename)
           }
         )
-
         # create visualization button
         output[[view_output]] <- renderUI({
           actionButton(inputId = view_str, label = "View", icon = icon("eye"), style = "color: #fff; background-color: #6c757d; border-color: #6c757d")
         })
+
+        output$table_footer <- renderText({
+          paste(
+            p("ID: Cavity ID, Area: Cavity area, Vol: Cavity volume, Dep: Cavity average depth, Hyd: Cavity average hydropathy.")
+          )
+        })
         # create list to store results
         result_list <- list(
           retrieve_input_pdb = retrieve_input_pdb,

kvfinder-web-portal/R/mod_server_colorCAVhyd.R

@@ -0,0 +1,51 @@
+#' Function that change background color in NGL viewer
+#'
+#' @param input shiny input
+#' @param output shiny output
+#' @param is_pg2 logical TRUE/FALSE. If TRUE, we calling to create result in page 2 (get latest results page).
+#' @param cav_rep_list
+#' @param result_pdb_list
+#' 
+#' 
+#' @import shiny
+#' @import NGLVieweR
+#'
+#' @export
+#'
+
+color_cavity_hyd <- function(input, output, is_pg2, cav_rep_list, result_pdb_list) {
+  if (is_pg2 == TRUE) {
+    input_cavity_hyd <- "input_cavity_hyd_pg2"
+    structure <- "structure_pg2"
+  } else {
+    input_cavity_hyd <- "input_cavity_hyd"
+    structure <- "structure"
+  }
+  #print(result_pdb_list$result_toml$MAX_DEPTH)
+  #print(max(unlist(result_pdb_list$result_toml$MAX_DEPTH)))
+  #NGLVieweR_proxy(structure) %>%
+  #  removeSelection(name = tail(cav_rep_list, n = 2)[1])
+  # After the initial structure is invisible, we can add a new representation to the current scene
+
+  if(input[[input_cavity_hyd]] == TRUE){
+    NGLVieweR_proxy(structure) %>%
+      addSelection("point",
+                   param =
+                     list(
+                       name = "hyd", # now the created selection is named "sel3"
+                       sele = paste(result_pdb_list$result_cav_names, collapse = " or "),
+                       colorScheme = 'occupancy',
+                       colorScale = c('blue', 'white', 'yellow'),
+                       colorReverse = TRUE,
+                       colorDomain = c(-1.42, 2.6)
+                       #colorScheme = scheme_color_list[[tail(protein_col_scheme_list, n = 1)]]
+                     )
+      )
+  } else{
+    NGLVieweR_proxy(structure) %>%
+      removeSelection(name = "hyd")
+  }
+
+  # NGLVieweR_proxy(structure) %>%
+  #   updateColor(tail(cav_rep_list,n=1),color= "resname")
+}

kvfinder-web-portal/R/mod_server_createINITscene.R

@@ -32,6 +32,7 @@ create_init_scene <- function(input, output, result_pdb_list, is_pg2, scheme_col
     fullscreen_title <- "fullscreen_title_pg2"
     cavity_rep <- "cavity_rep_pg2"
     cavity_deep <- "cavity_deep_pg2"
+    cavity_hyd <- "cavity_hyd_pg2"
     # if in the main page
   } else {
     structure <- "structure"
@@ -50,6 +51,7 @@ create_init_scene <- function(input, output, result_pdb_list, is_pg2, scheme_col
     fullscreen_title <- "fullscreen_title"
     cavity_rep <- "cavity_rep"
     cavity_deep <- "cavity_deep"
+    cavity_hyd <- "cavity_hyd"
   }
 
   #-------------------------------------------------------------------------------------------------------
@@ -87,7 +89,7 @@ create_init_scene <- function(input, output, result_pdb_list, is_pg2, scheme_col
   output[[show_interface]] <- renderUI({
     div(
       style = "font-size:12px;",
-      checkboxInput(inputId = interface_res, label = div(style = "font-size:12px;display:inline-block", "Show interface residues"))
+      checkboxInput(inputId = interface_res, label = div(style = "font-size:12px;display:inline-block", "Interface AA"))
     )
   })
   # protein color scheme selector
@@ -184,7 +186,14 @@ create_init_scene <- function(input, output, result_pdb_list, is_pg2, scheme_col
   output[[cavity_deep]] <- renderUI({
     div(
       style = "font-size:12px;",
-      checkboxInput(inputId = paste("input_", cavity_deep, sep = ""), label = div(style = "font-size:12px;display:inline-block", "Cavity depth"))
+      checkboxInput(inputId = paste("input_", cavity_deep, sep = ""), label = div(style = "font-size:12px;display:inline-block", "Depth"))
+    )
+  })
+
+  output[[cavity_hyd]] <- renderUI({
+    div(
+      style = "font-size:12px;",
+      checkboxInput(inputId = paste("input_", cavity_hyd, sep = ""), label = div(style = "font-size:12px;display:inline-block", "Hydropathy"))
     )
   })
   #----------------------------------------------------------------------------------------------------------------