Dev

Dockerfile

@@ -7,7 +7,7 @@ RUN apt-get update && apt-get install -y \
     libxml2-dev
 
 # Install R depedencies
-RUN install2.r shiny pkgload remotes devtools bio3d bs4Dash config data.table DT golem NGLVieweR RcppTOML readr rjson shinyjs blogdown colourpicker shinyfullscreen shinycssloaders shinyWidgets
+RUN install2.r shiny pkgload remotes devtools bio3d bs4Dash config data.table DT golem NGLVieweR RcppTOML readr rjson shinyjs blogdown colourpicker shinyfullscreen shinycssloaders shinyWidgets ggplot2 ggpubr
 
 # Copy the app directory into the image
 COPY ./kvfinder-web-portal/ /srv/shiny-server/kvfinder-web-portal/

kvfinder-web-portal/DESCRIPTION

@@ -47,7 +47,9 @@ Imports:
     shinycssloaders,
     shinyfullscreen,
     shinyjs,
-    shinyWidgets
+    shinyWidgets,
+    ggplot2,
+    ggpubr
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.1.2

kvfinder-web-portal/NAMESPACE

@@ -38,6 +38,7 @@ import(blogdown)
 import(bs4Dash)
 import(colourpicker)
 import(data.table)
+import(ggplot2)
 import(golem)
 import(httr)
 import(jsonlite)

kvfinder-web-portal/R/app_server.R

@@ -4,6 +4,8 @@
 #'     DO NOT REMOVE.
 #' @import shiny
 #' @import shinyjs
+#' @import ggplot2
+#' 
 #'
 #' @noRd
 #'
@@ -174,6 +176,10 @@ app_server <- function(input, output, session) {
         id = "download2",
         time = 0
       )
+      hideElement(
+        id = "table_footer",
+        time = 0
+      )
       hideElement(
         id = "view_str",
         time = 0
@@ -247,6 +253,14 @@ app_server <- function(input, output, session) {
         id = "cavity_hyd",
         time = 0
       )
+      hideElement(
+        id = "scale_plot_deep",
+        time = 0
+      )
+      hideElement(
+        id = "scale_plot",
+        time = 0
+      )
     }
   })
   #----------------------------------------------------
@@ -288,6 +302,10 @@ app_server <- function(input, output, session) {
           id = "download2",
           time = 0
         )
+        showElement(
+          id = "table_footer",
+          time = 0
+        )
       }
     })
     # disable check button button to force the users to resubmit job and to avoid inconsistencies in the interface
@@ -361,6 +379,14 @@ app_server <- function(input, output, session) {
       id = "cavity_hyd_pg2",
       time = 0
     )
+    hideElement(
+      id = "scale_plot_deep",
+      time = 0
+    )
+    hideElement(
+      id = "scale_plot",
+      time = 0
+    )
   })
   #----------------------------------------------------
 
@@ -439,6 +465,14 @@ app_server <- function(input, output, session) {
         id = "cavity_hyd",
         time = 0
       )
+      showElement(
+        id = "scale_plot_deep",
+        time = 0
+      )
+      showElement(
+        id = "scale_plot",
+        time = 0
+      )
       # disable view button to avoid user to click on it multiple times
       disable("view_str")
     },
@@ -486,12 +520,10 @@ app_server <- function(input, output, session) {
 
   # Select cavity to be visualized from clicking on cavity selector button
   observeEvent(input$select_cavity, {
-    print('exeuting select')
     select_cav(input = input, output = output, result_pdb_list = result_pdb, is_pg2 = FALSE)
   })
 
   observeEvent(input$interface_res, {
-    print('exeuting select')
     interface_cav(input = input, output = output, result_pdb_list = result_pdb, is_pg2 = FALSE)
   })
 
@@ -528,35 +560,74 @@ app_server <- function(input, output, session) {
   })
 
   observeEvent(input$input_cavity_deep, {
+    if(input$input_cavity_deep == TRUE){
+      updateCheckboxInput(session, "input_cavity_hyd", value = FALSE)  
+    }
+
     color_cavity_deepth(input = input, output = output, is_pg2 = FALSE, cav_rep_list=cav_rep_list,result_pdb_list=result_pdb )
-  })
+
+    output$scale_plot_deep <- renderPlot({
+      depth_scale = c(0,result_pdb$list_depth, max(unlist(result_pdb$result_toml$MAX_DEPTH)))
+      df <- data.frame(x = seq(1,length(depth_scale)), y = depth_scale)
+      p <- ggplot2::ggplot(data = df, aes(x = x, y = y, colour = y)) +
+        geom_point() +
+        #scale_colour_gradient2(name = "Deepth (A)", low = "yellow", mid = "white", high = "blue", midpoint = 0.59,breaks = seq(-1,2.5,0.5))+
+        scale_color_gradientn(name = "Deepth (A)", colours = rev(rainbow(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",
+              panel.background = element_rect(fill='transparent'),
+              plot.background = element_rect(fill='transparent'),
+              legend.background = element_rect(fill='transparent'),
+              legend.box.background = element_rect(fill='transparent'))+
+        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 <- ggpubr::get_legend(p)
+      ggpubr::as_ggplot(leg)
+
+    }, bg="transparent") #, height =50, width = '100%'
+})
 
   observeEvent(input$input_cavity_hyd, {
+    if(input$input_cavity_hyd == TRUE){
+    updateCheckboxInput(session, "input_cavity_deep", value = FALSE)
+    }
     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)) + 
+      p <- ggplot2::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") +
+              legend.justification = "center",
+              panel.background = element_rect(fill='transparent'),
+              plot.background = element_rect(fill='transparent'),
+              legend.background = element_rect(fill='transparent'),
+              legend.box.background = element_rect(fill='transparent'))+
         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)
+      leg <- ggpubr::get_legend(p)
+      ggpubr::as_ggplot(leg)
 
-    }) #, height =50, width = '100%'
+    }, bg="transparent") #, 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
@@ -633,6 +704,14 @@ app_server <- function(input, output, session) {
       id = "cavity_hyd_pg2",
       time = 0
     )
+    showElement(
+      id = "scale_plot_deep_pg2",
+      time = 0
+    )
+    showElement(
+      id = "scale_plot_pg2",
+      time = 0
+    )
     disable("view_str_pg2")
   })
 
@@ -711,12 +790,81 @@ app_server <- function(input, output, session) {
     take_snapshot(input = input, output = output, is_pg2 = TRUE)
   })
 
+  observeEvent(input$interface_res_pg2, {
+    interface_cav(input = input, output = output, result_pdb_list = result_pdb, is_pg2 = TRUE)
+  })
+
   observeEvent(input$input_cavity_deep_pg2, {
+    if(input$input_cavity_deep_pg2 == TRUE){
+      updateCheckboxInput(session, "input_cavity_hyd_pg2", value = FALSE)  
+    }
+
     color_cavity_deepth(input = input, output = output, is_pg2 = TRUE, cav_rep_list=cav_rep_list,result_pdb_list=result_pdb )
+
+    output$scale_plot_deep_pg2 <- renderPlot({
+      depth_scale = c(0,result_pdb$list_depth, max(unlist(result_pdb$result_toml$MAX_DEPTH)))
+      df <- data.frame(x = seq(1,length(depth_scale)), y = depth_scale)
+      p <- ggplot2::ggplot(data = df, aes(x = x, y = y, colour = y)) +
+        geom_point() +
+        #scale_colour_gradient2(name = "Deepth (A)", low = "yellow", mid = "white", high = "blue", midpoint = 0.59,breaks = seq(-1,2.5,0.5))+
+        scale_color_gradientn(name = "Deepth (A)", colours = rev(rainbow(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",
+              panel.background = element_rect(fill='transparent'),
+              plot.background = element_rect(fill='transparent'),
+              legend.background = element_rect(fill='transparent'),
+              legend.box.background = element_rect(fill='transparent'))+
+        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 <- ggpubr::get_legend(p)
+      ggpubr::as_ggplot(leg)
+
+    }, bg="transparent") #, height =50, width = '100%'
+
+
+
   })
 
   observeEvent(input$input_cavity_hyd_pg2, {
+    if(input$input_cavity_hyd_pg2 == TRUE){
+      updateCheckboxInput(session, "input_cavity_deep_pg2", value = FALSE)
+    }
+
     color_cavity_hyd(input = input, output = output, is_pg2 = TRUE, cav_rep_list=cav_rep_list,result_pdb_list=result_pdb )
+
+    output$scale_plot_pg2 <- 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 <- ggplot2::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",
+              panel.background = element_rect(fill='transparent'),
+              plot.background = element_rect(fill='transparent'),
+              legend.background = element_rect(fill='transparent'),
+              legend.box.background = element_rect(fill='transparent'))+
+        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 <- ggpubr::get_legend(p)
+      ggpubr::as_ggplot(leg)
+
+    }, bg="transparent") #, height =50, width = '100%'
+
   })
 
   #----------------------------------------------------

kvfinder-web-portal/R/app_ui.R

@@ -162,6 +162,13 @@ app_ui <- function(request) {
                            plotOutput("scale_plot", height = '50', width = '50%'))
                   )
                     ),
+                  conditionalPanel(
+                    condition="input.input_cavity_deep==1",
+                    fluidRow(
+                      column(12, align='center',
+                             plotOutput("scale_plot_deep", height = '50', width = '50%'))
+                    )
+                  ),
                   fluidRow(
                     column(2, uiOutput("selection_pdb")),
                     column(2, uiOutput("cavity_rep")),
@@ -247,6 +254,20 @@ app_ui <- function(request) {
                   fluidRow(
                     NGLVieweROutput("structure_pg2", width = "100%", height = "600px")
                   ),
+                  conditionalPanel(
+                    condition="input.input_cavity_hyd_pg2==1",
+                    fluidRow(
+                      column(12, align='center',
+                             plotOutput("scale_plot_pg2", height = '50', width = '50%'))
+                    )
+                  ),
+                  conditionalPanel(
+                    condition="input.input_cavity_deep_pg2==1",
+                    fluidRow(
+                      column(12, align='center',
+                             plotOutput("scale_plot_deep_pg2", height = '50', width = '50%'))
+                    )
+                  ),
                   fluidRow(
                     column(2, uiOutput("selection_pdb_pg2")),
                     column(2, uiOutput("cavity_rep_pg2")),

kvfinder-web-portal/R/mod_server_changeCAVcolor.R

@@ -19,17 +19,14 @@ change_cav_color <- function(input, output, is_pg2, cav_rep_list) {
     input_cavity_color <- "input_cavity_color"
     structure <- "structure"
   }
-  print('inside cav color')
-  print(cav_rep_list)
-  # if(length(cav_rep_list) > 1){
-  #   NGLVieweR_proxy(structure) %>%
-  #     updateColor("point", input[[input_cavity_color]])
-  # } else{
-  #   NGLVieweR_proxy(structure) %>%
-  #     updateColor("sel3", input[[input_cavity_color]])
-  # }
-  # print(cav_rep_list)
-  # print(tail(cav_rep_list,n=1))
-  NGLVieweR_proxy(structure) %>%
+
+  if(!is.null(cav_rep_list)){ #this is to make sure that this will work on the second time loaded page
+    NGLVieweR_proxy(structure) %>%
       updateColor(tail(cav_rep_list,n=1), input[[input_cavity_color]])
+  } else {
+    NGLVieweR_proxy(structure) %>%
+      updateColor("point", input[[input_cavity_color]])
+  }
+
+
 }