From 6301a1b03b9e2350f11e3d2fce4d732a1415ec40 Mon Sep 17 00:00:00 2001
From: Helder Ribeiro <helder.ribeiro@lnbio.cnpem.br>
Date: Tue, 28 Feb 2023 16:51:50 -0500
Subject: [PATCH 01/19] add ggplot to dockerfile

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 4437be5..8289b16 100644
--- a/Dockerfile
+++ b/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 ggplot
 
 # Copy the app directory into the image
 COPY ./kvfinder-web-portal/ /srv/shiny-server/kvfinder-web-portal/

From b54108cfb6f7b83852a0cb36871890554a8f4e17 Mon Sep 17 00:00:00 2001
From: Helder Ribeiro <helder.ribeiro@lnbio.cnpem.br>
Date: Tue, 28 Feb 2023 16:54:55 -0500
Subject: [PATCH 02/19] add ggplot2 to dockerfile

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 8289b16..2ee2c40 100644
--- a/Dockerfile
+++ b/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 ggplot
+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
 
 # Copy the app directory into the image
 COPY ./kvfinder-web-portal/ /srv/shiny-server/kvfinder-web-portal/

From 9c21de9a4b2a49b6ad488a584a729b3ba18a90b4 Mon Sep 17 00:00:00 2001
From: Helder Ribeiro <helder.ribeiro@lnbio.cnpem.br>
Date: Tue, 28 Feb 2023 16:55:34 -0500
Subject: [PATCH 03/19] add gglpot2 to description

---
 kvfinder-web-portal/DESCRIPTION | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/kvfinder-web-portal/DESCRIPTION b/kvfinder-web-portal/DESCRIPTION
index 12177ae..623ed1f 100644
--- a/kvfinder-web-portal/DESCRIPTION
+++ b/kvfinder-web-portal/DESCRIPTION
@@ -47,7 +47,8 @@ Imports:
     shinycssloaders,
     shinyfullscreen,
     shinyjs,
-    shinyWidgets
+    shinyWidgets,
+    gglpot2
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.1.2

From de3e0e934eca24e730dc04d948929e2cd35225c9 Mon Sep 17 00:00:00 2001
From: Helder Ribeiro <helder.ribeiro@lnbio.cnpem.br>
Date: Tue, 28 Feb 2023 16:56:18 -0500
Subject: [PATCH 04/19] add ggplot2 correct to description

---
 kvfinder-web-portal/DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/kvfinder-web-portal/DESCRIPTION b/kvfinder-web-portal/DESCRIPTION
index 623ed1f..83169d7 100644
--- a/kvfinder-web-portal/DESCRIPTION
+++ b/kvfinder-web-portal/DESCRIPTION
@@ -48,7 +48,7 @@ Imports:
     shinyfullscreen,
     shinyjs,
     shinyWidgets,
-    gglpot2
+    ggplot
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.1.2

From 1ce0e562c2d7c8d0ed5e678e5731b1e6db3b2424 Mon Sep 17 00:00:00 2001
From: Helder Ribeiro <helder.ribeiro@lnbio.cnpem.br>
Date: Tue, 28 Feb 2023 17:06:05 -0500
Subject: [PATCH 05/19] fix read hyd bug

---
 kvfinder-web-portal/DESCRIPTION                 | 2 +-
 kvfinder-web-portal/R/mod_server_checkResults.R | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/kvfinder-web-portal/DESCRIPTION b/kvfinder-web-portal/DESCRIPTION
index 83169d7..0da702b 100644
--- a/kvfinder-web-portal/DESCRIPTION
+++ b/kvfinder-web-portal/DESCRIPTION
@@ -48,7 +48,7 @@ Imports:
     shinyfullscreen,
     shinyjs,
     shinyWidgets,
-    ggplot
+    ggplot2
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.1.2
diff --git a/kvfinder-web-portal/R/mod_server_checkResults.R b/kvfinder-web-portal/R/mod_server_checkResults.R
index ca60680..ed3390e 100644
--- a/kvfinder-web-portal/R/mod_server_checkResults.R
+++ b/kvfinder-web-portal/R/mod_server_checkResults.R
@@ -84,13 +84,14 @@ check_results <- function(input, output, run_id, is_pg2, url_address, session) {
         output[[results_table]] <- renderUI({
           DT::dataTableOutput(table_out)
         })
+        #print(result_toml$AVG_HYDROPATHY)
         output[[table_out]] <- DT::renderDataTable(
           data.table(
             `ID` = names(result_toml$AREA),
             `Area (A²)` = unlist(result_toml$AREA),
             `Vol. (A³)` = unlist(result_toml$VOLUME),
             `Dep. (A)` = unlist(result_toml$AVG_DEPTH),
-            `Hyd.` = unlist(result_toml$AVG_HYDROPATHY)
+            `Hyd.` = unlist(result_toml$AVG_HYDROPATHY[names(result_toml$AVG_HYDROPATHY) != 'EisenbergWeiss'])
           ),
           filter = c("none"),
           style = "auto",
@@ -98,7 +99,7 @@ check_results <- function(input, output, run_id, is_pg2, url_address, session) {
                          buttons = c("excel", "pdf"), 
                          autoWidth = TRUE,
                          scrollX = TRUE,
-                         columnDefs = list(list(targets=c(5), visible=TRUE, width='60'))
+                         columnDefs = list(list(targets=c(5), visible=TRUE, width='10%'))
                          ),
           extensions = "Buttons"
         )

From 38ad6550de49960c5f711e1136d26d37f615ea66 Mon Sep 17 00:00:00 2001
From: Helder Ribeiro <helder.ribeiro@lnbio.cnpem.br>
Date: Tue, 28 Feb 2023 17:15:51 -0500
Subject: [PATCH 06/19] fix table result width

---
 kvfinder-web-portal/R/mod_server_checkResults.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/kvfinder-web-portal/R/mod_server_checkResults.R b/kvfinder-web-portal/R/mod_server_checkResults.R
index ed3390e..238ef50 100644
--- a/kvfinder-web-portal/R/mod_server_checkResults.R
+++ b/kvfinder-web-portal/R/mod_server_checkResults.R
@@ -90,7 +90,8 @@ check_results <- function(input, output, run_id, is_pg2, url_address, session) {
             `ID` = names(result_toml$AREA),
             `Area (A²)` = unlist(result_toml$AREA),
             `Vol. (A³)` = unlist(result_toml$VOLUME),
-            `Dep. (A)` = unlist(result_toml$AVG_DEPTH),
+            `Avg Dep. (A)` = unlist(result_toml$AVG_DEPTH),
+            `Max Dep. (A)` = unlist(result_toml$MAX_DEPTH),
             `Hyd.` = unlist(result_toml$AVG_HYDROPATHY[names(result_toml$AVG_HYDROPATHY) != 'EisenbergWeiss'])
           ),
           filter = c("none"),
@@ -99,7 +100,7 @@ check_results <- function(input, output, run_id, is_pg2, url_address, session) {
                          buttons = c("excel", "pdf"), 
                          autoWidth = TRUE,
                          scrollX = TRUE,
-                         columnDefs = list(list(targets=c(5), visible=TRUE, width='10%'))
+                         columnDefs = list(list(targets=c(1), visible=TRUE, width='10%'))
                          ),
           extensions = "Buttons"
         )

From 5a3806ef0d2d8fdbd27720e8c9e908d62e51f420 Mon Sep 17 00:00:00 2001
From: Helder Ribeiro <helder.ribeiro@lnbio.cnpem.br>
Date: Tue, 28 Feb 2023 17:33:06 -0500
Subject: [PATCH 07/19] fix bug table footer

---
 kvfinder-web-portal/R/app_server.R              | 8 ++++++++
 kvfinder-web-portal/R/mod_server_checkResults.R | 4 ++--
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/kvfinder-web-portal/R/app_server.R b/kvfinder-web-portal/R/app_server.R
index 3b4f7d8..66684f8 100644
--- a/kvfinder-web-portal/R/app_server.R
+++ b/kvfinder-web-portal/R/app_server.R
@@ -174,6 +174,10 @@ app_server <- function(input, output, session) {
         id = "download2",
         time = 0
       )
+      hideElement(
+        id = "table_footer",
+        time = 0
+      )
       hideElement(
         id = "view_str",
         time = 0
@@ -288,6 +292,10 @@ 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
diff --git a/kvfinder-web-portal/R/mod_server_checkResults.R b/kvfinder-web-portal/R/mod_server_checkResults.R
index 238ef50..b0afb68 100644
--- a/kvfinder-web-portal/R/mod_server_checkResults.R
+++ b/kvfinder-web-portal/R/mod_server_checkResults.R
@@ -92,7 +92,7 @@ check_results <- function(input, output, run_id, is_pg2, url_address, session) {
             `Vol. (A³)` = unlist(result_toml$VOLUME),
             `Avg Dep. (A)` = unlist(result_toml$AVG_DEPTH),
             `Max Dep. (A)` = unlist(result_toml$MAX_DEPTH),
-            `Hyd.` = unlist(result_toml$AVG_HYDROPATHY[names(result_toml$AVG_HYDROPATHY) != 'EisenbergWeiss'])
+            `Avg Hyd.` = unlist(result_toml$AVG_HYDROPATHY[names(result_toml$AVG_HYDROPATHY) != 'EisenbergWeiss'])
           ),
           filter = c("none"),
           style = "auto",
@@ -140,7 +140,7 @@ check_results <- function(input, output, run_id, is_pg2, url_address, session) {
         
         output$table_footer <- renderText({
           paste(
-            p("ID: Cavity ID, Area: Cavity area, Vol: Cavity volume, Dep: Cavity average depth, Hyd: Cavity average hydropathy.")
+            p(strong("ID: "), "Cavity ID, ", strong("Area: "), "Cavity area, ", strong("Vol: "), "Cavity volume, ", strong("Avg Dep: "), "Cavity average depth ,", strong("Max Dep: "), "Cavity maximum depth, ", strong("Avg Hyd: "), "Cavity average hydropathy.")
           )
         })
         # create list to store results

From 72fd843f3d373a2f1e2fa9b05a1c6eec2f8a7c7c Mon Sep 17 00:00:00 2001
From: Helder Ribeiro <helder.ribeiro@lnbio.cnpem.br>
Date: Tue, 28 Feb 2023 17:37:16 -0500
Subject: [PATCH 08/19] import ggplot2 and add ggpubr to description and
 dockerfile

---
 Dockerfile                         | 2 +-
 kvfinder-web-portal/DESCRIPTION    | 3 ++-
 kvfinder-web-portal/NAMESPACE      | 1 +
 kvfinder-web-portal/R/app_server.R | 6 ++++--
 4 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 2ee2c40..fa4c57e 100644
--- a/Dockerfile
+++ b/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 ggplot2
+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/
diff --git a/kvfinder-web-portal/DESCRIPTION b/kvfinder-web-portal/DESCRIPTION
index 0da702b..96ddaef 100644
--- a/kvfinder-web-portal/DESCRIPTION
+++ b/kvfinder-web-portal/DESCRIPTION
@@ -48,7 +48,8 @@ Imports:
     shinyfullscreen,
     shinyjs,
     shinyWidgets,
-    ggplot2
+    ggplot2,
+    ggpubr
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.1.2
diff --git a/kvfinder-web-portal/NAMESPACE b/kvfinder-web-portal/NAMESPACE
index dfa1b29..79e89b9 100644
--- a/kvfinder-web-portal/NAMESPACE
+++ b/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)
diff --git a/kvfinder-web-portal/R/app_server.R b/kvfinder-web-portal/R/app_server.R
index 66684f8..1e59ef2 100644
--- a/kvfinder-web-portal/R/app_server.R
+++ b/kvfinder-web-portal/R/app_server.R
@@ -4,6 +4,8 @@
 #'     DO NOT REMOVE.
 #' @import shiny
 #' @import shinyjs
+#' @import ggplot2
+#' 
 #'
 #' @noRd
 #'
@@ -546,7 +548,7 @@ app_server <- function(input, output, session) {
                                -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),
@@ -559,7 +561,7 @@ app_server <- function(input, output, session) {
                size = guide_legend(title.position="top", title.hjust = 0.5))
       
       # ggpubr does this for you
-      leg <- get_legend(p)
+      leg <- ggpubr::get_legend(p)
       as_ggplot(leg)
       
     }) #, height =50, width = '100%'

From b95182ba893c4be0d62f2e0301d97a6d36e24591 Mon Sep 17 00:00:00 2001
From: Helder Ribeiro <helder.ribeiro@lnbio.cnpem.br>
Date: Tue, 28 Feb 2023 17:38:53 -0500
Subject: [PATCH 09/19] add ggpubr one more time

---
 kvfinder-web-portal/R/app_server.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/kvfinder-web-portal/R/app_server.R b/kvfinder-web-portal/R/app_server.R
index 1e59ef2..c5fd464 100644
--- a/kvfinder-web-portal/R/app_server.R
+++ b/kvfinder-web-portal/R/app_server.R
@@ -562,7 +562,7 @@ app_server <- function(input, output, session) {
       
       # ggpubr does this for you
       leg <- ggpubr::get_legend(p)
-      as_ggplot(leg)
+      ggpubr::as_ggplot(leg)
       
     }) #, height =50, width = '100%'
   })

From 83620b1749f9aaa2ee78381c90dae9c1d803ef7b Mon Sep 17 00:00:00 2001
From: Helder Ribeiro <helder.ribeiro@lnbio.cnpem.br>
Date: Tue, 28 Feb 2023 18:34:48 -0500
Subject: [PATCH 10/19] improve bar hyd scale

---
 kvfinder-web-portal/R/app_server.R | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/kvfinder-web-portal/R/app_server.R b/kvfinder-web-portal/R/app_server.R
index c5fd464..6ecb9f4 100644
--- a/kvfinder-web-portal/R/app_server.R
+++ b/kvfinder-web-portal/R/app_server.R
@@ -556,7 +556,11 @@ app_server <- function(input, output, session) {
               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))
       
@@ -564,7 +568,7 @@ app_server <- function(input, output, session) {
       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)

From ac469a8eb8f739a2e92b0763e8e499243c1b27fc Mon Sep 17 00:00:00 2001
From: Helder Ribeiro <helder.ribeiro@lnbio.cnpem.br>
Date: Tue, 28 Feb 2023 20:18:02 -0500
Subject: [PATCH 11/19] add depth scale

---
 kvfinder-web-portal/R/app_server.R            | 37 ++++++++++++++++++-
 kvfinder-web-portal/R/app_ui.R                |  7 ++++
 .../R/mod_server_checkResults.R               |  9 ++++-
 3 files changed, 51 insertions(+), 2 deletions(-)

diff --git a/kvfinder-web-portal/R/app_server.R b/kvfinder-web-portal/R/app_server.R
index 6ecb9f4..a262660 100644
--- a/kvfinder-web-portal/R/app_server.R
+++ b/kvfinder-web-portal/R/app_server.R
@@ -538,10 +538,43 @@ 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,
@@ -571,6 +604,8 @@ app_server <- function(input, output, session) {
     }, 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
diff --git a/kvfinder-web-portal/R/app_ui.R b/kvfinder-web-portal/R/app_ui.R
index 67c011b..3955659 100644
--- a/kvfinder-web-portal/R/app_ui.R
+++ b/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")),
diff --git a/kvfinder-web-portal/R/mod_server_checkResults.R b/kvfinder-web-portal/R/mod_server_checkResults.R
index b0afb68..366506f 100644
--- a/kvfinder-web-portal/R/mod_server_checkResults.R
+++ b/kvfinder-web-portal/R/mod_server_checkResults.R
@@ -143,12 +143,19 @@ check_results <- function(input, output, run_id, is_pg2, url_address, session) {
             p(strong("ID: "), "Cavity ID, ", strong("Area: "), "Cavity area, ", strong("Vol: "), "Cavity volume, ", strong("Avg Dep: "), "Cavity average depth ,", strong("Max Dep: "), "Cavity maximum depth, ", strong("Avg Hyd: "), "Cavity average hydropathy.")
           )
         })
+        
+        #get values of depth for each atom 
+        str_cav = strsplit(result_pdb_cav, "\n")[[1]]
+        get_atoms = str_cav[sapply(str_cav, function(x) startsWith(x, 'ATOM'))]
+        #print(get_atoms[1:10])
+        list_depth = as.numeric(sapply(get_atoms, function(x) strsplit(x, '\\s+')[[1]][10]))
         # create list to store results
         result_list <- list(
           retrieve_input_pdb = retrieve_input_pdb,
           result_pdb_cav = result_pdb_cav,
           result_cav_names = cav_out_names,
-          result_toml = result_toml
+          result_toml = result_toml,
+          list_depth = list_depth
         )
         return(result_list)
       }

From c1b62c686370f0692189c5436ca1d0dbfc1a2367 Mon Sep 17 00:00:00 2001
From: Helder Ribeiro <helder.ribeiro@lnbio.cnpem.br>
Date: Tue, 28 Feb 2023 21:27:12 -0500
Subject: [PATCH 12/19] add color scales in pg2

---
 kvfinder-web-portal/R/app_server.R | 65 ++++++++++++++++++++++++++++++
 kvfinder-web-portal/R/app_ui.R     | 14 +++++++
 2 files changed, 79 insertions(+)

diff --git a/kvfinder-web-portal/R/app_server.R b/kvfinder-web-portal/R/app_server.R
index a262660..d3808da 100644
--- a/kvfinder-web-portal/R/app_server.R
+++ b/kvfinder-web-portal/R/app_server.R
@@ -761,11 +761,76 @@ app_server <- function(input, output, session) {
   })
   
   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%'
+    
   })
 
   #----------------------------------------------------
diff --git a/kvfinder-web-portal/R/app_ui.R b/kvfinder-web-portal/R/app_ui.R
index 3955659..c7b25f8 100644
--- a/kvfinder-web-portal/R/app_ui.R
+++ b/kvfinder-web-portal/R/app_ui.R
@@ -254,6 +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")),

From 76b7bee50aa69df4f4b799e72961c71a0f60041f Mon Sep 17 00:00:00 2001
From: Helder Ribeiro <helder.ribeiro@lnbio.cnpem.br>
Date: Tue, 28 Feb 2023 21:33:52 -0500
Subject: [PATCH 13/19] add interface res pg2

---
 kvfinder-web-portal/R/app_server.R | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/kvfinder-web-portal/R/app_server.R b/kvfinder-web-portal/R/app_server.R
index d3808da..8b71873 100644
--- a/kvfinder-web-portal/R/app_server.R
+++ b/kvfinder-web-portal/R/app_server.R
@@ -760,6 +760,11 @@ app_server <- function(input, output, session) {
     take_snapshot(input = input, output = output, is_pg2 = TRUE)
   })
   
+  observeEvent(input$interface_res_pg2, {
+    print('exeuting select')
+    interface_cav(input = input, output = output, result_pdb_list = result_pdb, is_pg2 = TRUE)
+  })
+  
   observeEvent(input$input_cavity_deep_pg2, {
     if(input$input_cavity_deep_pg2 == TRUE){
       updateCheckboxInput(session, "input_cavity_hyd_pg2", value = FALSE)  

From 271bf2e567b089540b9af0141d407601b63c82ee Mon Sep 17 00:00:00 2001
From: Helder Ribeiro <helder.ribeiro@lnbio.cnpem.br>
Date: Tue, 28 Feb 2023 22:25:02 -0500
Subject: [PATCH 14/19] improve select cav, depth and hyd relationship

---
 kvfinder-web-portal/R/mod_server_selectCAV.R | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/kvfinder-web-portal/R/mod_server_selectCAV.R b/kvfinder-web-portal/R/mod_server_selectCAV.R
index ab6251b..1835582 100644
--- a/kvfinder-web-portal/R/mod_server_selectCAV.R
+++ b/kvfinder-web-portal/R/mod_server_selectCAV.R
@@ -27,8 +27,21 @@ select_cav <- function(input, output, result_pdb_list, is_pg2) {
     NGLVieweR_proxy(structure) %>%
       updateSelection("point", sele = paste(result_pdb_list$result_cav_names, collapse = " or "))
   } else { # show one cavity to show and zoom it
-    NGLVieweR_proxy(structure) %>%
-      updateSelection("point", sele = input[[select_cavity]]) %>%
-      updateZoomMove(input[[select_cavity]], input[[select_cavity]], 2000, -20)
+    print(input$input_cavity_deep)
+    if(isTRUE(input$input_cavity_deep) | isTRUE(input$input_cavity_deep_pg2)){
+      NGLVieweR_proxy(structure) %>%
+        updateSelection("point", sele = "not all") %>%
+        updateSelection("deepth", sele = input[[select_cavity]]) %>%
+        updateZoomMove(input[[select_cavity]], input[[select_cavity]], 2000, -20)
+    } else if(isTRUE(input$input_cavity_hyd) | isTRUE(input$input_cavity_hyd_pg2)){
+      NGLVieweR_proxy(structure) %>%
+        updateSelection("hyd", sele = input[[select_cavity]]) %>%
+        updateZoomMove(input[[select_cavity]], input[[select_cavity]], 2000, -20)
+    } else{
+      NGLVieweR_proxy(structure) %>%
+        updateSelection("point", sele = input[[select_cavity]]) %>%
+        updateZoomMove(input[[select_cavity]], input[[select_cavity]], 2000, -20)
+    }
+
   }
 }

From 15bde3fee1d7e5a88f03fab3691614de83c08690 Mon Sep 17 00:00:00 2001
From: Helder Ribeiro <helder.ribeiro@lnbio.cnpem.br>
Date: Wed, 1 Mar 2023 08:15:45 -0500
Subject: [PATCH 15/19] adjust hyd selection

---
 kvfinder-web-portal/R/mod_server_selectCAV.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/kvfinder-web-portal/R/mod_server_selectCAV.R b/kvfinder-web-portal/R/mod_server_selectCAV.R
index 1835582..5808547 100644
--- a/kvfinder-web-portal/R/mod_server_selectCAV.R
+++ b/kvfinder-web-portal/R/mod_server_selectCAV.R
@@ -35,6 +35,7 @@ select_cav <- function(input, output, result_pdb_list, is_pg2) {
         updateZoomMove(input[[select_cavity]], input[[select_cavity]], 2000, -20)
     } else if(isTRUE(input$input_cavity_hyd) | isTRUE(input$input_cavity_hyd_pg2)){
       NGLVieweR_proxy(structure) %>%
+        updateSelection("point", sele = "not all") %>%
         updateSelection("hyd", sele = input[[select_cavity]]) %>%
         updateZoomMove(input[[select_cavity]], input[[select_cavity]], 2000, -20)
     } else{

From 6367534696da232dbb3108a2176f74926dff21bd Mon Sep 17 00:00:00 2001
From: Helder Ribeiro <helder.ribeiro@lnbio.cnpem.br>
Date: Wed, 1 Mar 2023 08:24:25 -0500
Subject: [PATCH 16/19] fix scale not being hidden

---
 kvfinder-web-portal/R/app_server.R | 35 +++++++++++++++++++++++++++---
 1 file changed, 32 insertions(+), 3 deletions(-)

diff --git a/kvfinder-web-portal/R/app_server.R b/kvfinder-web-portal/R/app_server.R
index 8b71873..6b61436 100644
--- a/kvfinder-web-portal/R/app_server.R
+++ b/kvfinder-web-portal/R/app_server.R
@@ -253,6 +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
+      )
     }
   })
   #----------------------------------------------------
@@ -371,6 +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
+    )
   })
   #----------------------------------------------------
 
@@ -449,6 +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")
     },
@@ -496,12 +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)
   })
   
@@ -682,6 +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")
   })
 
@@ -761,7 +791,6 @@ app_server <- function(input, output, session) {
   })
   
   observeEvent(input$interface_res_pg2, {
-    print('exeuting select')
     interface_cav(input = input, output = output, result_pdb_list = result_pdb, is_pg2 = TRUE)
   })
   

From 562626ac2d40b982030e8c0787429dc12d4541d3 Mon Sep 17 00:00:00 2001
From: Helder Ribeiro <helder.ribeiro@lnbio.cnpem.br>
Date: Wed, 1 Mar 2023 08:38:00 -0500
Subject: [PATCH 17/19] fix colro cavity load pg 2nd time

---
 .../R/mod_server_changeCAVcolor.R             | 21 ++++++++-----------
 1 file changed, 9 insertions(+), 12 deletions(-)

diff --git a/kvfinder-web-portal/R/mod_server_changeCAVcolor.R b/kvfinder-web-portal/R/mod_server_changeCAVcolor.R
index ceb30f3..9995e15 100644
--- a/kvfinder-web-portal/R/mod_server_changeCAVcolor.R
+++ b/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]])
+  }
+  
+
 }

From 9288dbf43a916666bdb3e5e36728b6948a1b4575 Mon Sep 17 00:00:00 2001
From: Helder Ribeiro <helder.ribeiro@lnbio.cnpem.br>
Date: Wed, 1 Mar 2023 08:45:12 -0500
Subject: [PATCH 18/19] remove print

---
 kvfinder-web-portal/R/mod_server_createWORKscene.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/kvfinder-web-portal/R/mod_server_createWORKscene.R b/kvfinder-web-portal/R/mod_server_createWORKscene.R
index 35ccf51..29c1ff9 100644
--- a/kvfinder-web-portal/R/mod_server_createWORKscene.R
+++ b/kvfinder-web-portal/R/mod_server_createWORKscene.R
@@ -63,7 +63,6 @@ create_work_scene <- function(input, output, protein_rep_list, protein_col_list,
   } 
   
   if(prot_or_cav == 'cav' & length(cav_rep_list) >1) { #cav mode
-    print("inside cavity mode")
     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

From 1791e64525c9e90aa3b58d96ba9d995bdd972e32 Mon Sep 17 00:00:00 2001
From: Helder Ribeiro <helder.ribeiro@lnbio.cnpem.br>
Date: Wed, 1 Mar 2023 13:01:15 -0500
Subject: [PATCH 19/19] fix table width bug

---
 kvfinder-web-portal/R/mod_server_checkResults.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/kvfinder-web-portal/R/mod_server_checkResults.R b/kvfinder-web-portal/R/mod_server_checkResults.R
index 366506f..d51d968 100644
--- a/kvfinder-web-portal/R/mod_server_checkResults.R
+++ b/kvfinder-web-portal/R/mod_server_checkResults.R
@@ -98,7 +98,7 @@ check_results <- function(input, output, run_id, is_pg2, url_address, session) {
           style = "auto",
           options = list(dom = "lBfrtip", 
                          buttons = c("excel", "pdf"), 
-                         autoWidth = TRUE,
+                         #autoWidth = TRUE,
                          scrollX = TRUE,
                          columnDefs = list(list(targets=c(1), visible=TRUE, width='10%'))
                          ),