0.4.0

app.R

@@ -4,7 +4,7 @@
 
 # shiny::runApp("./")
 # Setup
-rtemisseq_version <- "0.3.0"
+rtemisseq_version <- "0.4.0"
 library(rtemis)
 library(rtemisbio)
 library(shiny)
@@ -29,31 +29,50 @@ source("data.R")
 #' @return A shiny app that can be converted to a shinylive app
 
 rtemisseq <- function(
-    default_theme = "dark",
-    protein_plotly_height = "900px",
-    jsonedit_height = "900px",
-    verbosity = 0) {
+  default_theme = "dark",
+  protein_plotly_height = "900px",
+  jsonedit_height = "900px",
+  verbosity = 0L
+) {
   # Logo
   logo <- base64enc::dataURI(
-    file = "./www/rtemisseq_gray.png", mime = "image/png"
+    file = "./www/rtemisseq_gray.png",
+    mime = "image/png"
   )
   # Version
   platform <- sessionInfo()[["platform"]]
   svl <- paste0(
-    "rtemisseq v", rtemisseq_version,
-    " | ", "rtemisbio v", utils::packageVersion("rtemisbio"),
-    " | ", "rtemis v", utils::packageVersion("rtemis"),
-    " | R v", version$major, ".", version$minor,
-    " | running on ", platform
+    "rtemisseq v",
+    rtemisseq_version,
+    " | ",
+    "rtemisbio v",
+    utils::packageVersion("rtemisbio"),
+    " | ",
+    "rtemis v",
+    utils::packageVersion("rtemis"),
+    " | R v",
+    version$major,
+    ".",
+    version$minor,
+    " | running on ",
+    platform
   )
 
   # Shinylive info
   shinylive_info <- if (substr(platform, 1, 4) == "wasm") {
     paste0(
       "<br><br>This application has been compiled to ",
-      as.character(a("WebAssembly", href = "https://webassembly.org/", target = "_blank")),
+      as.character(a(
+        "WebAssembly",
+        href = "https://webassembly.org/",
+        target = "_blank"
+      )),
       " using ",
-      as.character(a("shinylive", href = "https://posit-dev.github.io/r-shinylive/", target = "_blank")),
+      as.character(a(
+        "shinylive",
+        href = "https://posit-dev.github.io/r-shinylive/",
+        target = "_blank"
+      )),
       "<br>and is best viewed with the latest version of Chrome."
     )
   } else {
@@ -107,10 +126,18 @@ rtemisseq <- function(
             br(),
             HTML(paste0(
               "rtemisSeq is a web interface for ",
-              as.character(a("rtemisbio", href = "https://rtemis.org/rtemisbio", target = "_blank")),
+              as.character(a(
+                "rtemisbio",
+                href = "https://rtemis.org/rtemisbio",
+                target = "_blank"
+              )),
               ", <br>providing interactive visualization of sequence data.",
               "<br>Created for the ",
-              as.character(a("FTD CWOW", href = "https://cwow.ucsf.edu/", target = "_blank")),
+              as.character(a(
+                "FTD CWOW",
+                href = "https://cwow.ucsf.edu/",
+                target = "_blank"
+              )),
               ".<br><br>",
               rthelp_inline(
                 "To get started, use the navigation tabs at the top.",
@@ -118,7 +145,8 @@ rtemisseq <- function(
               ),
               shinylive_info
             )),
-            br(), br(),
+            br(),
+            br(),
             bslib::card_image(
               file = "./www/rtemisseq-splash.webp",
               alt = "rtemisseq",
@@ -191,6 +219,37 @@ rtemisseq <- function(
         #   ) # /nav_panel jsonedit
         # ) # /navset_card_tab
       ), # /nav_panel Protein Visualization
+      ## [] PDB Viewer ----
+      bslib::nav_panel(
+        title = "PDB Viewer",
+        icon = bsicons::bs_icon("box"),
+        card(
+          full_screen = TRUE,
+          class = "p-0",
+          # allow items side by side ----
+          card_header(
+            class = "d-flex justify-content-end",
+            # tooltip UI output ----
+            # uiOutput("ui_pdb_tooltip"),
+            # popover UI output ----
+            # uiOutput("ui_pdb_popover")
+          ),
+          layout_sidebar(
+            fillable = TRUE,
+            # Data Load Sidebar ----
+            sidebar = bslib::sidebar(
+              uiOutput("ui_pdb_settings"), # PDB settings
+              # uiOutput("ui_a3_load_switch"), # Switch between file upload and built-in data
+              # uiOutput("ui_a3_data_load"), # File upload or built-in data selection depending on switch
+              # uiOutput("ui_a3_data_info"), # Shows dataset info
+              # uiOutput("ui_a3_plot_button"), # Click to plot
+              # uiOutput("ui_a3_tooltip")
+            ),
+            # Plot Output ----
+            NGLVieweR::NGLVieweROutput("pdb", width = "100%", height = "900px")
+          )
+        ) # /card
+      ), # /nav_panel PDB Viewer
       ## [] About ----
       bslib::nav_panel(
         title = "About",
@@ -202,10 +261,18 @@ rtemisseq <- function(
               class = "text-center",
               HTML(paste0(
                 "Created by the ",
-                as.character(a("FTD CWOW", href = "https://cwow.ucsf.edu/", target = "_blank")),
+                as.character(a(
+                  "FTD CWOW",
+                  href = "https://cwow.ucsf.edu/",
+                  target = "_blank"
+                )),
                 " Genomics & Transcriptomics core.<br/>",
                 "Powered by rtemis & rtemisbio (",
-                as.character(a("rtemis.org", href = "https://rtemis.org", target = "_blank")),
+                as.character(a(
+                  "rtemis.org",
+                  href = "https://rtemis.org",
+                  target = "_blank"
+                )),
                 ")."
               ))
             ), # /div
@@ -288,10 +355,14 @@ rtemisseq <- function(
 
     # GitHub files runs when github_files_update_button is clicked ----
     github_files <- reactive({
-      get_github_files(repo_owner = "rtemis-org", repo_name = "seq-data", verbosity = verbosity)
+      get_github_files(
+        repo_owner = "rtemis-org",
+        repo_name = "seq-data",
+        verbosity = verbosity
+      )
     }) |>
       bindEvent(input$github_files_update_button)
-    
+
     # GitHub file list output ----
     output$ui_github_files <- shiny::renderUI({
       req(github_files())
@@ -337,8 +408,16 @@ rtemisseq <- function(
         shiny::selectizeInput(
           inputId = "a3_builtin_data",
           label = "Select built-in a3 dataset",
-          choices = c("MAPT_Annot", "MAPT_Cleavage", "MAPT_Citrullination"),
-          selected = "MAPT_Annot"
+          choices = c(
+            "MAPT_PTM",
+            "MAPT_Cathepsin_Cleavage",
+            "MAPT_APP_Cleavage_3_4",
+            "MAPT_APP_Cleavage_4_5",
+            "MAPT_APP_Cleavage_5_5",
+            "MAPT_APP_Cleavage_7_4",
+            "MAPT_Citrullination"
+          ),
+          selected = "MAPT_PTM"
         )
       }
     }) # /ui_a3_data_load
@@ -396,8 +475,12 @@ rtemisseq <- function(
         }
         # index with input$github_file
         jsondat <- httr::GET(
-          github_files()[github_files()$file_name == input$github_file, "download_url"]
-        ) |> httr::content(as = "text", encoding = "UTF-8")
+          github_files()[
+            github_files()$file_name == input$github_file,
+            "download_url"
+          ]
+        ) |>
+          httr::content(as = "text", encoding = "UTF-8")
         dat <- as.a3(jsonlite::parse_json(
           jsondat,
           simplifyVector = TRUE,
@@ -435,7 +518,11 @@ rtemisseq <- function(
     output$dplot3_protein <- plotly::renderPlotly({
       req(a3_obj())
       if (verbosity > 0) {
-        message("Rendering dplot3_protein of object with class '", class(a3_obj())[1], "'")
+        message(
+          "Rendering dplot3_protein of object with class '",
+          class(a3_obj())[1],
+          "'"
+        )
       }
       plot(
         a3_obj(),
@@ -447,7 +534,8 @@ rtemisseq <- function(
         bg = input$plot.bg, # legend.bg defaults to transparent, this sets paper bg
         plot.bg = input$plot.bg,
         marker.col = input$marker.col,
-        n.per.row = if (input$n.per.row == "auto") NULL else as.integer(input$n.per.row)
+        n.per.row = if (input$n.per.row == "auto") NULL else
+          as.integer(input$n.per.row)
       )
     }) |> # /dplot3_protein
       bindEvent(input$a3_plot_button, input$a3_plot_update_button)
@@ -462,7 +550,8 @@ rtemisseq <- function(
     output$ui_a3_tooltip <- shiny::renderUI({
       bslib::tooltip(
         trigger = span(
-          "Plot help", bsicons::bs_icon("info-circle", class = "text-info"),
+          "Plot help",
+          bsicons::bs_icon("info-circle", class = "text-info"),
           style = "text-align: right;",
           class = "rtanihi"
         ),
@@ -490,10 +579,36 @@ rtemisseq <- function(
           #   "Plot settings", bsicons::bs_icon("gear", class = "ms-auto"),
           #   style = "text-align: right;"
           # shiny::selectizeInput("a3.theme", label = "Theme", choices = c("dark", "light"), selected = default_theme),
-          shiny::sliderInput("marker.size", label = "Marker size", min = 1, max = 100, value = 28),
-          shiny::sliderInput("font.size", label = "Font size", min = 1, max = 72, value = 18),
-          if (length(a3_obj()$Annotations$PTM) > 0) shiny::sliderInput("ptm.marker.size", label = "PTM Marker size", min = .1, max = 36, value = 28 / 4.5),
-          if (length(a3_obj()$Annotations$Cleavage_site) > 0) shiny::sliderInput("clv.marker.size", label = "Cleavage Site Marker size", min = .1, max = 36, value = 28 / 4),
+          shiny::sliderInput(
+            "marker.size",
+            label = "Marker size",
+            min = 1,
+            max = 100,
+            value = 28
+          ),
+          shiny::sliderInput(
+            "font.size",
+            label = "Font size",
+            min = 1,
+            max = 72,
+            value = 18
+          ),
+          if (length(a3_obj()$Annotations$PTM) > 0)
+            shiny::sliderInput(
+              "ptm.marker.size",
+              label = "PTM Marker size",
+              min = .1,
+              max = 36,
+              value = 28 / 4.5
+            ),
+          if (length(a3_obj()$Annotations$Cleavage_site) > 0)
+            shiny::sliderInput(
+              "clv.marker.size",
+              label = "Cleavage Site Marker size",
+              min = .1,
+              max = 36,
+              value = 28 / 4
+            ),
           shinyWidgets::colorPickr(
             "plot.bg",
             label = "Plot background",
@@ -529,7 +644,6 @@ rtemisseq <- function(
       }
     }) # /ui_a3_popover
 
-
     # UI dplot3_protein ----
     output$ui_dplot3_protein <- renderUI({
       if (clicked() == FALSE || is.null(a3_obj())) {
@@ -559,6 +673,73 @@ rtemisseq <- function(
         height = jsonedit_height
       )
     })
+
+    # UI PDB settings ----
+    output$ui_pdb_settings <- renderUI({
+      list(
+        shiny::textInput(
+          inputId = "pdbcode",
+          label = "PDB code",
+          value = "2MZ7"
+        ),
+        shiny::selectInput(
+          inputId = "pdbrepresentation",
+          label = "Representation type",
+          choices = c(
+            "cartoon",
+            "ball+stick",
+            "line",
+            "surface",
+            "ribbon"
+          ),
+          selected = "cartoon"
+        ),
+        shiny::selectInput(
+          inputId = "pdbcolorscheme",
+          label = "Color Scheme",
+          choices = c(
+            "residueindex",
+            "element",
+            "hydrophobicity",
+            "occupancy",
+            "partialcharge"
+          ),
+          selected = "residueindex"
+        ),
+        shiny::radioButtons(
+          inputId = "pdbanimate",
+          label = hilite1("Animation"),
+          choices = c("Off", "Rock", "Spin"),
+          selected = "Off",
+          inline = TRUE
+        )
+      ) # /list
+    })
+
+    # PDB Viewer ----
+    output$pdb <- NGLVieweR::renderNGLVieweR({
+      req(input$pdbcode, input$pdbrepresentation, input$pdbcolorscheme)
+      NGLVieweR::NGLVieweR(input$pdbcode) |>
+        NGLVieweR::addRepresentation(
+          input$pdbrepresentation,
+          param = list(color = input$pdbcolorscheme)
+        ) |>
+        NGLVieweR::stageParameters(backgroundColor = "#161616") |>
+        NGLVieweR::setQuality("high") |>
+        NGLVieweR::setFocus(0)
+    })
+
+    observeEvent(input$pdbanimate, {
+      if (input$pdbanimate == "Rock") {
+        NGLVieweR::NGLVieweR_proxy("pdb") |> NGLVieweR::updateRock(TRUE)
+      } else if (input$pdbanimate == "Spin") {
+        NGLVieweR::NGLVieweR_proxy("pdb") |> NGLVieweR::updateSpin(TRUE)
+      } else {
+        NGLVieweR::NGLVieweR_proxy("pdb") |>
+          NGLVieweR::updateRock(FALSE) |>
+          NGLVieweR::updateSpin(FALSE)
+      }
+    })
   } # /server
 
   # Shiny app ----