initial commit

tb_host/app.R

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+#
+# This is a Shiny web application. You can run the application by clicking
+# the 'Run App' button above.
+#
+# Find out more about building applications with Shiny here:
+#
+#    http://shiny.rstudio.com/
+#
+
+library(shiny)
+library(shinyjs)
+library(shinydashboard)
+#library("wesanderson") # ayyyy lmao hipster af
+library(dplyr)
+library(DT)
+library(ggplot2)
+library(grid) # for the info box
+library(plotly)
+library(shinycssloaders)
+library(NGLVieweR)
+
+# 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"
+
+genes = c("Gene 1", "Gene 2", "Gene 3", "Gene 4", "Gene 5")
+
+# Define UI for application that draws a histogram
+ui=dashboardPage(skin="purple",
+                 dashboardHeader(title="Tuberculosis Host"),
+                 dashboardSidebar(
+                   radioButtons("gene",
+                                label="Gene",
+                                choices = genes,
+                                selected="Gene 1" # "none" is a value
+                   )
+                 ),
+                 dashboardBody(
+                   useShinyjs(),
+                   fluidRow(
+                     box(
+                       title="Crystallised Structure",
+                       column(
+                         NGLVieweROutput("structure"),
+                         width=12
+                       )
+                     ),
+                     box(
+                       title="AlphaFold Structure",
+                       column(
+                         NGLVieweROutput("af_structure"),
+                         width=12
+                       )
+                     )
+                   ),
+                   fluidRow(
+                     column(
+                       DT::dataTableOutput('table'),
+                       width=12
+                     )
+                   ),
+                   verbatimTextOutput("debug")
+                 )
+)
+
+# Define server logic required to draw a histogram
+server <- function(input, output) {
+  
+  output$distPlot <- renderPlot({
+    # generate bins based on input$bins from ui.R
+    x    <- faithful[, 2]
+    bins <- seq(min(x), max(x), length.out = input$bins + 1)
+    
+    # draw the histogram with the specified number of bins
+    hist(x, breaks = bins, col = 'darkgray', border = 'white',
+         xlab = 'Waiting time to next eruption (in mins)',
+         main = 'Histogram of waiting times')
+  })
+  ### NGLViewer ####
+  # Structure Viewer WebGL/NGLViewR window
+  output$structure <- renderNGLVieweR({
+    #ngl_gene=isolate(input$switch_target)
+    #ngl_gene=input$switch_target
+    #ngl_drug=target_map[[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"
+                                     #, colorScheme = "chainid"
+                        )
+      ) %>%
+      stageParameters(backgroundColor = "lightgrey") %>%
+      setQuality("high") %>%
+      setFocus(0) %>%
+      setSpin(FALSE)
+  })
+  output$af_structure <- renderNGLVieweR({
+    #ngl_gene=isolate(input$switch_target)
+    #ngl_gene=input$switch_target
+    #ngl_drug=target_map[[ngl_gene]]
+    #ngl_pdb_file=paste0(load_dir, "Data/", ngl_drug, '/output/depth/', ngl_gene, '_complex.pdb')
+    #print(ngl_pdb_file)
+    #NGLVieweR(ngl_pdb_file) %>%
+    NGLVieweR("3pl1") %>%
+      addRepresentation("cartoon",
+                        param = list(name = "cartoon",
+                                     color="tan"
+                                     #, colorScheme = "chainid"
+                        )
+      ) %>%
+      stageParameters(backgroundColor = "lightgrey") %>%
+      setQuality("high") %>%
+      setFocus(0) %>%
+      setSpin(FALSE)
+  })
+  output$table = DT::renderDataTable(mtcars)
+  
+  
+}
+
+# Run the application 
+shinyApp(ui = ui, server = server)