fixed problem

.gitignore

@@ -0,0 +1,6 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+*.Rproj
+*.cache

app/server.r

@@ -1,8 +1,8 @@
 function(input, output) {
-  
+
   #keeping track of he inserted UIs
   inserted <- c()
-  
+
   #Adding the UI after choosing the UserID and clicking on the button
   observeEvent(input$start_btn, {
     id <- input$start_btn
@@ -18,39 +18,38 @@ function(input, output) {
     else{
       user <- input$user_key
       showNotification(deepblue_echo(user_key = input$user_key), type = "message", duration = 10)
-    }    
-    
+    }
+
     #progress bar for loading the UI
     withProgress(message = "Getting Projects, Epigenetics Marks, Chromosomes and Tests",min = 0,
                  max = 2, value = 0,
                  {
-                   
+
                    incProgress(amount = 1, message = "building input interface")
-                   
+
                    insertUI(selector = '#addOptions',
                             where = "afterBegin",
                             #We wrap the element in a div with id to remove it when the restart buttong pressed
                             ui = tags$div(
-                              
+
                               id = id,
 
                               selectInput('genome', "Select Genome", c(deepblue_list_genomes(user_key = user)$name,"NULL"),
                                           selected = "NULL"),
-                              
+
                               selectInput('project', 'Select Project', c(deepblue_list_projects(user_key = user)$name,
                                                                          "NULL"), selected = "NULL"),
-                              
+
                               selectInput('epigenetic_mark', 'Select an Epigenetic Mark',
                                           c(deepblue_list_epigenetic_marks(user_key = user)$name, "NULL"), multiple = TRUE,
                                           selected = "NULL"),
-                              
+
                               actionButton('list_exper_btn', "List Experiments"),
-
-
+
                               radioButtons("type_of_score", "Choose method to calculate scoring matrix",choices=
                                              c("Annotations" = "annotation", "Tiling Regions" = "tiling")),
-                              
-                              
+
+
                               conditionalPanel(
                                 condition = "input.type_of_score == 'tiling'",
                                 radioButtons("tiling_size", "Select Tiling Region Size", choices =
@@ -60,16 +59,16 @@ function(input, output) {
                    )
                    inserted <<- c(id, inserted)
                    incProgress(amount = 1, message = "done")
-                   
+
                  })
   })
-  
+
   #Adding a small UI for choosing the chromosome according the genome chosen
   observeEvent(input$genome, {
     if(input$genome != "NULL"){
       # chromsome <- input$genome
       genomes <- deepblue_list_genomes(user_key = input$user_key)
-      
+
       insertUI(selector = '#addChromosomes',
                where = "afterEnd",
                ui = tags$div(
@@ -82,8 +81,8 @@ function(input, output) {
       )
     }
   })
-  
-  
+
+
   #To remove the inserted UI and start again
   observeEvent(input$end_btn, {
     removeUI(
@@ -95,37 +94,33 @@ function(input, output) {
       selector = '#add_chr', multiple = TRUE
     )
   })
-  
-  
+
+
   #List experiments and info for experiments in a list
   all_experiments <- eventReactive(input$list_exper_btn, {
     #getting experments
-    browser()
     all_experiments <- list_experiments(genome = input$genome, epigenetic_mark = input$epigenetic_mark, project = input$project,
                      user_key = input$user_key)
 
   })
-
-  eventReactive(input$list_exper_btn, {
-    output$table <- renderTable(all_experiments())
-
-  })
-
+
+  output$table <- renderTable(all_experiments()[[1]])
+
+
   #make a table of metadata
   experiments_info_meta <- eventReactive(input$plot_btn, {
-    browser()
     #extract metadata
     experiments_info_meta <- extract_metadata(all_experiments()[[2]])
-    
+
   })
-  
+
   #Get the score matrix
   filtered_score_matrix <- eventReactive(input$plot_btn, {
     #get scoring matrix
     score_matrix_tiling_regions(experiments = all_experiments()[[1]], experiments_info_meta =  experiments_info_meta(),
-                                genome = input$genome, chr = input$chr, user_key = input$user_key) 
+                                genome = input$genome, chr = input$chr, user_key = input$user_key)
   })
-  
+
   #plot data
   plot_pca <- eventReactive(input$plot_btn, {
     #get plot
@@ -134,7 +129,7 @@ function(input, output) {
                     filtered_score_matrix = filtered_score_matrix(),
                     epigenetic_mark = input$epigenetic_mark)
   })
-  
+
   output$plot <- renderPlotly(plot_pca())
-  
+
 }

app/ui.r

@@ -12,36 +12,36 @@ library(stats)
 library(plotly)
 library(shiny)
 
-source("/home/fawaz/Desktop/Max_Planck_Job/shiny_apps/shinyApp/functions/extract_metadata.r")
-source("/home/fawaz/Desktop/Max_Planck_Job/shiny_apps/shinyApp/functions/list_experiments.r")
-source("/home/fawaz/Desktop/Max_Planck_Job/shiny_apps/shinyApp/functions/score_matrix_tiling_regions.r")
-source("/home/fawaz/Desktop/Max_Planck_Job/shiny_apps/shinyApp/functions/plot_pca_labels.r")
-source("/home/fawaz/Desktop/Max_Planck_Job/shiny_apps/shinyApp/functions/plot_correlation.r")
+source("../functions/extract_metadata.r")
+source("../functions/list_experiments.r")
+source("../functions/score_matrix_tiling_regions.r")
+source("../functions/plot_pca_labels.r")
+source("../functions/plot_correlation.r")
 
 #JvkPLwsTHbb3Fyi4
 
 fluidPage(
-  
+
   sidebarPanel(
-    
+
     textInput("user_key", "User Key", value = "anonymous_key"),
-   
+
     actionButton('start_btn', "Log-in with your ID and start"),
     actionButton('end_btn', 'Start Again'),
-    
+
     tags$div(id = 'addOptions'),
     tags$div(id = 'addChromosomes'),
-    
-    actionButton("plot_btn", "Caclulate and Plot")
-    
+
+    actionButton("plot_btn", "Calculate and Plot")
+
   ),
-  
+
   mainPanel(
     tabsetPanel(type = "tabs",
                 tabPanel("Table", tableOutput("table")),
                 tabPanel("Summary", tableOutput("summary")),
                 tabPanel("Plot", plotlyOutput('plot', width = "100%", height = "600px"))
-                
+
     )
   )
-)
+)