Inicialización

2022-07-12 12:52:25 +02:00
commit 4efb48600f
2 changed files with 72 additions and 0 deletions
@@ -0,0 +1,72 @@
+library(shiny)
+library(seqRFLP)
+library(reversetranslate)
+
+# Define UI 
+ui <- fluidPage(
+
+  # Application title
+  titlePanel("Reverse tranlation"),
+  
+  navbarPage("Apps",
+     tabPanel("Translation",
+        sidebarPanel(
+          fileInput("file1", "Sube fichero mfasta", multiple = FALSE),
+          selectInput("spec", label = h3("Specie"), 
+                      choices = list("Human" = 1, "E. Coli" = 2), 
+                      selected = 1),
+          actionButton("calab", "Analizar")
+        ),
+
+        mainPanel(
+          textAreaInput("seqText", label="Enter mFasta text", width = "100%", height = "500px", value=""),
+          # tags$head(tags$style(HTML("pre { white-space: pre-wrap; word-break: break-all; }"))),
+          htmlOutput("seqDNA")
+        )
+    ),
+    tabPanel("Codon Frequency Table",
+      mainPanel(
+        tableOutput("tbl")
+      )
+    )
+  )
+)
+
+# Define server
+server <- function(input, output) {
+
+    output$seqDNA <- renderText({
+        if (input$seqText == ""){
+          print("Result")
+        }else{
+          seqs<-strsplit(input$seqText,"\n")[[1]]
+          names_seqs<-seqs[grepl("^>",seqs)]
+          names_seqs<-gsub(">","", names_seqs)
+          seqs<-seqs[!grepl("^>", seqs)]
+          
+          if(input$spec == 1){spec<-hsapien_tbl}
+          if(input$spec == 2){spec<-ecoli_tbl}
+          
+          seqs_DNA<-c()
+          progress <- shiny::Progress$new(min=0, max=length(seqs))
+          for (i in 1:length(seqs)){
+            set.seed(123)
+            seqs_DNA<-c(seqsDNA<-reverse_translate(seqs[i],spec))
+            progress$set(message = "Reverse Translating", value = i)
+          }
+          
+          paste(dataframe2fas(data.frame(names=names_seqs, 
+                                         seqs=seqs_DNA)), collapse="<br>")
+        }
+    })
+    {
+      output$tbl <- renderTable({
+        if(input$spec == 1){spec<-hsapien_tbl}
+        if(input$spec == 2){spec<-ecoli_tbl}
+        spec %>% arrange(aa)
+      })
+    }
+}
+
+# Run the application 
+shinyApp(ui = ui, server = server)