add dname server

amitjavilaventura · Jan 9, 2021 · 3a27878 · 3a27878
1 parent 22453de
commit 3a27878
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Showing 7 changed files with 152 additions and 19 deletions.
diff --git a/src/app_server.R b/src/app_server.R
@@ -2,4 +2,12 @@
 ### DNApp SERVER FUNCTION ###
 #############################
 
-server <- function(input, output) {}
+source("src/app_server_dname.R")
+
+server <- function(input, output, session) {
+
+  dname_server(input, output, session)
+
+}
+
+
diff --git a/src/app_server_dname.R b/src/app_server_dname.R
@@ -0,0 +1,73 @@
+# ========================= #
+#   DNAme server function   #
+# ========================= #
+
+# Render input name in text        
+dname_input <- function(input, output, session) {
+
+    output$name <-  renderText({
+      isolate({input$dna_name})
+    })
+}
+
+# Render output name (dna name) in text
+dname_outname <- function(input, output, session) {
+    output$text_output <- renderText({
+
+      nucl_acid <- isolate({input$nucleicacid})
+      if(nucl_acid == "DNA"){ table = dna_codon_aa }
+      else if(nucl_acid == "mRNA"){ table = rna_codon_aa }
+
+      DNAme <- name2dna(input = isolate({input$dna_name}), nucleic_acid = nucl_acid,
+                        table = table, codon_usage = isolate({input$codon_usage}), 
+                        sep = isolate({input$separator}))
+      if(is.list(DNAme)){ paste(DNAme$name) }
+      else{ paste(DNAme) }
+    })
+}
+
+# Render table with all 1-letter, 3-letter aa, aa names and most frequent codons for several species.
+dname_table <- function(input, output, session) {
+  output$table_output <- renderTable({
+
+    nucl_acid <- isolate({input$nucleicacid})
+    if(nucl_acid == "DNA"){ table = dna_codon_aa }
+    else if(nucl_acid == "mRNA"){ table = rna_codon_aa }
+
+    DNAme <- name2dna(input = isolate({input$dna_name}), nucleic_acid = nucl_acid,
+                      table = table, codon_usage = isolate({input$codon_usage}), 
+                      sep = isolate({input$separator}))    
+
+    if(is.list(DNAme)){ DNAme$df }
+    else{ paste(DNAme) }
+  })
+}
+
+dname_dsDNA <- function(input, output, session) {
+  output$dsDNA_name <- renderTable({
+
+    nucl_acid <- isolate({input$nucleicacid})
+    if(nucl_acid == "DNA"){ table = dna_codon_aa }
+    else if(nucl_acid == "mRNA"){ table = rna_codon_aa }
+
+    DNAme <- name2dna(input = isolate({input$dna_name}), nucleic_acid = nucl_acid,
+                      table = table, codon_usage = isolate({input$codon_usage}), 
+                      sep = isolate({input$separator}))
+
+    if(is.list(DNAme)){ DNAme$ds_name }
+    else{ paste(DNAme) }
+  }, spacing = "xs")
+}
+
+# DNAme server function complete
+dname_server <- function(input, output, session) {
+
+  observeEvent(input$submit_dname, {
+    dname_input(input, output, session)
+    dname_outname(input, output, session)
+    dname_table(input, output, session)
+    dname_dsDNA(input, output, session)
+  })
+
+}
+
diff --git a/src/app_ui_body_about.R b/src/app_ui_body_about.R
@@ -14,7 +14,7 @@ dnapp_body_about <-
           tags$p("The apps currently present in DNApp are:",
                  tags$ul(tags$li("DNAme"),
                          tags$li("sNAP+"))),
-          br(),br(),br(),br(),
+          br(),br(),br(),br(),br(),br(),br(),br(),
           HTML('<center><a rel="license" href="http://creativecommons.org/licenses/by-nc-nd/4.0/">
                <img alt="Creative Commons Licence" style="border-width:0" 
                src="https://i.creativecommons.org/l/by-nc-nd/4.0/88x31.png" />

diff --git a/src/app_ui_body_dname.R b/src/app_ui_body_dname.R
@@ -1,5 +1,9 @@
+# ======================== #
+#   DNAme user interface   #
+# ======================== #
 
-
+############
+# UI ABOUT #
 
 dnapp_body_dname_about <- tabItem(tabName = "dname_about",
                                   HTML('<p style="font-size:30px;font-family:Helvetica;color:black;"><u>Welcome to DNAme!</u></p>'),
@@ -76,22 +80,33 @@ dnapp_body_dname_about <- tabItem(tabName = "dname_about",
 
 
 
+##########
+# UI APP #
+
 dnapp_body_dname_app  <- tabItem("dname_app",
                                  splitLayout(cellWidths = c("30%", "70%"),
                                     column(width = 12,
                                       box(title = tagList(icon("dna"), "DNA your name"), width = 12, solidHeader = T,
-                                          textInput(inputId = "name", label = "Write your name", value = "DNAme"),
-                                          actionButton(inputId = "submit", label = "DNAme")),
+                                          textInput(inputId = "dna_name", label = "Write your name", value = "DNAme"),
+                                          actionButton(inputId = "submit_dname", label = "DNAme")),
                                       box(title = tagList(icon("gear"), "Parameters"), width = 12, collapsible = T, collapsed = T,
                                           selectInput(inputId = "nucleicacid", label = "Select the nucleic acid:", choices = c("DNA", "mRNA"), selected = "DNA", selectize = T),
                                           selectInput(inputId = "codon_usage", label = "Select an organism:", selected = "Human", choices = list("Human" = "Human", "Mouse" = "Mouse","C. elegans" = "Celegans", "A. thaliana" = "Athaliana", "E. coli" = "Ecoli")),
-                                          textInput(inputId = "separator", label = "Write a separator:", value = "-"))),
+                                          textInput(inputId = "separator", label = "Write a separator:", value = ""))),
 
-                                  conditionalPanel(condition = "input.submit > 0",
-                                          h4("This is your DNA name!"),
-                                          tags$div(HTML(paste(tags$span(style="color:blue", textOutput(outputId = "name"))))),
-                                          tags$div(HTML(paste(tags$span(style="color:red; font-face:bold; font-size:30px", textOutput("text_output"))))),
-                                          br(),br(),
-                                          h4("Information"),
-                                          helpText("This is all the information in the letters of your name."),
-                                          tableOutput(outputId = "table_output"))))
+                                  conditionalPanel(condition = "input.submit_dname > 0",
+                                          h4("Input name:"),
+                                          tags$div(HTML(paste(tags$span(style="color:blue; font-size:20px; font-family:courier;", textOutput(outputId = "name"))))),
+                                          br(),
+                                          h4("DNA name:"),
+                                          tags$div(HTML(paste(tags$span(style="color:red; font-face:bold; font-size:30px; font-family:courier;", 
+                                                                        textOutput("text_output"))))),
+                                          br(),
+                                          conditionalPanel(condition = "input.nucleicacid == 'DNA'",
+                                                           h4("dsDNA name:"),
+                                                           tags$div(tableOutput("dsDNA_name"), style = "font-family:courier; font-size:25px"),
+                                                           br()),
+                                          h4("Information:"),
+                                          tableOutput("table_output"))))
+
+
diff --git a/src/app_ui_body_snap.R b/src/app_ui_body_snap.R
@@ -1,3 +1,6 @@
+# ======================== #
+#   sNAP+ user interface   #
+# ======================== #
 
 dnapp_body_snap_about <-
 tabItem(tabName = "snap_about", 

diff --git a/src/functions_dname.R b/src/functions_dname.R
@@ -36,7 +36,7 @@ is.letter.normal <- function(input){
 
 # ----- is.aa.letter ----- # 
 # function to check if all letters in input have an associated amino acid
-is.aa.letter <- function(input){
+is.not.aa <- function(input){
 
   library(dplyr)
 
@@ -46,11 +46,35 @@ is.aa.letter <- function(input){
   return(check.aa.letter)
 }
 
+# ----- Get complementary sequence ----- # 
+# function to make the complementary sequence of an input
+dna_complementary <- function(input, sep=""){
+
+  query <- str_to_upper(input) %>% str_split(pattern = "") %>% unlist()
+  complement <- character(length = length(query))
+
+  for(i in 1:length(query)){
+      complement[i] <- if_else(str_detect(query[i], "A"), "T",
+                               if_else(str_detect(query[i], "G"), "C",
+                                       if_else(str_detect(query[i], "T"), "A",
+                                               if_else(str_detect(query[i], "C"), "G", " ")))) 
+  }
+
+  ds_name <- data_frame(`5' -> 3'` = paste(query, collapse = sep),
+                        `3' <- 5'` = paste(complement, collapse = sep)) %>% 
+    t() %>% 
+    as.data.frame() %>%
+    set_colnames(c(" "))
+
+  return(ds_name)
+
+}
+
 
 # ----- Convert Name to DNA ----- #
-name2dna <- function(input="DNAmeà", table = dna_codon_aa, codon_usage = "Human", sep = "-"){
+name2dna <- function(input="DNAme", nucleic_acid = "DNA", table = dna_codon_aa, codon_usage = "Human", sep = "-"){
 
-  #library(Biostrings)
+  library(Biostrings)
   library(stringr)
   library(dplyr)
   library(magrittr)
@@ -68,7 +92,7 @@ name2dna <- function(input="DNAmeà", table = dna_codon_aa, codon_usage = "Human
   else{
 
     # if there are not allowed letters --> stop
-    if(TRUE %in% is.aa.letter(input)){
+    if(TRUE %in% is.not.aa(input)){
 
       message <- paste("One of the letters in", input, "does not have an associated amminoacid.")
       return(message)
@@ -92,11 +116,15 @@ name2dna <- function(input="DNAmeà", table = dna_codon_aa, codon_usage = "Human
 
       DNAme$name <- paste((dna_name %>% select(codon_usage))[1:length(name),1], collapse = sep)
 
+      if(nucleic_acid == "DNA"){
+        DNAme$ds_name <- dna_complementary(paste((dna_name %>% select(codon_usage))[1:length(name),1], collapse = ""), sep = "")
+      }
+
       # return list
       return(DNAme)
       }
-
   }
 
 }
 
+
diff --git a/src/tables_dname.R b/src/tables_dname.R
@@ -32,4 +32,10 @@ rna_codon_aa <- data.frame(one_letter = c("A", "C", "D", "E", "F", "G", "H", "I"
                                            "AAU", "CCU", "CAA", "AGA", "UCU", "ACU", "GUU", "UGG", "UAU", "  "), 
                            Ecoli       = c("GCG", "UGC", "GAU", "GAA", "UUU", "GGC", "CAU", "AUU", "AAA", "CUG", "AUG",
                                            "AAC", "CCG", "CAG", "CGU", "AGC", "ACC", "GUG", "UGG", "UAU", "  "),
+
+
+
+
+
+
                            stringsAsFactors = F)