Minor dings in lab 9 exercises

R/central_dogma_assignment.R

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+# Load the shiny library --------------------------------------------------
+library("shiny")
+
+
+
+# Load the library containing the `card()`-function -----------------------
+library("bslib")
+
+
+
+# Define app functions ----------------------------------------------------
+gene_dna <- function(length, base_probs = c(0.25, 0.25, 0.25, 0.25)) {
+  if (length %% 3 != 0) {
+    stop("The argument to the parameter 'length' has to be divisible by 3")
+  }
+  if (!(abs(sum(base_probs) - 1) < 1e-10)) {
+    stop("The sum of the vector-argument to the base_probs-parameter must be 1")
+  }
+  dna_vector <- sample(
+    x = c("A", "T", "C", "G"),
+    size = length,
+    replace = TRUE,
+    prob = base_probs
+  )
+  dna_string <- paste0(x = dna_vector, collapse = "")
+  return(dna_string)
+}
+transcribe_dna <- function(dna){
+  rna <- gsub(
+    pattern = "T",
+    replacement = "U",
+    x = dna)
+  return(rna)
+}
+translate_rna <- function(rna){
+  if( is.null(rna) || rna == "" ){ return("") }
+  l <- nchar(x = rna)
+  firsts <- seq(
+    from = 1,
+    to = l,
+    by = 3)
+  lasts <- seq(
+    from = 3,
+    to = l,
+    by = 3)
+  codons <- substring(
+    text = rna,
+    first = firsts,
+    last = lasts)
+  codon_table <- c(
+    "UUU" = "F", "UCU" = "S", "UAU" = "Y", "UGU" = "C",
+    "UUC" = "F", "UCC" = "S", "UAC" = "Y", "UGC" = "C",
+    "UUA" = "L", "UCA" = "S", "UAA" = "_", "UGA" = "_",
+    "UUG" = "L", "UCG" = "S", "UAG" = "_", "UGG" = "W",
+    "CUU" = "L", "CCU" = "P", "CAU" = "H", "CGU" = "R",
+    "CUC" = "L", "CCC" = "P", "CAC" = "H", "CGC" = "R",
+    "CUA" = "L", "CCA" = "P", "CAA" = "Q", "CGA" = "R",
+    "CUG" = "L", "CCG" = "P", "CAG" = "Q", "CGG" = "R",
+    "AUU" = "I", "ACU" = "T", "AAU" = "N", "AGU" = "S",
+    "AUC" = "I", "ACC" = "T", "AAC" = "N", "AGC" = "S",
+    "AUA" = "I", "ACA" = "T", "AAA" = "K", "AGA" = "R",
+    "AUG" = "M", "ACG" = "T", "AAG" = "K", "AGG" = "R",
+    "GUU" = "V", "GCU" = "A", "GAU" = "D", "GGU" = "G",
+    "GUC" = "V", "GCC" = "A", "GAC" = "D", "GGC" = "G",
+    "GUA" = "V", "GCA" = "A", "GAA" = "E", "GGA" = "G",
+    "GUG" = "V", "GCG" = "A", "GAG" = "E", "GGG" = "G")
+  protein <- paste0(
+    x = codon_table[codons],
+    collapse = "")
+  return(protein)
+}
+base_freqs <- function(dna){
+  if (is.null(dna) || dna == "" ){
+    return( data.frame(dna_vec = factor(c("A", "C", "G", "T")),
+                       Freq = c(0, 0, 0, 0)) ) }
+  dna_vec <- strsplit(x = dna,
+                      split = "")
+  base_counts <- table(dna_vec)
+  return( as.data.frame.table(base_counts) )
+}
+
+
+
+# Define the User Interface (Frontend) ------------------------------------
+ui <- page_fluid(
+  layout_columns(
+    col_widths = 12,
+    card(
+      titlePanel("Virtual Central Dogma"),
+      style = "background-color: #f0f0f0; padding: 15px;"
+    )),
+  layout_columns(
+    col_widths = 12,
+    card(
+      titlePanel("About"),
+      helpText("This Shiny app emulates the central dogma of biology:",
+               "DNA => RNA => Protein")
+    )),
+  layout_columns(
+    col_widths = 12,
+    card(
+      card_header("Virtual Gene Generator"),
+      sliderInput(inputId = "n_bases",
+                  label = "Number of bases:",
+                  min = 1,
+                  max = 60,
+                  value = 30,
+                  width = "100%"),
+      layout_columns(
+        col_widths = c(3, 3, 3, 3),
+        numericInput(inputId = "prob_A",
+                     label = "Probability of A",
+                     value = 0.25,
+                     min = 0,
+                     max = 1,
+                     step = 0.1),
+        numericInput(inputId = "prob_T",
+                     label = "Probability of T",
+                     value = 0.25,
+                     min = 0,
+                     max = 1,
+                     step = 0.1),
+        numericInput(inputId = "prob_C",
+                     label = "Probability of C",
+                     value = 0.25,
+                     min = 0,
+                     max = 1,
+                     step = 0.1),
+        numericInput(inputId = "prob_G",
+                     label = "Probability of G",
+                     value = 0.25,
+                     min = 0,
+                     max = 1,
+                     step = 0.1)
+    ))),
+  layout_columns(
+    col_widths = 12,
+    card(
+      card_header("Virtual Gene output"),
+      mainPanel(
+        verbatimTextOutput(outputId = "dna")
+      )
+    )),
+  layout_columns(
+    col_widths = 12,
+    card(
+      card_header("Virtual RNA polymerase"),
+      textInput(inputId = "gene_dna",
+                label = "Copy/paste the virtual gene to here",
+                value = "",
+                width = "100%")
+    )),
+  layout_columns(
+    col_widths = 12,
+    card(
+      card_header("Virtual RNA polymerase output"),
+      mainPanel(
+        verbatimTextOutput(outputId = "rna")
+      )
+    )),
+  layout_columns(
+    col_widths = 12,
+    card(
+      card_header("Virtual Ribosome"),
+      textInput(inputId = "gene_rna",
+                label = "Copy/paste the virtual RNA to here",
+                value = "",
+                width = "100%")
+    )),
+  layout_columns(
+    col_widths = 12,
+    card(
+      card_header("Virtual RNA polymerase output"),
+      mainPanel(
+        verbatimTextOutput(outputId = "protein")
+      )
+    )),
+  layout_columns(
+    col_widths = 12,
+    card(
+      card_header("Analyse Nucleotide Frequencies"),
+      mainPanel(
+        plotOutput(outputId = "freq_analysis_plot")
+      )
+    ))
+)
+
+
+
+# Define the Server (Backend) ---------------------------------------------
+server <- function(input, output) {
+  output$dna <- renderText({
+    gene_dna(length = input$n_bases,
+             base_probs = c(input$prob_A, input$prob_T, input$prob_C, input$prob_G))
+  })
+  output$rna <- renderText({
+    transcribe_dna(dna = input$gene_dna)
+  })
+  output$protein <- renderText({
+    translate_rna(rna = input$gene_rna)
+  })
+  output$freq_analysis_plot <- renderPlot({
+    input$gene_dna |> 
+      base_freqs() |> 
+    ggplot2::ggplot(
+      mapping = ggplot2::aes(
+        x = dna_vec,
+        y = Freq / sum(Freq),
+        fill = dna_vec,
+        label = stringr::str_c(round(Freq / sum(Freq) * 100,
+                                     digits = 2), "%"))) +
+      ggplot2::geom_col(colour = "black") +
+      ggplot2::geom_hline(yintercept = 0) +
+      ggplot2::geom_text(nudge_y = 0.05) +
+      ggplot2::scale_y_continuous(limits = c(0, 1)) +
+      ggplot2::theme_minimal() +
+      ggplot2::theme(legend.position = "none") +
+      ggplot2::labs(x = "Nucleotide",
+                    y = "Relative Frequency")
+  })
+}
+
+
+
+# Launch the shiny app ----------------------------------------------------
+shinyApp(ui = ui, server = server)