inst/app/server.R

In thierrycnam/igfuns: Analyzes of Ig sequencing data

library(igfuns)
library(dplyr)
library(kableExtra)
server <- function(input, output, session) {

  # Tables
  output$table_bregs <- renderDataTable({
    bregs
  })

  output$chisq_table_1 <- function(){
    react_chisq_test()$observed %>%
      kable() %>%
      kable_styling("striped")
  }

  output$chisq_table_2 <- function(){
    react_chisq_test()$expected %>%
      kable() %>%
      kable_styling("striped")
  }

  output$fisher_table_1 <- function(){
    react_fisher_test()$observed %>%
      kable() %>%
      kable_styling("striped")
  }

  output$fisher_table_2 <- function(){
    react_fisher_test()$expected %>%
      kable() %>%
      kable_styling("striped")
  }

  ## Gene frequencies
  output$v_gene_table <- renderDataTable({
    get_freq(v)
  })

  output$j_gene_table <- renderDataTable({
    get_freq(j)
  })



  # Render prints
  output$chisq_result <- renderPrint({
    react_chisq_test()
  })

  output$fisher_result <- renderPrint({
    react_fisher_test()
  })

  output$text_bregs <- renderPrint({
    summary(react_df_charges_gravy())
  })

  output$print_select_input_1 <- renderPrint({
    input$select_input_1
  })

  # Render UI
  output$ui_select_input_1 <- renderUI({
    choices <-
      react_df_charges_gravy() %>%
      select(-c(v, j, b_cell_subset, sample))
    list_choices <-
      as.list(setNames(choices, choices))
    selectInput("select_input_1",
                label = "Select a qualitative variable",
                choices = list_choices,
                multiple = FALSE)
  })
  # Reactives
  react_df_1 <- reactive({
    df_1 <-
      bregs %>%
      select(v, j) %>%
      table()
    df_1
  })

  react_chisq_test <- reactive({
    chisq.test(react_df_1())
  })

  react_fisher_test <- reactive({
    fisher.test(react_df_1())
  })

  #
  react_df_charges_gravy <- reactive({
    bregs %>%
      select(sample, b_cell_subset,
             pos_ch_cdr3, neg_ch_cdr3,
             pos_ch_vreg, neg_ch_vreg,
             gravy_cdr3, gravy_vreg,
             length, length_v,
             v, j)
  })

  # Plots
  output$donut_v_plot <- renderPlot({
    df_1 <- get_freq(v)
    get_donut_plot(df_1, freq, v)
  })

  output$donut_j_plot <- renderPlot({
    df_1 <- get_freq(j)
    get_donut_plot(df_1, freq, j)
  })
}