Code Editor for app.R

library(magrittr)
library(shiny)
library(dplyr)
library(ggplot2)
library(DT)
library(archs4)

ui <- fluidPage(
    titlePanel("Differential Analysis with ARCHS4 Data"),
    sidebarLayout(
        sidebarPanel(
            numericInput("n", "Number of genes to display:", value = 10, min = 1),
            actionButton("analyze", "Perform Analysis")
        ),
        mainPanel(
            tabsetPanel(
                tabPanel("Results", DTOutput("results_table")),
                tabPanel("Visualization", plotOutput("results_plot"))
            )
        )
    )
)

server <- function(input, output, session) {
    # Reactive value to store the analysis results
    results <- reactiveVal(NULL)
    
    observeEvent(input$analyze, {
        # Simulated differential analysis (replace this with actual analysis)
        # Fetch data from ARCHS4
        gene_expression_data <- archs4::get_archs4_data()
        
        # Perform differential expression analysis
        analysis_results <- gene_expression_data %>% 
            top_n(input$n, wt = abs(effect_size)) %>% 
            arrange(desc(effect_size))
        
        # Update the reactive value
        results(analysis_results)
    })

    output$results_table <- renderDT({
        req(results())  # Ensure results are available
        datatable(results())
    })
    
    output$results_plot <- renderPlot({
        req(results())
        ggplot(results(), aes(x = gene, y = effect_size)) +
            geom_col() +
            coord_flip() +
            labs(title = "Top Differentially Expressed Genes", x = "Gene", y = "Effect Size")
    })
}