Code Editor for app.R

library(shiny)
library(ggplot2)

# Generate mock data
set.seed(123)
experiment_data <- data.frame(
    Time = seq(0, 11, by=1),
    Control = cumsum(rnorm(12, mean=0.5, sd=0.2)),
    Treatment_A = cumsum(rnorm(12, mean=0.8, sd=0.2)), 
    Treatment_B = cumsum(rnorm(12, mean=1.2, sd=0.3))
)

# Define UI
ui <- fluidPage(
    theme = bslib::bs_theme(bootswatch = "flatly"),
    
    titlePanel("Gene Expression Analysis"),
    
    sidebarLayout(
        sidebarPanel(
            selectInput("treatment", "Select Treatment Group:",
                choices = c("Control", "Treatment_A", "Treatment_B")),
            
            radioButtons("scale", "Y-axis Scale:",
                choices = c("Linear" = "linear", "Log" = "log"),
                selected = "linear"),
                
            checkboxInput("show_ci", "Show Confidence Interval", TRUE),
            
            hr(),
            
            helpText("This interactive visualization shows relative gene expression levels over time for different treatment conditions.")
        ),
        
        mainPanel(
            h3("Expression Profile"),
            plotOutput("expression_plot"),
            br(),
            div(style = "color: #666;",
                "Note: Data shown represents a simulated time-course experiment measuring relative gene expression levels.",
                br(),
                "Statistical analysis includes locally-weighted regression (LOESS) with 95% confidence intervals.")
        )
    )
)

# Define server logic
server <- function(input, output) {
    output$expression_plot <- renderPlot({
        treatment <- input$treatment
        
        p <- ggplot(experiment_data, aes(x = Time, y = .data[[treatment]])) +
            geom_point(size = 3, color = "#2c3e50") +
            labs(
                x = "Time (hours)",
                y = "Relative Expression Level",
                title = paste(gsub("_", " ", treatment), "Group"),
                subtitle = "Time Course Analysis"
            ) +
            theme_minimal() +
            theme(
                plot.title = element_text(size = 16, face = "bold"),
                plot.subtitle = element_text(size = 12, color = "#666666"),
                axis.title = element_text(size = 12),
                panel.grid.minor = element_blank()
            )
            
        if(input$scale == "log") {
            p <- p + scale_y_log10()
        }
            
        p <- p + geom_smooth(
            method = "loess",
            se = input$show_ci,
            color = "#e74c3c",
            fill = "#e74c3c40"
        )
        
        p
    })
}

# Run the application
shinyApp(ui = ui, server = server)