Auto_PlotR

Automated temperature curve plotting from RDS file

#we need to increase the maximum upload size to 1GB options(shiny.maxRequestSize=1000*1024^2) #load necessary libraries library(shiny) library(ggplot2)

Define UI for application that draws a histogram

ui <- fluidPage( titlePanel("Abundance vs Temperature Plotter for Multiple Dataframes"),

sidebarLayout( sidebarPanel( fileInput("dataFile", "Choose RDS File", accept = c(".rds")) ), mainPanel( plotOutput("plots") ) ) )

#define server server <- function(input, output) {

output$plots <- renderPlot({ req(input$dataFile)

df_list <- tryCatch({
  readRDS(input$dataFile$datapath)
}, error = function(e) {
  cat("Error in reading RDS file:", e$message, "\n")
  return(NULL)
})

if(is.null(df_list) || !is.list(df_list)) {
  cat("Uploaded file is not a valid list of dataframes\n")
  return(NULL)
}

process_and_plot <- function(df, name) {
  if(!all(c("Temperature", "Abundance", "collapsed_uniprot") %in% names(df))) {
    cat(paste("Dataframe", name, "does not have the required columns.\n"))
    return(NULL)
  }
  
  # Filter for the first collapsed_uniprot entry
  first_uniprot <- unique(df$collapsed_uniprot)[1]
  df <- df[df$collapsed_uniprot == first_uniprot, ]
  
  ggplot(df, aes(x = Temperature, y = Abundance, color = collapsed_uniprot)) +
    geom_line() +
    theme_minimal() +
    labs(title = paste("Abundance vs Temperature for", first_uniprot, "in", name), 
         x = "Temperature", y = "Abundance")
}

num_dataframes <- length(df_list)
plot_list <- list()

withProgress(message = 'Plotting in progress...', {
  for (i in seq_along(df_list)) {
    setProgress(message = sprintf("Plotting dataframe %d of %d", i, num_dataframes),
                value = i / num_dataframes)
    plot_list[[i]] <- process_and_plot(df_list[[i]], names(df_list)[i])
  }
})

plot_list <- Filter(Negate(is.null), plot_list)

if(length(plot_list) > 0) {
  do.call(gridExtra::grid.arrange, c(plot_list, ncol = 1))
} else {
  cat("No valid plots to display.\n")
}

})

}

Run the application

shinyApp(ui = ui, server = server)