inst/shinyapp/script/mod_advplot.R

In BioVizSeq: Visualizing the Elements Within Bio-Sequences

mod_advplot_ui <- function(id){
  ns <- NS(id)
  tagList(
    sidebarPanel(
      width = 4,
      h3(strong("The main options:")),
      radioButtons(
        inputId = ns("ordertype"),
        label = "File",
        choices = c("Tree (.newk)" = "tree", "Order (.csv/.txt)" = "orderfile"),
        selected = "tree",
        inline = TRUE 
      ),
      fileInput(ns("filetree"),label = NULL, accept = NULL),
      fileInput(ns("filegroup"),"Choose Group File to Upload(.csv/.txt/.xlsx/.xls):", accept = NULL),
      
      fileInput(ns("filegff"),"Choose Annotation File to Upload(.gff/.gtf):", accept = NULL),
      fileInput(ns("filememe"),"Choose MEME File to Upload(.xml):", accept = NULL),
      fileInput(ns("filepfam"),"Choose PFAM File to Upload(.tsv):", accept = NULL),
      fileInput(ns("filecdd"),"Choose CDD File to Upload(.txt):", accept = NULL),
      fileInput(ns("filepep"),"Choose Protein File to Upload(.fa/.fasta):", accept = NULL),
      selectInput(ns("filesmart"), label = "Do SMART:",
                  c("FALSE", "TRUE")),
      
      fileInput(ns("fileplantcare"),"Choose Plantcare File to Upload(.tab):", accept = NULL),
      numericInput(ns("prolength"),label = "Promoter Length",value = 2000),
      
      fileInput(ns("filename"),"Choose Renamed File to Upload(.csv/.txt/.xlsx/.xls):", accept = NULL),
      selectInput(ns("shapemotif"), label = "Element shape:",
                  c("RoundRect", "Rect")),
      
      numericInput(ns("roundr"),label = "RoundRect r value",value = 0.3),
      numericInput(ns("legendsize"),label = "Legend size",value = 12),
      
      textAreaInput(ns("code_input"),"Combination select:", placeholder = "e.g. p_tree + p_gff + p_pfam"),
      
      actionButton(ns("file_submit"), strong("Submit All Data"), styleclass = "success"),
      br(),
      br(),
      h3(strong("Download options:")),
      numericInput(ns("picheigh"),label = "Graph heigh value",value = 9.5),
      numericInput(ns("picwidth"),label = "Graph width value",value = 9.5),
      downloadButton(ns("downloadpic"),label = "Download Picture!"),
      radioButtons(ns("format"), "Figure type:", 
                   choices = c("PNG" = "png", "PDF" = "pdf"), 
                   selected = "png")
    ),
    
    mainPanel(
      h3("Advanced Plot:"),
      withSpinner(plotOutput(ns("plot_result"), width='100%', height='700px'))
    )
  )
}


mod_advplot_server <- function(input, output, session){
  ns <- session$ns

  filedata <- eventReactive(input$file_submit,{
    infile <- input$filename
    if (is.null(infile)){
      return(NULL)
    }else{
      if (grepl(".xls$|.xlsx$", infile$datapath, ignore.case = TRUE)) {
        read.xlsx(infile$datapath,1, header=T)
      } else if (grepl(".csv$", infile$datapath, ignore.case = TRUE)) {
        read.csv(infile$datapath,sep=',', header=T)
      } else if(grepl(".txt$", infile$datapath, ignore.case = TRUE)){
        read.table(infile$datapath,sep = "\t", header = T,)
      }
    }
  })
  
  groupdata <- eventReactive(input$file_submit,{
    infile <- input$filegroup
    if (is.null(infile)){
      return(NULL)
    }else{
      if (grepl(".xls$|.xlsx$", infile$datapath, ignore.case = TRUE)) {
        read.xlsx(infile$datapath,1, header=T)
      } else if (grepl(".csv$", infile$datapath, ignore.case = TRUE)) {
        read.csv(infile$datapath,sep=',', header=T)
      } else if(grepl(".txt$", infile$datapath, ignore.case = TRUE)){
        read.table(infile$datapath,sep = "\t", header = T,)
      }
    }
  })
  
  dosmart <- eventReactive(input$file_submit,{
    smart_do <- input$filesmart
    if (smart_do == "FALSE")
      return( FALSE )
    else
      return( TRUE )
  })
  
  element_plot <- eventReactive(input$file_submit,{
    if(input$ordertype == "tree"){
      plot_file <- combi_p(tree_path=input$filetree$datapath, gff_path = input$filegff$datapath,
                           meme_path = input$filememe$datapath, pfam_path = input$filepfam$datapath,
                           cdd_path = input$filecdd$datapath, fa_path = input$filepep$datapath,
                           plantcare_path = input$fileplantcare$datapath,
                           smart_path = dosmart(),
                           promoter_length = input$prolength,
                           renamefile = filedata(), groupfile = groupdata(),
                           shape = input$shapemotif,
                           r = input$roundr, legend_size= input$legendsize
      )
      
      p_tree <- plot_file$p_tree
      p_gff <- plot_file$p_gff
      p_smart <-plot_file$p_smart
      p_pfam <- plot_file$p_pfam
      p_cdd <- plot_file$p_cdd
      p_plantcare <- plot_file$p_plantcare
      p_meme <- plot_file$p_meme
      
      code_str <- input$code_input
      ele_num <- str_count(code_str, "\\+") +1
      code_loc <- paste(" + plot_layout(ncol = ", ele_num,
                        ", guides = 'collect') + plot_annotation(tag_levels = 'A')")
      code_combi <- paste(code_str, code_loc)
      eval(parse(text = code_combi))
    }else{
      plot_file <- combi_p2(order_path=input$filetree$datapath, gff_path = input$filegff$datapath,
                           meme_path = input$filememe$datapath, pfam_path = input$filepfam$datapath,
                           cdd_path = input$filecdd$datapath, fa_path = input$filepep$datapath,
                           plantcare_path = input$fileplantcare$datapath,
                           smart_path = dosmart(),
                           promoter_length = input$prolength,
                           renamefile = filedata(),
                           shape = input$shapemotif,
                           r = input$roundr, legend_size= input$legendsize
      )
      
      p_gff <- plot_file$p_gff
      p_smart <-plot_file$p_smart
      p_pfam <- plot_file$p_pfam
      p_cdd <- plot_file$p_cdd
      p_plantcare <- plot_file$p_plantcare
      p_meme <- plot_file$p_meme
      
      code_str <- input$code_input
      ele_num <- str_count(code_str, "\\+") +1
      
      first_element <- strsplit(code_str, split = "\\+")[[1]][1]
      
      code_change <- paste(first_element,"<-", first_element, 
      '+ theme(axis.text.y = element_text(color = "black", size = 10, angle = 0 ))')
      
      eval(parse(text = code_change))
      
      code_loc <- paste(" + plot_layout(ncol = ", ele_num,
                        ", guides = 'collect') + plot_annotation(tag_levels = 'A')")
      code_combi <- paste(code_str, code_loc)
      eval(parse(text = code_combi))
    }
    
  })
  
  output$plot_result <- renderPlot({
    element_plot()
  })
  
  
  
  
  output$downloadpic <- downloadHandler(
    filename = function() { 
      paste("Advanced_plot", input$format, sep = ".")
    },
    content = function(file) {
      ggsave(
        filename = file,
        plot = element_plot(),
        device = input$format,
        path = NULL,
        scale = 1,
        width = input$picwidth,
        height = input$picheigh,
        units = "in",
        dpi = 400,
        limitsize = TRUE
      )
    }
  )
}