annotate DrawFunctions.R @ 2:5e64657b4fe5 draft

planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e

require(ggplot2)
require(gridExtra)
require(reshape2)


Draw <- function(Signal_data, type.draw = c("signal", "pca"), output = c("default", 
                                                                         "window", "png", "pdf"), dirpath = ".", filename = "%003d", height = 480, 
                 width = 640, pdf.onefile = TRUE, ...) {
  
  # Data initialisation and checks ----------------------------------------------
  type.draw <- match.arg(type.draw)
  output <- match.arg(output)
  fullpath <- paste(file.path(dirpath, filename), output, sep = ".")
  createFile <- TRUE
  createWindow <- FALSE
  
  # Drawing --------------------------------------------------------------------
  # output
  switch(output, default = {
    createFile <- FALSE
  }, window = {
    createWindow <- TRUE
    createFile <- FALSE
  }, png = {
    grDevices::png(fullpath, width, height)
  }, pdf = {
    grDevices::pdf(fullpath, width = width/72, height = height/72, 
                   onefile = pdf.onefile)
  }, {
    stop("Unknown output type.")
  })
  
  # Drawing type (signal/spectrum or PCA)
  funs <- list(signal = DrawSignal, pca = DrawPCA)
  if (type.draw %in% names(funs)) {
    fun <- funs[[type.draw]]
  } else {
    stop(paste("Unknown type:", type.draw))
  }
  
  # Plot finalisation ----------------------------------------------
  if (is.vector(Signal_data)) {
    Signal_data <- vec2mat(Signal_data)
  }
  fun(Signal_data, createWindow = createWindow, ...)
  if (createFile) {
    grDevices::dev.off()
  }
}



#####   DrawSignal

DrawSignal <- function(Signal_data, subtype = c("stacked", "together", 
                                                "separate", "diffmean", "diffmedian", "diffwith"), 
                       ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T, 
                       xlab = "rowname", RowNames = NULL, row = 1, num.stacked = 4, 
                       main = NULL, createWindow) {
  # nticks
  
  # Data initialisation and checks ----------------------------------------------
  
  subtype <- match.arg(subtype)
  vec <- is.vector(Signal_data)
  if (vec) {
    Signal_data <- vec2mat(Signal_data)
  }
  
  n <- nrow(Signal_data)
  m <- ncol(Signal_data)
  
  if (n < num.stacked){
    num.stacked <- n
  }
  
  scale <- colnames(Signal_data)
  
  num.plot <- sum(ReImModArg)
  
  Var <- rowname <- value <- NULL  # only for R CMD check
  
  # Drawing array
  if (num.plot <= 0) {
    stop("Nothing selected in ReImModArg.")
  } else if (num.plot <= 2) {
    if (vertical)  {
      nrow <- num.plot
      ncol <- 1
    } else  {
      nrow <- 1
      ncol <- num.plot
    }
  } else {
    nrow <- 2
    ncol <- 2
  }
  
  # RowNames 
  if (is.null(RowNames))  {
    RowNames <- rownames(Signal_data)
    if (is.null(RowNames))  {
      RowNames <- 1:n
    }
  } else {
    if (!is.vector(RowNames)) {
      stop("RowNames is not a vector")
    }
    if (length(RowNames) != n)  {
      stop(paste("RowNames has length", length(RowNames), "and there are", n, "FIDs."))
    }
  }
  
  if (n == 1) {
    RowNames <- deparse(substitute(Signal_data))
  }
  
  elements <- list()
  if (ReImModArg[1]) {
    elements[["Re"]] <- Re(Signal_data)
    rownames(elements[["Re"]]) <- RowNames
  }
  if (ReImModArg[2]) {
    elements[["Im"]] <- Im(Signal_data)
    rownames(elements[["Im"]]) <- RowNames
  }
  if (ReImModArg[3]) {
    elements[["Mod"]] <- Mod(Signal_data)
    rownames(elements[["Mod"]]) <- RowNames
  }
  if (ReImModArg[4]) {
    elements[["Arg"]] <- Arg(Signal_data)
    rownames(elements[["Arg"]]) <- RowNames
  }
  
  
  
  
  # Drawing --------------------------------------------------------------------
  
  y = x = NULL # only for R CMD check
  
  
  # SEPARATE or STACKED ===============
  if (subtype == "separate" | subtype == "stacked")  {
    
    i <- 1
    while (i <= n)  {
      if (createWindow)  {
        grDevices::dev.new(noRStudioGD = TRUE)
      }
      if (subtype == "separate")  {
        # The other uses gridExtra to do that
        graphics::par(mfrow = c(nrow, ncol))
      }
      plots <- list()
      if (subtype == "separate")  {
        last <- i
      } else  {
        last <- min(i + num.stacked - 1, n)
      }
      for (name in names(elements))  {
        if (subtype == "separate")   {
          if (n == 1) {
            df <- data.frame(x = as.numeric(scale), y = elements[[name]])
          } else {df <- data.frame(x = as.numeric(scale), y = elements[[name]][i, ])
          }
          
          plots[[name]] <- ggplot2::ggplot(data = df, ggplot2::aes(x = x, y = y)) + 
            ggplot2::geom_line(size = 1) + 
            ggplot2::theme(legend.position = "none") + 
            ggplot2::labs(x = xlab, y = name) +
            ggplot2::ggtitle(RowNames[i]) +
            ggplot2::theme_bw()
          
          if ((df[1, "x"] - df[(dim(df)[1]), "x"]) > 0) {
            plots[[name]] <- plots[[name]] + ggplot2::scale_x_reverse()
          }
          
        } else   {
          
          if (n == 1 ) {
            melted <- data.frame(rowname = rep(name, m), 
                                 Var = as.numeric(scale), value = elements[[name]][i,])
          } else if (last==i){ 
            melted <- data.frame(rowname = rep(rownames(elements[[name]])[i], m), 
                                 Var = as.numeric(scale), value = elements[[name]][i,])
          } else {melted <- reshape2::melt(elements[[name]][i:last, ], 
                                           varnames = c("rowname", "Var"))
          }
          
          
          plots[[name]] <- ggplot2::ggplot(data = melted, ggplot2::aes(x = Var, y = value)) + 
            ggplot2::geom_line(size = 0.3) + 
            ggplot2::facet_grid(rowname ~ ., scales = "free_y") + 
            ggplot2::theme(legend.position = "none") + 
            ggplot2::labs(x = xlab, y = name) +
            ggplot2::ggtitle(label = main) +
            ggplot2::theme_bw()
          
          if ((melted[1, "Var"] - melted[(dim(melted)[1]), "Var"]) > 0) {
            plots[[name]] <- plots[[name]] + ggplot2::scale_x_reverse()
          }
        }
      }
      
      if (subtype == "stacked")  {
        do.call(gridExtra::grid.arrange, c(plots, list(nrow = nrow, ncol = ncol)))
      } 
      
      i <- last + 1
    }
  } else if (subtype %in% c("together", "diffmean", "diffmedian", "diffwith")) {
    
    # TOGHETER or DIFFMEAN or DIFFMEDIAN or DIFFWITH ===============
    
    rainbow_colors <- grDevices::rainbow(n)
    
    if (createWindow) {
      grDevices::dev.new(noRStudioGD = TRUE)
    }
    graphics::par(mfrow = c(nrow, ncol))
    
    plots <- list()
    
    # Loop for Re, Im, Mod and Arg
    for (name in names(elements)) {
      # Get this part of the signal
      element <- elements[[name]]
      
      # Express the signal according to a reference if asked by `subtype'
      if (subtype == "diffmean")  {
        element <- sweep(element, MARGIN = 2, colMeans(element),  `-`)
      } else if (subtype == "diffmedian") {
        element <- sweep(element, MARGIN = 2, matrixStats::colMedians(element), `-`)
      } else if (subtype == "diffwith")  {
        element <- sweep(element, MARGIN = 2, element[row, ], `-`)
        if (row == 1 & n > 1)  {
          # Since we use plot on the first row and lines on the following, the y
          # scale is calculated at the first row so if the first row is all 0, it
          # causes problems
          tmp <- element[1, ]
          element[1, ] <- element[2, ]
          element[2, ] <- tmp
        }
      }
      
      
      melted <- reshape2::melt(elements[[name]], varnames = c("rowname", "Var"))
      
      
      plots[[name]] <- ggplot2::ggplot(melted, ggplot2::aes(x = Var, 
                                                            y = value, group = rowname, colour = rowname)) + ggplot2::geom_line() + 
        ggplot2::labs(x = xlab, y = name) + ggplot2::scale_colour_discrete(name = NULL) + 
        ggplot2::ggtitle(main)
      
      if ((melted[1, "Var"] - melted[(dim(melted)[1]), "Var"]) > 
          0)  {
        plots[[name]] <- plots[[name]] + ggplot2::scale_x_reverse()
      }
      
      do.call(gridExtra::grid.arrange, c(plots, list(nrow = nrow, 
                                                     ncol = ncol)))
    }
  }
  
  
}