R/sampleProfile2metdna.R

In jaspershen/sampleProfile2metdna: sampleProfile2metdna

# path <- "V:/workreport/Shen Xiaotao/MetDNA demo data/metDNA/fly20180712/POS"
#' @title sampleProfile2metdna
#' @description sampleProfile2metdna
#' @author Xiaotao Shen
#' \email{shenxt1990@@163.com}
#' @param path Absolute directory
#' @param polarity polarity
#' @param width width, in
#' @param height height, in
#' @return A png figure
#' @export

sampleProfile2metdna <- function(path = ".",
                                 polarity = c("positive", "negative"),
                                 width = 10,
                                 height = 6){
  file.name <- dir(path)
  polarity <- match.arg(polarity)

  return.info <- NULL

  if(any(file.name == "data.csv")){
    data <- readr::read_csv(file.path(path, "data.csv"))
    return.info <- c(return.info,
                     paste("There are ", nrow(data), " peaks and ", ncol(data) - 3, " samples in your data",
                           sep = "")
                     )

    int <- log(apply(data[,-c(1:3)], 1, mean), 10)
    data <- data.frame(data, int, stringsAsFactors = FALSE)
    data$mz <- as.numeric(data$mz)
    data$rt <- as.numeric(data$rt)

    plot <-  ggplot2::ggplot(data, ggplot2::aes(x = rt, y = mz, colour = int)) +
      ggplot2::geom_point(alpha = 0.5) +
      # ggplot2::scale_color_gradient2(low = "blue", mid = "white", high = "red") +
      # modified by zhiwei 20190310
      ggplot2::scale_color_gradient(low = "dodgerblue", high = "orange") +
      ggplot2::labs(x = "Retention time (RT, second)",
                    y = "Mass to charge ratio (m/z)",
                    colour = "log10(intensity)")+
      ggplot2::ggtitle(ifelse(polarity == "positive",
                              "Peak Intensity Profile(POS)", "Peak Intensity Profile(NEG)"))+
      my.theme

    ggplot2::ggsave(filename = "plot.png", plot = plot, path = path,
                    width = width, height = height,
                    units = "in")
  }else{

    return.info <- c(return.info, "No data")

   plot <- ggplot2::ggplot()+
     ggplot2::labs(x = "Retention time (RT, second)",
                   y = "Mass to charge ratio (m/z)",
                   colour = "log10(intensity)")+
     ggplot2::ggtitle(ifelse(polarity == "positive",
                             "Peak Intensity Profile(POS)", "Peak Intensity Profile(NEG)"))+
     ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5, size = 20))+
     my.theme
   ggplot2::ggsave(filename = "plot.png", plot = plot, path = path,
                   width = width, height = height,
                   units = "in")
  }

  if(any(file.name == "sample.info.csv")){
    # modified by Zhiwei 20190310
    sample.info <- readr::read_csv(file.path(path, "sample.info.csv"))
    return.info <- c(return.info,
                     paste("The samples are classified into ",
                           length(unique(sample.info$group)),
                           " groups: ",
                           paste(unique(sample.info$group), collapse = ","),
                           sep = "")
    )
  }else{
    return.info <- c(return.info, "No sample information")
  }


  if(length(grep(".msp|.mgf", file.name)) > 0){
    return.info <- c(return.info,
                     paste(length(grep(".msp|.mgf", file.name)), " MS/MS files are provided")
    )
  }else{
    return.info <- c(return.info, "No MS/MS data")
  }

  return(return.info)

}






my.theme <- ggplot2::theme_bw()+
  ggplot2::theme(axis.title.x = ggplot2::element_text(size = 18),
                 axis.title.y = ggplot2::element_text(size = 18)) +
  ggplot2::theme(axis.text.x = ggplot2::element_text(size = 15),
                 axis.text.y = ggplot2::element_text(size = 15)) +
  ggplot2::theme(legend.title = ggplot2::element_text(size = 12)) +
  ggplot2::theme(legend.text = ggplot2::element_text(size = 10))