R/plot_function.R

In jaspershen/MetNormalizer: MetNormalizer

#' @title peak_plot
#' @description peak_plot
#' @author Xiaotao Shen
#' \email{shenxt@@sioc.ac.cn}
#' @param index index
#' @param sample sample.
#' @param sample.nor sample.nor.
#' @param QC QC
#' @param QC.nor QC.nor
#' @param tags tags
#' @param sample.order sample.order
#' @param QC.order QC.order
#' @param tags tags
#' @param path path
#' @param sample.rsd sample.rsd
#' @param QC.rsd QC.rsd
#' @param sample.nor.rsd sample.nor.rsd
#' @param QC.nor.rsd QC.nor.rsd
#' @importFrom magrittr %>%


setGeneric(
  name = "peak_plot",
  def = function(index,
                 sample,
                 sample.nor,
                 QC,
                 QC.nor,
                 sample.order,
                 QC.order,
                 tags,
                 path = ".",
                 sample.rsd = sample.rsd,
                 QC.rsd = QC.rsd,
                 sample.nor.rsd = sample.nor.rsd,
                 QC.nor.rsd = QC.nor.rsd) {
    # Sys.sleep(1)

    for (i in index) {
      cat(i, " ")
      temp_data <-
        rbind(
          data.frame(
            order = sample.order,
            raw = sample[, i],
            normalization = sample.nor[, 1],
            class = "Subject",
            stringsAsFactors = FALSE
          ),
          data.frame(
            order = QC.order,
            raw = QC[, i],
            normalization = QC.nor[, 1],
            class = "QC",
            stringsAsFactors = FALSE
          )
        )

      plot_raw <-
      ggplot2::ggplot(temp_data, ggplot2::aes(x = order, y = raw)) +
        ggplot2::geom_point(ggplot2::aes(colour = class)) +
        ggplot2::labs(x = "Inction order",
                      y = "Intensity",
                      title = paste("Peak:", tags["name", i]),
                      subtitle = "Before") +
        ggsci::scale_colour_lancet() +
        ggplot2::geom_smooth(ggplot2::aes(colour = class)) +
        ggplot2::annotate(
          geom = "text",
          x = Inf,
          y = Inf,
          hjust = 1,
          vjust = 1,
          label = paste(
            "QC RSD:",
            round(QC.rsd[i], 2),
            "%\n",
            "Sample RSD:",
            round(sample.rsd[i], 2),
            "%"
          )
        ) +
        ggplot2::theme_bw()


      plot_normalization <-
        ggplot2::ggplot(temp_data, ggplot2::aes(x = order, y = normalization)) +
        ggplot2::geom_point(ggplot2::aes(colour = class)) +
        ggplot2::labs(x = "Inction order",
                      y = "Intensity",
                      title = paste("Peak:", tags["name", i]),
                      subtitle = "After") +
        ggsci::scale_colour_lancet() +
        ggplot2::geom_smooth(ggplot2::aes(colour = class)) +
        ggplot2::annotate(
          geom = "text",
          x = Inf,
          y = Inf,
          hjust = 1,
          vjust = 1,
          label = paste(
            "QC RSD:",
            round(QC.nor.rsd[i], 2),
            "%\n",
            "Sample RSD:",
            round(sample.nor.rsd[i], 2),
            "%"
          )
        ) +
        ggplot2::theme_bw()

      # plot <-
      #   see::plots(plot_raw, plot_normalization,
      #              tags = c("Before", 'After'))

      suppressMessages(require(patchwork))
      plot <-
        plot_raw + plot_normalization +
        patchwork::plot_layout(nrow = 2, byrow = FALSE)

      ggplot2::ggsave(
        plot,
        filename = file.path(path, paste(tags["name", i], "png", sep = ".")),
        width = 10,
        height = 7
      )
    }
  }
)