R/boxplot_data.R

In jankinsan/BatchEC: Evaluates and corrects batch effects in gene expression data

#' @title Plots boxplots showing Gene Expression across samples
#'
#' @description Plots boxplots that can be used to see the change in gene expression after
#' adjustment for batch effects using ComBat
#'
#' @param expr A dataframe containing gene expression values.
#' Rows are genes, columns are samples. Could be the dataframe before or after correction
#' @param NameString  String that will be added in all output filenames. Default=NA.
#' @param batch The title of the batch for which you want to evaluate and do the
#'  correction. Default = "Batch"
#' @param when String indicating if the expression data is from before or after correction. Use "before" or "after"
#' @param return.plot Should the plot be returned as an object to the environment?
#' If FALSE, plot is saved to a pdf file, if TRUE, plot is returned to the environment.
#' Default = FALSE
#'
#'
#' @import grDevices
#'
#' @export
boxplot_data <- function(expr, when, NameString, batch = "Batch", return.plot=FALSE){

  print(paste0("================Plotting boxplot ", when, "====================="))

  #plotting gene expression
  data <- reshape2::melt(expr)

  #boxplot expression
  boxplot_expression <- ggplot2::ggplot(data, ggplot2::aes(x=data[,dim(data)[2]-1],
                                                           y= data[,dim(data)[2]])) +

    ggplot2::scale_x_discrete(guide = ggplot2::guide_axis(check.overlap = TRUE))+

    ggplot2::labs(title = paste0("Gene Expression ", when, " Correction for ", batch),
                  x = "Samples",
                  y = "Expression") +

    ggplot2::theme(
      #adjusting axis lines and text
      axis.line.x = ggplot2::element_line(size =0.75),
      axis.line.y = ggplot2::element_line(size =0.75),
      axis.text.x = ggplot2::element_text(size =15, colour ="black"),
      axis.text.y = ggplot2::element_text(size=15, colour ="black"),

      #Center align the title
      plot.title = ggplot2::element_text(face = "bold", hjust =0.5, size = 20),

      # Remove panel grid lines
      panel.grid.major = ggplot2::element_blank(),
      panel.grid.minor = ggplot2::element_blank(),

      # Remove panel background
      panel.background = ggplot2::element_blank())

  if(when == "before"){
    boxplot_exp <- boxplot_expression +
      ggplot2::geom_boxplot(color = "dodgerblue3",
                            inherit.aes = TRUE,
                            outlier.size = 0.5,
                            outlier.color = "limegreen")
  }
  else if (when == "after"){
    boxplot_exp <- boxplot_expression +
      ggplot2::geom_boxplot(color = "orange",
                            inherit.aes = TRUE,
                            outlier.size = 0.5,
                            outlier.color = "limegreen")
  } else{
    stop("Please specify the string 'when', should be either 'before' or 'after'")
  }

  if(return.plot==FALSE){
  date <- as.character(format(Sys.Date(), "%Y%m%d"))
  if (NameString == ""){
    plotFile <- paste0(date, "_", batch, "_gene_expression_boxplot_", when,".pdf")
  }else {
    plotFile <- paste0(date, "_", NameString, "_", batch, "_gene_expression_boxplot_", when,".pdf")
  }

  #plotting both the boxplots in a pdf file
  pdf(plotFile, height= 6.5, width = 13)
  plot (boxplot_exp)
  dev.off()
  print(paste0("Boxplot ", when, " Batch Correction plotted to ", plotFile))
  } else if(return.plot==TRUE){

    return(boxplot_exp)
  }
}