R/plot_RelativetoIsland.R

In isglobal-brge/EASIER: EwAS: quality control, meta-analysIs and EnRichment

#' Relative to Island Plot
#'
#' Relative to Island plot
#'
#' @param x Dataframe with Relative to Island data
#' @param outputdir string with relative path
#' @param main optional, string with title
#' @param xlab optional, string with xlab text
#'
#' @return distribution plot
#'
#' @export
plot_RelativetoIsland <- function(x, outputdir = '.', outputfile = NULL, main='', xlab='',...)
{

   if( !'RelIsland' %in% colnames(x)) {
      x$RelIsland <- rownames(x)
   }

   x$RelIsland <- factor(x[,"RelIsland"], levels = (as.character(x[,"RelIsland"])))
   x <- melt(x, id.vars = c("RelIsland"), measure.vars = c("depletion", "enrichment"), value.name = 'OR' )


   nms <- names(x)
   x.plot <- nms['RelIsland']

   p <- ggplot(x, aes(x = RelIsland, y = OR, fill = factor(variable)  )) +
      geom_bar(stat="identity",  width = 0.5, position=position_dodge()) +
      theme_classic(base_size = 20) +
      theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
      geom_hline(yintercept = 1) +
      xlab(paste0("Relation to ",names(x)[1]))

   if(!is.null(outputfile)) {
      if(!is.null(outputdir) & !is.na(outputdir) & outputdir!='.')
         dir.create(outputdir, showWarnings = FALSE, recursive = TRUE)

      # Output filename
      filename <- tools::file_path_sans_ext(basename(outputfile))

      ggplot2::ggsave(paste0(file.path( outputdir),"/OR_",filename,"_",names(x)[1],".pdf"), p)
   }

   return(p)
}