R/enrichplot.R

In mrbakhsh/HPiP: Host-Pathogen Interaction Prediction

    #' enrichplot
    #' @title Plot the Enrichment Reuslt
    #' @param x A data.frame with the enrichment analysis results.
    #' @param low Colours for low.
    #' @param high Colours for high.
    #' @param cex.size Text size.
    #' @return An enrichment plot.
    #' @seealso See \code{\link{enrichfindP}} for functional enrichment
    #' analysis.
    #' @author Matineh Rahmatbakhsh, \email{matinerb.94@gmail.com}
    #' @importFrom ggplot2 scale_colour_gradient2
    #' @importFrom ggplot2 scale_x_continuous
    #' @importFrom ggplot2 element_rect
    #' @description This function plots the enrichment result.
    #' @export
    #' @examples
    #' data('enrich.df')
    #' #select enrichment for one of the example (e.g., E protein)
    #' enrich.df <-
    #' enrich.df[enrich.df$id == "E:P0DTC4", ]
    #' enrichplot(enrich.df, low = "blue", high = "red", cex.size = 10)

    enrichplot <-
      function(x,
               low = "blue",
               high = "red",
               cex.size = 15) {
        xaxis <- NULL
        term_name <- NULL
        intersection_size <- NULL
        p_value <- NULL

        x$xaxis <- 1

        print(ggplot(x, aes(xaxis, term_name, color = -log10(p_value))) +
          geom_point(aes(xaxis, term_name, size = intersection_size),
            stroke = 1, show.legend = TRUE
          ) +
          scale_colour_gradient2(low = low, high = high) +
          theme_bw() +
          scale_x_continuous(expand = c(0, 0), limits = c(1, 1)) +
          theme(text = element_text(size = cex.size, color = "#000000")) +
          theme(axis.text.y = element_text(color = "#000000")) +
          theme(axis.ticks.x = element_blank()) +
          theme(axis.text.x = element_blank()) +
          labs(title = "", x = "", y = "term_name"))
      }