R/bb_goscatter.R

In blaserlab/blaseRtools: R Tools for Blaser Lab Data Analysis

#' Make a scatter plot of GO term associations
#'
#' @param simMatrix Take from output of bb_gosummary
#' @param reducedTerms Also take from output of bb_gosummary
#' @param size Variable to map to point size.  Defaults to "score".
#' @param addLabel Boolean; whether or not to add text labels
#' @param labelSize Optional label size
#' @return A ggplot
#' @export
#' @import tidyverse ggrepel
#' @importFrom stats cmdscale as.dist
bb_goscatter <-
  function (simMatrix,
            reducedTerms,
            size = "score",
            addLabel = TRUE,
            labelSize = 4) {
    x <- stats::cmdscale(as.matrix(stats::as.dist(1 - simMatrix)),
                         eig = TRUE,
                         k = 2)
    df <-
      cbind(as.data.frame(x$points), reducedTerms[match(rownames(x$points),
                                                        reducedTerms$go), c("term", "parent", "parentTerm", "size", "score")])
    p <-
      ggplot(df, aes(x = V1, y = V2, color = parentTerm)) +
      geom_point(aes(size = !!sym(size)), alpha = 0.5) +
      scale_color_discrete(guide = FALSE) +
      scale_size_continuous(guide = FALSE, range = c(0, 10))
    if (addLabel) {
      p <- p +
        geom_text_repel(
          aes(label = parentTerm),
          segment.size = 0.25,
          data = subset(df, parent == rownames(df)),
          box.padding = grid::unit(0.5, "lines"),
          size = labelSize,
          color = "black",
          max.overlaps = 100,
          force = 2,
          seed = 1234,
          segment.curvature = -0.1,
          segment.square = TRUE,
          segment.inflect = TRUE,
          min.segment.length = 0
        )

    }
    p <- p + labs(x = "PCoA 1", y = "PCoA 2")

    return(p)
  }