R/cohort_scatterplot.R

In vdumeaux/mixtR: Matched Interaction across Tissues (MIxT) data analysis

#' Plot scatterplot of ranksums
#'
#' Generate scatterplot of ranksums obtained from two gene sets/modules
#'
#' @param mixt.ranksum  output of sig.ranksum()
#' @param x.tissue character string providing the name of tissue on the x axis
#' @param x.module character string providing the name of module on the x axis
#' @param y.tissue character string providing the name of tissue on the y axis
#' @param y.module character string providing the name of module on the y axis
#' @param cohort.name character string that provides the name of the patient cohort.
#' Defaults is set to 'all'
#'
#' @export

cohort_scatterplot <- function(mixt.ranksum, x.tissue, x.module, y.tissue, y.module,
                               cohort.name = "all") {

  if (!x.tissue %in% names(mixt.ranksum))
    stop ("tissue1 should be a name of mixt.ranksum")
  if (!x.module %in% names(mixt.ranksum[[x.tissue]]))
    stop ("ranksums were not computed for x.module in x.tissue")

  if (!y.tissue %in% names(mixt.ranksum))
    stop ("y.tissue should be a name of mixt.ranksum")
  if (!y.module %in% names(mixt.ranksum[[y.tissue]]))
    stop ("ranksums were not computed for y.module in y.tissue")


  # we need to swap around these to fix accessing the perm_cor_p object
  if (x.tissue != names(mixt.ranksum)[1]) {
    tmp = NULL
    xmodule = NULL
    ymodule = NULL
    tmp = x.module
    xmodule = y.module
    ymodule = tmp
    xtissue = y.tissue
    ytissue = x.tissue
  } else {
    xmodule = x.module
    ymodule = y.module
    xtissue = x.tissue
    ytissue = y.tissue
  }

  ### data for scatterplot
  x.ranksum = mixt.ranksum[[x.tissue]][[x.module]][[cohort.name]]$ranksum
  y.ranksum = mixt.ranksum[[y.tissue]][[y.module]][[cohort.name]]$ranksum
  plot.data <- data.frame(x.ranksum = x.ranksum,
                          y.ranksum = y.ranksum)


  p1 <- ggplot2::ggplot(plot.data, ggplot2::aes(x = x.ranksum, y = y.ranksum)) +
    ggplot2::geom_smooth(method = "lm", colour = "white", alpha = 0.2, size = 0.4) +
    ggplot2::geom_point(size = 2) +
    ggplot2::labs(y = paste(y.module, y.tissue, "module ranksum"), x = paste(x.module,x.tissue, "module ranksum"),
                  title = paste(cohort.name, " patients", " (cor=", as.character(signif(stats::cor.test(plot.data$x.ranksum, plot.data$y.ranksum)$estimate, digits = 1)),
                                ")", sep = "")) +
    ggplot2::theme(legend.position = "none",
                   panel.background = ggplot2::element_rect(fill = "transparent", colour = NA),
                   axis.line.x = ggplot2::element_line(colour = "grey60"),
                   axis.line.y = ggplot2::element_line(colour = "grey60"),
                   axis.title = ggplot2::element_text(size = 10),
                   plot.title = ggplot2::element_text(hjust = 0, vjust = 1, size = 12))

  print(p1)
}