R/dotplot_pwys.R

In jdreyf/ezlimmaplot: Bioinformatics plots using limma and ggplot2, some from output of ezlimma

#' Make dot plots for the significance and DE proportion of pathway analysis
#'
#' Make dot plots like clusterProfiler showing the significance and proportion of genes in each pathway
#' with significance below cutoff.
#'
#' @param tab Table of output from \code{ezlimma::roast_*}.
#' @param prefix.v A vector of prefixes that prefix \code{.p}, \code{.FDR}, or \code{.logFC} in \code{colnames(tab)}.
#' These will be the comparisons shown in the plot. If \code{NULL} these are inferred from \code{colnames(tab)} that end with \code{.p}.
#' @param name Name of file to create. Set to \code{NA} to plot to screen instead of to file; otherwise, "_dotplot.pdf" is appended to the name.
#' @param type.sig Either "p" or "FDR"; type of significance to show.
#' @param cut.sig Numeric in [0, 1]. Pathways need to have significance of type \code{type.sig < cut.sig} in a comparison to be shown on the dot plot.
#' @param ntop Integer; number of top pathway-by-comparison statistics to select.
#' @param font.size Numeric font size of pathway names e.g. 12.
#' @param mixed Character string. Should mixed statistics be included, should they be the only statistics included, or should they be excluded?
#' @param reorder.rows Boolean; reorder pathways by significance before selecting \code{ntop} pathways? If not, order of \code{tab} is retained.
#' @param caption Logical; should the caption explaining the color bar title be included?
#' @param colorbar.title Character title of color bar.
#' @inheritParams ezheat
#' @inheritParams ezvenn
#' @inheritParams barplot_pwys
#' @return Invisibly, the ggplot object.
#' @export

# 3 columns per contrast: up, down, mixed
# color is prop; size is -log10 of p or q
# https://github.com/YuLab-SMU/enrichplot/blob/0a01deaa5901b8af37d78c561e5f8200b4748b59/R/dotplot.R
# prefix.v=NULL; name = NA; type.sig="p"; cut.sig=0.05; ntop = 20; pwys_nm_size = 100; width = 8; height = 8; mixed="include"; caption=TRUE; colorbar.title = "Prop P<5%"
dotplot_pwys <- function(tab, prefix.v=NULL, name = NA, type.sig=c("p", "FDR"), cut.sig=0.05, ntop = 20, pwys_nm_size = 100, font.size = 12,
                         width = 8, height = 8, mixed = c("include", "exclude", "only"), reorder.rows=TRUE, caption=TRUE, colorbar.title = "Prop P<5%"){
  type.sig <- match.arg(type.sig)
  mixed <- match.arg(mixed)
  stopifnot(mixed == "exclude" | any(grepl("Mixed", colnames(tab))), cut.sig > 0, cut.sig <= 1)
  tab <- as.data.frame(tab)
  rownames(tab) <- gsub("_", " ", substr(rownames(tab), 1, pwys_nm_size))
  # extract prefix
  if (is.null(prefix.v)){
    p.colnms <- ezlimma:::grep_cols(tab=tab, p.cols="p")
    p.colnms <- p.colnms[!grepl("Mixed", p.colnms)]
    prefix.v <- gsub(pattern = "(\\.|^)p$", replacement = "", x=p.colnms)
  }
  stopifnot(sapply(tab[, paste0(prefix.v, ".Direction"), drop=FALSE], FUN=function(vv) all(vv %in% c("Up", "Down") )))

  if (!is.na(name)){
    name <- paste0(name, "_dotplot.pdf")
    grDevices::pdf(name, width=width, height=height)
    on.exit(grDevices::dev.off())
  }

  dir.v <- switch(mixed, include = c("Up", "Down", "Mixed"), exclude = c("Up", "Down"), only = "Mixed")
  col.labs <- paste(rep(prefix.v, each=length(dir.v)), dir.v, sep=".")

  ds <- pivot_roast_longer(tab=tab, prefix.v = prefix.v, direction.v = dir.v)

  # filter out non-significant comparison x pathway rows
  # could do this in for loop separately for Mixed and not Mixed, but here I only need to do it once
  # then subset to 1st ntop rows: this does not cause error or warning even if ntop > nrow(ds)
  if (reorder.rows) ds <- ds |> dplyr::arrange(!!rlang::sym(type.sig))
  ds <- ds |> dplyr::filter(!!rlang::sym(type.sig) < cut.sig)
  ds <- ds |> dplyr::filter(Pwy %in% (ds |> dplyr::slice(1:ntop) |> dplyr::pull(Pwy)))
  if (nrow(ds) == 0) stop("No pathways had ", type.sig, " < ", cut.sig, ".")
  pwy.max.nchar <- ds |> dplyr::pull(Pwy) |> nchar() |> max()

  # i probably need to modify the font and/or use str_wrap() for long pwy nms
  # enrichplot::dotplot uses theme_dose(font.size) w/ default font size 12
  # angle axis labels: https://stackoverflow.com/questions/1330989/rotating-and-spacing-axis-labels-in-ggplot2
  # order legends: https://stackoverflow.com/questions/11393123/controlling-ggplot2-legend-display-order, but `color=guide_legend(order=1)` treats it as factor
  # add padding to label_wrap(width) to prevent splitting onto 3 lines, but not sure how to calculate it efficiently
  # enrichplot has own str_wrap: https://github.com/YuLab-SMU/yulab.utils/blob/946215d1aad07bb3bd0f8712d634a73e0a71fb34/R/str-utils.R, but
  # it looks like it could split onto >2 lines
  ggp <- ggplot2::ggplot(data = ds, mapping=ggplot2::aes(x=factor(Comparison, levels = col.labs, ordered = TRUE),
                                                         y=factor(Pwy, levels = rev(unique(Pwy)), ordered = TRUE),
                                                         size = -log10(!!rlang::sym(type.sig)), color=Prop_p05)) +
    ggplot2::geom_point() + ggplot2::xlab(NULL) + ggplot2::ylab(NULL) + ggplot2::labs(color = colorbar.title) +
    ggplot2::scale_size(range = c(4, 10)) +
    ggplot2::scale_x_discrete(guide = ggplot2::guide_axis(angle = 45)) +
    ggplot2::scale_y_discrete(labels = scales::label_wrap(width = ceiling(pwy.max.nchar/2) + 10)) +
    ggplot2::guides(size = ggplot2::guide_legend(order = 2)) + ggplot2::theme_bw() +
    ggplot2::theme(axis.text.x = ggplot2::element_text(color = "black"), axis.text.y = ggplot2::element_text(color = "black", size = font.size))
  if (caption){
    capt <- paste(colorbar.title, "= proportion of genes in pwy with P < 0.05 in given direction or for *Mixed* in either direction")
    ggp <- ggp + ggplot2::labs(caption = capt)
  }
  graphics::plot(ggp)
  return(invisible(ggp))
}