R/summary_barplot.R

In elimereu/matchSCore2: What the Package Does TODOELI

#' Cumulative barplot of cell mapped compositions
#'
#' This function identifies true label groups between reference groups and clusters.
#'
#' @param class.fac A named vector of classified cells (e.g. the `output$ids`
#' from the [identity_map()] function).
#' @param obs.fac A named vector of clusters.
#'
#' @return A cumulative barplot describing the cell identity compositions of the
#' observed clusters onto the reference
#'
#' @export
#'
#' @examples
#' # TODO
summary_barplot <- function(class.fac,
                            obs.fac) {

  # library(reshape2) # TODO: really needed?
  # library(grid) # TODO: really needed?

  t <- table(class.fac, obs.fac)
  df <- data.frame(t)
  n <- colSums(t)
  percentage.cell_type <- sapply(
    names(n),
    function(x) round(t[, x] / n[x] * 100, digits = 2)
  )
  df2 <- data.frame(percentage.cell_type)

  y <- melt(df2)
  y$class.fac <- df$class.fac
  y$obs.fac <- df$obs.fac
  y$Freq <- df$Freq
  names(y)[2] <- "Cell.type.percent"

  gg <- ggplot(y, aes_string(x = "obs.fac", y = "Cell.type.percent")) +
    geom_bar(aes_string(y = "Cell.type.percent", x = "obs.fac", fill = "class.fac"), stat = "identity") +
    theme_bw() +
    theme(
      axis.title = element_blank(),
      legend.title = element_blank(),
      legend.text = element_text(size = 13),
      axis.text.x = element_text(colour = "black", size = 14, angle = 45, hjust = 1, vjust = 1),
      axis.text.y = element_text(colour = "black", size = 16),
      axis.line = element_line(colour = "black", size = 1),
      panel.grid.major = element_blank(), panel.border = element_blank()
    )

  return(gg)
}