R/plot_density.R

In thierrycnam/igfuns: Analyzes of Ig sequencing data

#' plot_density
#'
#' Deprecated. Use plot_density_facet.
#'
#' @param df_ data frame
#' @param mode mode
#'
#' @return
#' @export
#' @import RColorBrewer
#' @import ggplot2
#'
#' @examples
#' plot_density(subset(pbmc_div_mut, V != "2"))
plot_density <- function(df_, mode=1) {
  # to silent warnings
  div_germ <- NULL
  density  <- NULL
  V        <- NULL
  label_subtype <- NULL
  status <- NULL


  my_theme <- igfuns::my_theme()
  my_colors_vh <- brewer.pal(n = 9, name = "Set1")
  my_scale_fill_vh <- scale_fill_manual(values=my_colors_vh,
                                        labels=paste0("IGHV", seq(7)))
  ggplot(df_, aes(x=div_germ, y=stat(density), fill=V, lty=status)) +
    geom_line(stat="density", aes(color=V)) +
    my_scale_fill_vh +
    scale_color_manual(name="V", values=my_colors_vh) +
    my_theme +
    xlab("Divergence germline (%)") +
    ylab("Density") +
    facet_grid(rows=vars(V), cols=vars(label_subtype))
}