R/cell_bar_plot.R

In IOBR/IOBR: Immune Oncology Biological Research

#'  Visualize the results as a stacked bar chart with tidyverse/ggplot2.
#'
#' @param input input  result of `CIBERSORT` or `quantiseq`
#' @param id patient identifier of input
#' @param title plot title
#' @param legend.position legend position
#' @param coord_filp logical variables, `coord_filp` of ggplot2
#' @param palette default is palette3
#' @param show_col default is FALSE
#' @param cols default is NULL, user can define colors manually
#' @param features default is NULL, user can define which column to draw
#' @param pattern patterns of features
#'
#' @return
#' @export
#'
#' @examples
#' # Loading TCGA-STAD microenvironment data
#' data("sig_stad", package = "IOBR")
#' # showing 20 tumor microenvironment cell proportion deconvoluted by CIBERSORT algorithm
#' cell_bar_plot(input = sig_stad[1:20, ], id = "ID", features = colnames(sig_stad)[25:46])

cell_bar_plot<- function(input, id = "ID", title = "Cell Fraction", features = NULL, pattern = NULL, legend.position = "bottom",
                         coord_filp = TRUE, palette = 3, show_col = F, cols = NULL){

  input<-as.data.frame(input)
  colnames(input)[which(colnames(input)==id)]<-"ID"

  if(is.null(features)){

    if(is.null(pattern)) stop(">>>=== The 'pattern' parameter must be defined...")
    feas <- colnames(input)[str_detect(colnames(input), pattern = pattern)]
  }else{

    feas <- features
  }

  input <- input[, c("ID", feas)]

  input<-remove_names(input_df = input, variable = "colnames", patterns_to_na = patterns_to_na, patterns_space = "_")
  ##################
  if(legend.position == "top"|legend.position=="bottom") {
    legend.direction<-"horizontal"
  }else{
    legend.direction<-"vertical"
  }


  if(!is.null(cols)){
    cols<-cols
  }else{
    if(is.null(palette)){
      cols<-IOBR::palettes(category = "random", palette = 4, show_col = show_col, show_message = T)
    }else{
      cols<-IOBR::palettes(category = "random", palette = palette, show_col = show_col, show_message = T)
    }
  }


  if(coord_filp){
    pp<-input %>%
      tidyr::gather(cell_type,fraction, -ID) %>%
      # plot as stacked bar chart
      ggplot(aes(x=ID, y=fraction, fill=cell_type)) +
      geom_bar(stat='identity') +
      coord_flip() +
      theme_light()+
      scale_fill_manual(values = cols) +
      scale_x_discrete(limits = rev(levels(input)))+
      ggtitle(paste0(title))+
      theme(plot.title=element_text(size=rel(2),hjust=0.5),
            axis.text.x= element_text(face="plain",angle=0,hjust = 1,color="black"),
            axis.text.y= element_text(face="plain",angle= 30,hjust = 1,color="black"))+
      theme(legend.title = element_blank(),
            legend.position= legend.position,
            legend.direction= legend.direction,
            legend.justification=c(.5,.5),
            legend.box="horizontal",
            legend.box.just="top")
  }else{
   pp<- input %>%
     tidyr::gather(cell_type,fraction, -ID) %>%
      # plot as stacked bar chart
      ggplot(aes(x=ID, y=fraction, fill=cell_type)) +
      geom_bar(stat='identity') +
      # coord_flip() +
      theme_light()+
      scale_fill_manual(values = cols) +
      scale_x_discrete(limits = rev(levels(input)))+
      ggtitle(paste0(title))+
      theme(plot.title=element_text(size=rel(2),hjust=0.5),
            axis.text.x= element_text(face="plain",angle=0,hjust = 1,color="black"),
            axis.text.y= element_text(face="plain",angle=30,hjust = 1,color="black"))+
      theme(legend.title = element_blank(),
            legend.position= legend.position,
            legend.direction= legend.direction,
            legend.justification=c(.5,.5),
            legend.box="horizontal",
            legend.box.just="top")
  }

 print(pp)
 return(pp)

}