R/cell_bar_plot.R

In IOBR/IOBR: Immune Oncology Biological Research

#' Visualize the results as a stacked bar chart with tidyverse/ggplot2.
#' 
#' @description cell_bar_plot() provides batch visualization of tumor microenvironment (TME) cell fractions. It supports input from deconvolution results generated by methodologies such as 'CIBERSORT', 'EPIC', and 'quanTIseq'. The function enables comparison of TME cell distributions within one sample or among different samples.
#'
#' @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 A ggplot2 object representing the bar plot of cell fractions.
#' @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)

}