R/boxplots.R

In lucyleeow/RPPA: Analyse RPPA Data From Zeptosens System

#' Generate boxplots of RFI values
#' 
#' Creates boxplots of raw RFI value for each antibody or each sample.
#' 
#' @return Creates plot in current graphics device.
#' 
#' @param tidydf Tidy dataframe of raw RFI values.
#' @param RFIcol Name of the column, as string, containing RFI values.
#' @param order Vector of sample names, in the order that they are to appear on
#'     the graph.
#' @param fill_by Optional argument. Name of the column, a string, to add to
#'     the \code{fill} argument in ggplot's \code{aes}.
#'     
#'     
#' @importFrom assertthat assert_that
#' @import ggplot2
#' 
#' @describeIn RFIperAB Creates a boxplot for each antibody.
#' @export
RFIperAB <- function(tidydf, RFIcol = "RFI", fill_by) {
  
  assert_that(RFIcol %in% colnames(tidydf) == 1,
              msg = "Check 'RFIcol' is correct")
  
  if (! missing(fill_by)){
    assert_that(fill_by %in% colnames(tidydf) == 1,
                msg = "Check 'fill_by' is correct")
  }
  
  assert_that("Antibody.Name" %in% colnames(tidydf) == 1,
              msg = "Check that an 'Antibody.Name' column exists in tidydf")
  
  
  # make plot
  if (missing(fill_by)){
    
    gg <- ggplot(tidydf, aes_string(y=RFIcol, x="Antibody.Name"))
    
  } else{
    
    gg <- ggplot(tidydf, aes_string(y=RFIcol, x="Antibody.Name", fill=fill_by))
  }
  
  # make rest of plot
  
  gg +
    geom_boxplot() + 
    labs(title = "RFI per AB", y = "RFI", x = "Antibody") +
    coord_flip() +
    theme(plot.title = element_text(hjust = 0.5), 
          title = element_text(size=14),
          axis.text.y = element_text(size = 8))
  
}

#' @describeIn RFIperAB Creates a boxplot for each sample.
#' @export
RFIperSample <- function(tidydf, RFIcol = "RFI", order, fill_by) {
  
  # check inputs
  assert_that(RFIcol %in% colnames(tidydf) == 1,
              msg = "Check 'RFIcol' is correct")
  
  if (! missing(fill_by)){
    assert_that(fill_by %in% colnames(tidydf) == 1,
                msg = "Check 'fill_by' is correct")
  }
  
  assert_that("Antibody.Name" %in% colnames(tidydf) == 1,
              msg = "Check that an 'Antibody.Name' column exists in tidydf")
  
  assert_that(is.atomic(order), sum(order %in% tidydf$X1) == length(order),
              msg = "Check 'order' is an atomic vector of sample names")
  
  
  if (missing(fill_by)){
    
    gg <- ggplot(tidydf, aes_string(y=RFIcol, x="X1"))
    
  } else{
    
    gg <- ggplot(tidydf, aes_string(y=RFIcol, x="X1", fill=fill_by))
  }
  
  # make plot
  
  gg + 
    geom_boxplot() + 
    labs(title = "RFI per Sample", y = "RFI", x = "Sample") +
    scale_x_discrete(limits = order) + 
    coord_flip() +
    theme(plot.title = element_text(hjust = 0.5), 
          title = element_text(size=14),
          axis.text.y = element_text(size = 8))
}