R/plot_maker.R

In PCAmatchR: Match Cases to Controls Based on Genotype Principal Components

#' Function to plot matches from match_maker output
#'
#' @param data match_maker output
#' @param x_var Principal component 1
#' @param y_var Principal component 2
#' @param case_control Case or control status
#' @param line draw line
#' @param ... Arguments passed to \code{plot}
#'
#' @return None
#' @importFrom graphics legend plot segments
#' @export
#'
#' @examples
#' \donttest{
#' # run match_maker()
#' # Create PC data frame by subsetting provided example dataset
#' pcs <- as.data.frame(PCs_1000G[,c(1,5:24)])
#' # Create eigenvalues vector using example dataset
#' eigen_vals <- c(eigenvalues_1000G)$eigen_values
#' # Create full eigenvalues vector using example dataset
#' all_eigen_vals<- c(eigenvalues_all_1000G)$eigen_values
#' # Create Covarite data frame
#' cov_data <- PCs_1000G[,c(1:4)]
#' # Generate a case status variable using ESN 1000 Genome population
#' cov_data$case <- ifelse(cov_data$pop=="ESN", c(1), c(0))
#' # With 1 to 1 matching
#'  if(requireNamespace("optmatch", quietly = TRUE)){
#'  library(optmatch)
#'  match_maker_output<- match_maker(PC = pcs,
#'                                  eigen_value = eigen_vals,
#'                                  data = cov_data,
#'                                  ids = c("sample"),
#'                                  case_control = c("case"),
#'                                  num_controls = 1,
#'                                  eigen_sum = sum(all_eigen_vals),
#'                                  weight_dist=TRUE
#'                                  )
#'
#' # run plot_maker()
#'  plot_maker(data=match_maker_output,
#'             x_var="PC1",
#'             y_var="PC2",
#'             case_control="case",
#'             line=TRUE)
#'  }
#' }
#'
plot_maker <- function(data=NULL, x_var=NULL, y_var=NULL, case_control=NULL, line=T, ...)
{
  # Check function input
  if(is.null(data))
  {
    stop("Please specify the match_maker data frame.")
  }
  if(is.null(x_var))
  {
    stop("Please specify the X variable for plotting.")
  }
  if(is.null(y_var))
  {
    stop("Please specify the Y variable for plotting.")
  }
  if(is.null(case_control))
  {
    stop("Please specify the case indicator variable for plotting.")
  }

  plot(data$PC_matches[,x_var], data$PC_matches[,y_var], pch=20, xlab=x_var, ylab=y_var, col=c("blue","red")[factor(data$PC_matches[,case_control])], ...)
  legend("bottomright", legend=(c("Controls","Cases")), pch=20, col=c("blue","red"), bty = "n")

  if(line==T)
  {
    pair <- 0
    for (i in 1:length(data$PC_matches[,1]))
    {
      if (data$PC_matches$match_final[i]!=pair)
      {
        case_x <- data$PC_matches[,x_var][i]
        case_y <- data$PC_matches[,y_var][i]
        pair <- data$PC_matches$match_final[i]
      }
      else
      {
        segments(case_x,case_y,data$PC_matches[,x_var][i],data$PC_matches[,y_var][i], col="gray", lty=3)
      }
    }
  }

}