R/genomicRiskSummaryPlot.R

In JakeConway/ClinPlots: ClinPlots

#' Function to generate the genomic risk summary plot, as seen in the README.
#'
#' @description A function to generate the genomic risk summary plot, which is a series of text plots accompanied
#' by a line plot displaying the values from one of the columns, usually post-test probability.
#' @param data A data.frame of the variables to use in the plots. The column that is used for the line plot must
#'        have one additional value than the other columns. The names of the columns in the data.frame will be
#'        used for the names of the columns in the plot.
#' @param column The name or index of the column to be used for the line plot.
#' @examples
#' require(ggplot2); require(grid); require(gridExtra); require(scales);
#'
#' MI.df <- read.csv(system.file("extdata", "MI.genomic.risk.txt", package = "ClinPlots"), sep='\t')
#' genomicRiskSummaryPlot(MI.df, "pt.probability")
#' #running genomicRiskSummaryPlot(MI.df, 7) will produce same result
#' @export
genomicRiskSummaryPlot <- function(data, column) {
  data <- colsToCharacter(data)
  columns <- colnames(data)
  data <- adjustGeneLabels(data, columns)
  line.data <- genomicFlattenToX(data, column)
  line.plot <- generateGenomicLinePlot(line.data)
  data <- initGgplots(data, columns, nrow(data))
  data <- addLineData(data, line.plot)
  grobs <- alignGenomicHeights(data, 4)
  drawGenomicRiskSummary(grobs)
}