R/plotSNPs.R

In ttriche/sesamizeGEO: the poor man's methylation suite (cf. `sesamizer`)

#' another oldie but goodie
#' 
#' plot SNPs living in metadata(x)$SNPs, provided they match sampleNames(x)
#' 
#' @param x       a grSet with SNPs in its metadata(), or a SNP matrix 
#' @param rotate  rotate the subjects onto the side? (FALSE)
#' @param ...     other arguments passed on to Heatmap
#' 
#' @import ComplexHeatmap
#' 
#' @export
plotSNPs <- function(x, rotate=FALSE, ...) { 
  if (is(x, "GenomicRatioSet") | is(x, "RGChannelSet")) { 
    SNPs <- as.matrix(metadata(x)$SNPs)
    if (is.null(SNPs) | !all(colnames(x) %in% colnames(SNPs))) {
      stop("Your SNPs don't match your samples. Aborting.")
    }
    SNPs <- SNPs[, colnames(x)]
  } else { 
    SNPs <- as.matrix(x)
  }
  if (rotate) SNPs <- t(SNPs)
  Heatmap(SNPs, name="BAF", 
          clustering_method_columns='ward.D2', 
          clustering_distance_columns='manhattan', 
          clustering_method_rows='ward.D2', 
          clustering_distance_rows='manhattan',
          ...)
}