R/heatmapify.R

In maxconway/metabex: Metabolic Model Explorer

#' Produce a heatmap
#' 
#' Produces a heatmap of the genes (hierachically clustered) against the first principal component of the phenotype
#' 
#' @param dataset a dataframe with some columns prefixed by \code{genotype.},
#'   and some by \code{phenotype.}
#' @param colour the colour for the resulting heatmap
#' 
#' @export
heatmapify <- function(dataset, colour='purple'){
  
  v=as.matrix(1*dataset[order(princomp(dataset[,grep(pattern='phenotype.*',setdiff(colnames(dataset),'phenotype.kos'))])$scores[,'Comp.1']),
                              grep(pattern='genotype.*',
                                   colnames(dataset)
                              )
                              ]
  )
  
  # jitter v slightly to avoid a stack overflow from too many identical values
  vmod <- v+matrix(rnorm(prod(dim(v)),sd = 0.0001), nrow = nrow(v), ncol = ncol(v))
  
  # cluster rows
#   hc.rows <- hclust(dist(vmod))
  
  # transpose the matrix and cluster columns
#   hc.cols <- hclust(dist(t(vmod)))
  
  r <- vmod[,]
  
  heatmap(x=r,
          Rowv=NA,
          Colv=NULL,
          labRow=NA,
          labCol=NA,
          ylab='strain',
          xlab='gene (clustered)',
          col=c('ghostwhite',colour),
          scale='none',
          distfun=function(x){dist(x)}
  )
  
}