#' Plot heatmap
#'
#' @param dat matrix
#' @param filename (optional)
#' @param height of pdf file
#' @param width of pdf file
#'
#' @return
#' @export
#'
#' @examples
plot.heatmap = function(dat, filename = NULL, height = 10, width =7, scale="none", showRowDendro=F, showColDendro=F, cexRow=0.9, cexCol=0.9){
hc = hclust(as.dist(1-cor(dat, method="spearman", use= "pairwise.complete.obs")), method="complete")
hr = hclust(as.dist(1-cor(t(dat), method="spearman", use= "pairwise.complete.obs")), method="complete")
require(heatmap3)
p = heatmap3(dat, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc), scale=scale, balanceColor=T, showRowDendro=showRowDendro, showColDendro=showColDendro, cexRow = cexRow, cexCol = cexCol)
if (!is.null(filename)) {
pdf( filename, height = height, width =width)
print(p)
dev.off()
}
}
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