I am trying to take my dataset, which consists of the interaction of a dna protein, to cluster data and generate a heat map that displays the resulting data, so that the data looks grouped with clusters lining up on a diagonal. I can group the data and generate a dendrogram of this data, however, when I generate a heat map of the data using the heat map function in R, the clusters are not visible. If you look at the first 2 images, then one of the dendrograms that I can generate, the second from the heat map that I can generate, and the third is just an example of a cluster heat map that shows how I expect the result to look rude. As can be seen from the comparison of the second and third images, it is clear that in the third there are clusters, but not in the second image.
:
http://pastebin.com/wQ9tYmjy
R:
args <- commandArgs(TRUE);
matrix_a <- read.table(args[1], sep='\t', header=T, row.names=1);
location <- args[2];
matrix_d <- dist(matrix_a);
hc <- hclust(matrix_d,"average");
mypng <- function(filename = "mydefault.png") {
png(filename)
}
options(device = "mypng")
plot(hc);
:
matrix_a <- read.table("Arda_list.txt.binary.matrix.txt", sep='\t', header=T, row.names=1);
mtscaled <- as.matrix(scale(matrix_a))
heatmap(mtscaled, Colv=F, scale='none')
:
http://digitheadslabnotebook.blogspot.com/2011/06/drawing-heatmaps-in-r.html
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