heatmap_ChIP-seq_2.r

#The X axis is -3 kb to 3 kb around TSS.

#It turns out that the heatmap.2 function use default hclust ( Hierachical Clustering) to cluster the #matrix.
#alternatively, we can use K-means clustering to cluster the data and to see what's the pattern look like.

km<- kmeans(m1,2)   # determine how many cluster you want, I specify 2 here

m1.kmeans<- cbind(m1, km$cluster)   # combine the cluster with the matrix

dim(m1.kmeans)
# [1] 903  602
# the last column is 602

o<- order(m1.kmeans[,602])  # order the last column

m1.keans<- m1.kmeans[o,]   # order the matrix according to the order of the last column


pheatmap( m1.kmeans[,1:601], cluster_rows = F, cluster_cols = F, col= hmcols, breaks = bk, legend=FALSE, show_rownames=FALSE, show_colnames=FALSE)

# no need to cluster by pheatmap, so I set cluster_rows and cluster_cols to FALSE