silhouette width

library(cluster)
setwd("E:\\Projects\\8.ComBAT\\ComBat248")
rmafile <- "ComBat248T_filtered.stdized.txt"
data <- read.table(rmafile, header = T, sep = "\t", row.names=1)

setwd("E:\\Projects\\8.ComBAT\\ComBat248\\CCP_FIS_SG248_top10000_ZL20120301\\Run3")
feature.file <- "K3_limma_geneset4.txt"
feature <- read.table(feature.file, header = T, sep = "\t", row.names=1)

data <- data[feature$ID,]
plot (hclust(dist(t(data)))) # Hclust plot of data

dmat <- dist(t(data))
hc <- hclust(dmat, "average")
hsil <- silhouette(cutree(hc, k=3), dmat)
plot(hsil)
write.table(hsil, "silhouette_width.avg_linkage.txt", sep="\t")