I'm using pheatmap with large data. My purpose is to clusterize rows and columns and to analyze main clusters. I upload the data table and perform the heatmap as follows:
library (pheatmap)
data<-read.table ("example.txt", header = TRUE)
pheatmap(data)
By this I get the heatmap of my data. My example.txt look like this:
a b c d e f
a 1 0.1 0.9 0.5 0.65 0.9
b 0.1 1 0.39 0.83 0.47 0.63
c 0.9 0.39 1 0.42 0.56 0.84
d 0.5 0.83 0.42 1 0.95 0.43
e 0.65 0.47 0.56 0.95 1 0.14
f 0.9 0.63 0.84 0.43 0.14 1
May be this is a very stupid question, but anyway I'll post it. After running pheatmap(data), how can I get the elements corresponding to the clusters? Do I have to save the results in some specific ways and analyse them by other R packages?
Answer
Grab the result of pheatmap and use cutree. To extract 10 clusters e.g. you could do:
library(pheatmap)
res <- pheatmap(mtcars)
mtcars.clust <- cbind(mtcars,
cluster = cutree(res$tree_row,
k = 10))
head(mtcars.clust)
# mpg cyl disp hp drat wt qsec vs am gear carb cluster
# Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4 1
# Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4 1
# Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1 2
# Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1 3
# Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2 4
# Valiant 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1 3
See ?pheatmap, ?hclust and ?cutree for the help.