pheatmap in R. How to get clusters

Question

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:

Answer 1

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.