ggplot2 - R: How do I display clustered matrix heatmap (similar color patterns are grouped)

Question

I searched a lot of questions about heatmap throughout the site and packages, but I still have a problem.
I have clustered data (kmeans/EM/DBscan..), and I want to create a heatmap by grouping the same cluster. I want the similar color patterns to be grouped in the heatmap, so generally, it looks like a block-diagonal.
I tried to order the data by the cluster number and display it,

k = kmeans(data, 3)
d = data.frame(data)
d = data.frame(d, k$cluster)
d = d[order(d$k.cluster),]
heatmap(as.matrix(d))

but it is still not sorted and looks like this link:
But, I want it to be sorted by its cluster number and looked like this:
Can I do this in R?
I searched lots of packages and tried many ways, but I still have a problem.
Thanks a lot.

Answer 1

You can do this using reshape2 and ggplot2 as follows:

library(reshape2)
library(ggplot2)

# Create dummy data
set.seed(123)
df <- data.frame(
        a = sample(1:5, 1000, replace=TRUE),
        b = sample(1:5, 1000, replace=TRUE),
        c = sample(1:5, 1000, replace=TRUE)
)

# Perform clustering
k <- kmeans(df, 3)

# Append id and cluster
dfc <- cbind(df, id=seq(nrow(df)), cluster=k$cluster)

# Add idsort, the id number ordered by cluster 
dfc$idsort <- dfc$id[order(dfc$cluster)]
dfc$idsort <- order(dfc$idsort)

# use reshape2::melt to create data.frame in long format
dfm <- melt(dfc, id.vars=c("id", "idsort"))

ggplot(dfm, aes(x=variable, y=idsort)) + geom_tile(aes(fill=value))