Cluster data in heat map in R ggplot

Question

Please see my plot below:

my code:

 > head(data)
                  


        

Answer 1

You can achieve this by defining the order of Timepoints in a dendrogram after you have applied hclust to your data:

data <- scale(t(data))
ord <- hclust( dist(data, method = "euclidean"), method = "ward.D" )$order
ord
[1]  2  3  1  4  8  5  6 10  7  9

The only thing you have to do then is transforming your Time-column to a factor where the factor levels are ordered by ord:

pd <- as.data.frame( data )
pd$Time <- sub("_.*", "", rownames(pd))
pd.m <- melt( pd, id.vars = "Time", variable.name = "Gene" )

pd.m$Gene <- factor( pd.m$Gene, levels = colnames(data), labels = seq_along( colnames(data) ) )
pd.m$Time <- factor( pd.m$Time, levels = rownames(data)[ord],  labels = c("0h", "0.25h", "0.5h","1h","2h","3h","6h","12h","24h","48h") )

The rest is done by ggplot automatically:

ggplot( pd.m, aes(Time, Gene) ) +
  geom_tile(aes(fill = value)) +
  scale_fill_gradient2(low=muted("blue"), high=muted("red"))