R - heatmap.2: reorder rows and columns

Question

I generated a heatmap using heatmap.2 of the gplots package:

library(gplots)
abc <-read.csv(file="abc.txt", header=T, sep="\t", dec=".")
abcm<-as.matrix(abc)
def <-read.csv(file="def.txt", header=T, sep="\t", dec=".")
defm<-as.matrix(def)
mean <-read.csv(file="mean.txt", header=T, sep="\t", dec=".")
meanm<-as.matrix(mean)
distance.row = dist(as.matrix(def), method = "euclidean")
cluster.row = hclust(distance.row, method = "average")
distance.col = dist(t(as.matrix(abc)), method = "euclidean")
cluster.col = hclust(distance.col, method = "average")
my_palette <- colorRampPalette(c("red", "yellow", "green"))(n = 299)

heatmap.2(meanm, trace="none", dendrogram="both", Rowv=as.dendrogram(cluster.row), Colv=as.dendrogram(cluster.col), margins = c(7,7), col=my_palette)

with two different clustering methods for each dendrogram.

Now I want to reorder the objects, so that the green squares form a diagonal. How do I do that?

EDIT: my sample input here

structure(c(1, 0.6798, 0.6604, 0.7101, 0.6771, 0.6725, 0.6696, 
0.6548, 0.676, 0.6811, 0.6798, 1, 0.656, 0.6763, 0.8163, 0.781, 
0.7811, 0.6503, 0.7811, 0.855, 0.6604, 0.656, 1, 0.6532, 0.6498, 
0.6459, 0.6455, 0.7532, 0.6521, 0.6536, 0.7101, 0.6763, 0.6532, 
1, 0.672, 0.669, 0.6669, 0.6517, 0.6748, 0.6786, 0.6771, 0.8163, 
0.6498, 0.672, 1, 0.7828, 0.7838, 0.6441, 0.7736, 0.8227, 0.6725, 
0.781, 0.6459, 0.669, 0.7828, 1, 0.8361, 0.6447, 0.7574, 0.7796, 
0.6696, 0.7811, 0.6455, 0.6669, 0.7838, 0.8361, 1, 0.638, 0.7566, 
0.7772, 0.6548, 0.6503, 0.7532, 0.6517, 0.6441, 0.6447, 0.638, 
1, 0.6563, 0.6459, 0.676, 0.7811, 0.6521, 0.6748, 0.7736, 0.7574, 
0.7566, 0.6563, 1, 0.7778, 0.6811, 0.855, 0.6536, 0.6786, 0.8227, 
0.7796, 0.7772, 0.6459, 0.7778, 1), .Dim = c(10L, 10L), .Dimnames = list(
    c("sp1", "sp2", "sp3", "sp4", "sp5", "sp6", "sp7", "sp8", 
    "sp9", "sp10"), c("sp1", "sp2", "sp3", "sp4", "sp5", "sp6", 
    "sp7", "sp8", "sp9", "sp10")))

Answer 1

The function reorder.dendrogram flips the branches.

reorder(as.dendrogram(cluster.col), 10:1)
reorder(as.dendrogram(cluster.row), 10:1)

used in

heatmap.2(meanm, trace="none", dendrogram="both",
Rowv=reorder(as.dendrogram(cluster.row), 10:1),
Colv=reorder(as.dendrogram(cluster.col), 10:1),
margins = c(7,7), breaks=breaks,col=hm.colors, na.color="white",
main="mean(AAI+ANI)", xlab="AAI clustering", ylab="ANI clustering", srtCol=45)