i'm stuck with R, i don't know what package use to create the plot i would like. I have a pairwise matrix with the similiarity between genomes. Something like:
GENOMES genomeA genomeB genomeC
genomeA 100 75.5 13.2
genome B 42.3 100 47.3
genomeC 90 46 100
and at the end i would like to have the plots:
one with heatmap of correlation (triangular or full) with clustering
one with heatmap of correlation (triangular or full) with possibility to add my own phylogenetic tree to see the difference between the phylogeny and the clustering
i tried a lot of differents heatmap with differents packages but they are all classical heatmap and not correlation one. with heatmap i get something like this :
mtscaled = as.matrix(scale(test1))
heatmap(mtscaled, scale='none')
fun but not very accurate..
i would like more something like this + the possibility to add dendogram and tree, if someone can think about cool package!
like this it's "just" a clustering but if i want to add my own phylogenetic tree, how to reorder everyone according to the tree?