Hierarchical clustering in relative abundances plots about microviz HOT 2 CLOSED

Hi Brigitte,

Not currently possible unfortunately, but could be a nice feature for the future.
If you really need it, the code from inside ps_seriate can get you the seriation object which has the clustering dendrogram inside it. You could then plot this alongside the bar chart with ggdendro or dendextend http://andrie.github.io/ggdendro/

(but indeed this would be a bit of manual work)

Code below adapted from inside ps_seriate

method = "OLO_ward"
dist = "bray"
tax_transform = "identity"

# transform taxa for ordering 
ps_transformed <- ps_get(tax_transform(ps, trans = tax_transform))

# calculate distance between samples
distMat <- dist_get(dist_calc(data = ps_transformed, dist = dist))
ser <- seriation::seriate(x = distMat, method = method)

Out of interest, why do you want the clustering dendrogram?

from microviz.

Hi David,
Thanks for the suggestion! I want the clustering to see if there are some groups visible based on the microbiome composition. I am going to try to use your suggestion. Thanks!

from microviz.