I found a really great tutorial on the website about making dendrogram plots with heatmaps:

However, the create_dendrogram function is very much a black box, and the documentation doesn’t describe how distances between samples are actually computed (e.g., Euclidean distance?). It works both when I plug in a correlation matrix or the data or the data itself (see below, where df is a pandas datframe of my data). Is it computing the pairwise Euclidean distance for all rows, and using that as the data from the distances in the dendrogram?

Correlation matrix:

FF.create_dendrogram(df.corr(), orientation=‘bottom’, labels=labels)

Just the data itself:

FF.create_dendrogram(df.T, orientation=‘bottom’, labels=labels)

Thanks!

chris