Embedding alignment and clustering based on the embeddings from FAST

Source: R/iSCMEB.R

Embedding alignment and clustering using the Harmony and Louvain based on the ebmeddings from FAST as well as determining the number of clusters.

RunHarmonyLouvain(PRECASTObj, resolution = 0.5)

Arguments

PRECASTObj

a PRECASTObj object created by CreatePRECASTObject.

resolution

an optional real, the value of the resolution parameter, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities.

Value

Return a revised PRECASTObj object with slot PRECASTObj@resList added by a Harmony compoonent (including the aligned embeddings and embeddings of batch effects) and a Louvain component (including the clusters).