Generate multiple representations

Generate representations of the data to be used in lineage analysis.

RepresentationMap(
  flat_embedding = NULL,
  similarity_matrix,
  join_components = TRUE,
  normalize_S = TRUE,
  flat_embedding_method = "umap",
  ...
)

Arguments

flat_embedding	optionally provided low dim embedding, if not then 2d tsne will be used
similarity_matrix	the graphical embedding of the cells
join_components	boolean, whether or not to join disconnected components of the similarity matrix
normalize_S	whether or not to normalize the similarity matrix
flat_embedding_method	what method to use for flat embedding. Use umap by default. Can be umap or tsne.
...	arguments to called functions

Value

a list containing:

dist_flat

distance matrix on flat embedding

dist_graph

distance matrix on graph

adj_matrix

unweighted adjacency matrix

flat_embedding

the low dimensional embedding of the cells

similarity_graph

igraph object on the unweighted adjacency matrix

components

an igraph components object based on similarity_graph

n_components

number of components in components

sizes

sizes of components in components

members

list of members of components, sorted by component size and member index