multi2dend

igraph communities object, returned from igraph community detection functions

counts

boolean If TRUE, take (cl$memberships[1,]). Otherwise, uses as.integer(membership(cl)) (default=FALSE)

deep

Distance metric used (default='cor'). Eiether 'cor' for the correlation distance in log10 space, or 'JS' for the Jensen&lt;U+2013&gt;Shannon distance metric (i.e. the square root of the Jensen&lt;U+2013&gt;Shannon divergence)

dist

Translate multilevel segmentation into a dendrogram, with the lowest level of the dendrogram listing the cells

Core utilities for single-cell RNA-seq data analysis. Contained within are utility functions for working with differential expression (DE) matrices and count matrices, a collection of functions for manipulating and plotting data via 'ggplot2', and functions to work with cell graphs and cell embeddings. Graph-based methods include embedding kNN cell graphs into a UMAP <doi:10.21105/joss.00861>, collapsing vertices of each cluster in the graph, and propagating graph labels.

multi2dend: Translate multilevel segmentation into a dendrogram, with the lowest level of the dendrogram listing the cells

Description

Usage

Arguments

Value