multi2dend

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.

Evan Biederstedt

sccore

Core Utilities for Single-Cell RNA-Seq

Viktor Petukhov

Rasmus Rydbirk

Peter Kharchenko

multi2dend function

<dl><dt>cl</dt>
<dd>igraph communities object, returned from igraph community detection functions</dd>
<dt>counts</dt>
<dd>dgCmatrix of counts</dd>
<dt>deep</dt>
<dd>boolean If TRUE, take (cl$memberships[1,]). Otherwise, uses as.integer(membership(cl)) (default=FALSE)</dd>
<dt>dist</dt>
<dd>Distance metric used (default='cor'). Eiether 'cor' for the correlation distance in log10 space, or 'JS' for the Jensen–Shannon distance metric (i.e. the square root of the Jensen–Shannon divergence)</dd></dl>

Arguments

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

<dl>

<dt>cl</dt>
<dd>igraph communities object, returned from igraph community detection functions</dd>


<dt>counts</dt>
<dd>dgCmatrix of counts</dd>


<dt>deep</dt>
<dd>boolean If TRUE, take (cl$memberships[1,]). Otherwise, uses as.integer(membership(cl)) (default=FALSE)</dd>


<dt>dist</dt>
<dd>Distance metric used (default='cor'). Eiether 'cor' for the correlation distance in log10 space, or 'JS' for the Jensen–Shannon distance metric (i.e. the square root of the Jensen–Shannon divergence)</dd>

</dl>

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

Description

Usage

Value

Arguments