collapseGraphSum

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

collapseGraphSum function

<dl><dt>graph</dt>
<dd>igraph graph object Graph to be collapsed</dd>
<dt>groups</dt>
<dd>factor on vertices describing cluster assignment (can specify integer vertex ids, or character vertex names which will be matched)</dd>
<dt>normalize</dt>
<dd>boolean Whether to recalculate edge weight as observed/expected (default=TRUE)</dd></dl>

Arguments

Collapse Graph By Sum — collapseGraphSum

<dl>

<dt>graph</dt>
<dd>igraph graph object Graph to be collapsed</dd>


<dt>groups</dt>
<dd>factor on vertices describing cluster assignment (can specify integer vertex ids, or character vertex names which will be matched)</dd>


<dt>normalize</dt>
<dd>boolean Whether to recalculate edge weight as observed/expected (default=TRUE)</dd>

</dl>

collapseGraphSum: Collapse Graph By Sum

Description

Usage

Value

Arguments

Examples