knn_graph_from_dist

Build kNN graph from distance
(used in <code>"build_knn_graph"</code>)

Aggregates large single-cell data into metacell dataset by merging together gene expression of very similar cells. 'SuperCell' uses 'velocyto.R' <doi:10.1038/s41586-018-0414-6> <https://github.com/velocyto-team/velocyto.R> for RNA velocity. We also recommend installing 'scater' Bioconductor package <doi:10.18129/B9.bioc.scater> <https://bioconductor.org/packages/release/bioc/html/scater.html>.

Leonard Herault

SuperCell

Simplification of scRNA-Seq Data by Merging Together Similar
Cells

Mariia Bilous

knn_graph_from_dist function

<dl><dt>D</dt>
<dd>dist matrix or dist object (preferentially)</dd>
<dt>k</dt>
<dd>kNN parameter</dd>
<dt>return_neighbors_order</dt>
<dd>whether return order of neighbors (not available for nn2 option)</dd>
<dt>mode</dt>
<dd>mode of <a href="/link/graph_from_adj_list?package=SuperCell&version=1.0" data-mini-rdoc="SuperCell::graph_from_adj_list">graph_from_adj_list</a> ('all' -- undirected graph, 'out' -- directed graph)</dd></dl>

Arguments

Build kNN graph from distance
(used in "build_knn_graph") — knn_graph_from_dist

<dl>

<dt>D</dt>
<dd>dist matrix or dist object (preferentially)</dd>


<dt>k</dt>
<dd>kNN parameter</dd>


<dt>return_neighbors_order</dt>
<dd>whether return order of neighbors (not available for nn2 option)</dd>


<dt>mode</dt>
<dd>mode of <a href='https://rdrr.io/pkg/igraph/man/graph_from_adj_list.html'>graph_from_adj_list</a> ('all' -- undirected graph, 'out' -- directed graph)</dd>

</dl>

knn_graph_from_dist: Build kNN graph from distance (used in `"build_knn_graph"`)

Description

Usage

Value

Arguments