BuildNetwork

BuildNetwork,scDiffCom-method

Create and plot an interactive network that summarize how
cell-types and their interactions are over-represented.

Analysis tools to investigate changes in intercellular
communication from scRNA-seq data. Using a Seurat object as input,
the package infers which cell-cell interactions are present in the dataset
and how these interactions change between two conditions of interest
(e.g. young vs old). It relies on an internal database of ligand-receptor
interactions (available for human, mouse and rat) that have been gathered
from several published studies. Detection and differential analyses
rely on permutation tests. The package also contains several tools
to perform over-representation analysis and visualize the results. See
Lagger, C. et al. (2023) <doi:10.1038/s43587-023-00514-x> for a full
description of the methodology.

Cyril Lagger

scDiffCom

Differential Analysis of Intercellular Communication from
scRNA-Seq Data

Eugen Ursu

Anais Equey

BuildNetwork function

<dl><dt>object</dt>
<dd><code>scDiffCom</code> object</dd>
<dt>network_type</dt>
<dd>Type of network to display. Currently, only
<code>ORA_network</code> (default) is supported.</dd>
<dt>layout_type</dt>
<dd>Layout of the network to display. Can either be
<code>"bipartite"</code> (default) or <code>"conventional"</code>.</dd>
<dt>abbreviation_table</dt>
<dd>Table with abbreviations
for the cell types present in the <code>object</code>. If <code>NULL</code> (default),
full names of the cell-types are displayed. Otherwise, it must be a
data.frame or data.table with exactly two columns with names
<code>ORIGINAL_CELLTYPE</code> and <code>ABBR_CELLTYPE</code>.</dd></dl>

Arguments

Display cell-type to cell-type interactive networks — BuildNetwork

<dl>

<dt>object</dt>
<dd><code>scDiffCom</code> object</dd>


<dt>network_type</dt>
<dd>Type of network to display. Currently, only
<code>ORA_network</code> (default) is supported.</dd>


<dt>layout_type</dt>
<dd>Layout of the network to display. Can either be
<code>"bipartite"</code> (default) or <code>"conventional"</code>.</dd>


<dt>abbreviation_table</dt>
<dd>Table with abbreviations
for the cell types present in the <code>object</code>. If <code>NULL</code> (default),
full names of the cell-types are displayed. Otherwise, it must be a
data.frame or data.table with exactly two columns with names
<code>ORIGINAL_CELLTYPE</code> and <code>ABBR_CELLTYPE</code>.</dd>

</dl>

BuildNetwork: Display cell-type to cell-type interactive networks

Description

Usage

Value

Arguments