compfr

This functions performs the computation of a Fruchterman-Rheingold graph layout based on an adjacency matrix derived
from the distance object in slot <code>distances</code> using the igraph package.

Application of 'RaceID' allows inference of cell types and prediction of lineage trees by the 'StemID2' algorithm (Herman, J.S., Sagar, Grun D. (2018) <DOI:10.1038/nmeth.4662>). 'VarID2' is part of this package and allows quantification of biological gene expression noise at single-cell resolution (Rosales-Alvarez, R.E., Rettkowski, J., Herman, J.S., Dumbovic, G., Cabezas-Wallscheid, N., Grun, D. (2023) <DOI:10.1186/s13059-023-02974-1>).

Dominic Grc3<bc>n

RaceID

Identification of Cell Types, Inference of Lineage Trees, and
Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

Dominic Grün

compfr function

<dl><dt>object</dt>
<dd><code>SCseq</code> class object.</dd>
<dt>knn</dt>
<dd>Positive integer number of nearest neighbours used for the inference of the Fruchterman-Rheingold layout. Default is <code>10</code>.</dd>
<dt>rseed</dt>
<dd>Integer number. Random seed to enforce reproducible layouts.</dd></dl>

Arguments

Computation of a two dimensional Fruchterman-Rheingold representation — compfr

<dl>

<dt>object</dt>
<dd><code>SCseq</code> class object.</dd>


<dt>knn</dt>
<dd>Positive integer number of nearest neighbours used for the inference of the Fruchterman-Rheingold layout. Default is <code>10</code>.</dd>


<dt>rseed</dt>
<dd>Integer number. Random seed to enforce reproducible layouts.</dd>

</dl>

compfr: Computation of a two dimensional Fruchterman-Rheingold representation

Description

Usage

Value

Arguments

Examples