compfr: Computation of a two dimensional Fruchterman-Rheingold...

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

Computation of a two dimensional Fruchterman-Rheingold representation

Description

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

Usage

compfr(object, knn = 10, rseed = 15555)

Arguments

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

Value

SCseq object with layout coordinates stored in slot fr.

Examples

sc <- SCseq(intestinalDataSmall)
sc <- filterdata(sc)
sc <- compdist(sc)
sc <- clustexp(sc)
sc <- findoutliers(sc)
sc <- compfr(sc)

RaceID documentation built on April 4, 2025, 4:34 a.m.