plotmap: Plotting a dimensional reduction representation

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

Plotting a dimensional reduction representation

Description

This functions plots a two-dimensional t-SNE map, UMAP, or a Fruchterman-Rheingold graph layout of the singe-cell transcriptome data.

Usage

plotmap(object, final = TRUE, tp = 1, fr = FALSE, um = FALSE, cex = 0.5)

Arguments

object	SCseq class object.
final	logical. If TRUE, then highlight final clusters after outlier identification. If FALSE, then highlight initial clusters prior to outlier identification. Default is TRUE.
tp	Number between 0 and 1 to change transparency of dots in the map. Default is 1.
fr	logical. If TRUE then plot Fruchterman-Rheingold layout. Default is FALSE.
um	logical. If TRUE then plot umap dimensional reduction representation. Default is FALSE.
cex	size of data points. Default value is 0.5.

Value

None

RaceID documentation built on Sept. 28, 2023, 5:06 p.m.