plotgraph: StemID2 Lineage Graph

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

StemID2 Lineage Graph

Description

This function plots a graph of lineage trajectories connecting RaceID3 cluster medoids as inferred by StemID2 to approximate the lineage tree. The plot highlights significant links, where colour indicates the level of significance and width indicates the link score. The node colour reflects the level of transcriptome entropy.

Usage

plotgraph(
  object,
  showCells = FALSE,
  showMap = TRUE,
  tp = 0.5,
  scthr = 0,
  cex = 1
)

Arguments

object	Ltree class object.
showCells	logical. If TRUE, then projections of cells are shown in the plot. Default is FALSE.
showMap	logical. Tf TRUE, then show transparent t-SNE map (with transparency tp) of cells in the background. Default is TRUE.
tp	Real number between zero and one. Level of transparency of the t-SNE map. Deafault is 0.5. See showMap.
scthr	Real number between zero and one. Score threshold for links to be shown in the graph. For scthr=0 all significant links are shown. The maximum score is one. Default is 0.
cex	real positive number. Size of data points. Deault is 1.

Value

None.

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