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.
plotgraph(object, showCells = FALSE, showTsne = TRUE, tp = 0.5,
scthr = 0)Ltree class object.
logical. If TRUE, then projections of cells are shown in the plot. Default is FALSE.
logical. Tf TRUE, then show transparent t-SNE map (with transparency tp) of cells in the background. Default is TRUE.
Real number between zero and one. Level of transparency of the t-SNE map. Deafault is 0.5. See showTsne.
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.
None.