Plotting a dimensional reduction representation
This functions plots a two-dimensional t-SNE map, UMAP, or a Fruchterman-Rheingold graph layout of the singe-cell transcriptome data.
plotmap(object, final = TRUE, tp = 1, fr = FALSE, um = FALSE, cex = 0.5)
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.None
Useful links