pseudotime.tree {iCellR} | R Documentation |
This function takes an object of class iCellR and marker genes for clusters and performs pseudotime for differentiation or time course analysis.
pseudotime.tree( x = NULL, marker.genes = "NULL", clust.names = "NULL", dist.method = "euclidean", clust.method = "complete", label.offset = 0.5, type = "classic", hang = 1, cex = 1 )
x |
An object of class iCellR. |
marker.genes |
A list of marker genes for clusters. |
clust.names |
A list of names for clusters. |
dist.method |
Choose from "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski", default = "euclidean". |
clust.method |
Choose from "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median" or "centroid", default = "complete". |
label.offset |
Space between names and tree, default = 0.5. |
type |
Choose from "classic", "jitter", "unrooted", "fan", "cladogram", "radial", default = "classic". |
hang |
Hang, default = 1. |
cex |
Text size, default = 1. |
An object of class iCellR.
marker.genes <- findMarkers(demo.obj,fold.change = 2,padjval = 0.1,uniq = TRUE) MyGenes <- top.markers(marker.genes, topde = 10, min.base.mean = 0.8) pseudotime.tree(demo.obj, marker.genes = MyGenes, type = "unrooted", clust.method = "complete")