iCellR (version 1.6.1)

pseudotime.tree: Pseudotime Tree

Description

This function takes an object of class iCellR and marker genes for clusters and performs pseudotime for differentiation or time course analysis.

Usage

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
)

Arguments

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.

Value

An object of class iCellR.

Examples

# NOT RUN {
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")

# }