pseudotime.tree: Pseudotime Tree
In rezakj/iCellR: Analyzing High-Throughput Single Cell Sequencing Data

pseudotime.tree

R Documentation

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.