pseudotime.tree: Pseudotime Tree

In iCellR: Analyzing High-Throughput Single Cell Sequencing Data

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.

iCellR documentation built on May 29, 2024, 5:14 a.m.