pseudotime.tree: Pseudotime Tree

In rezakj/scSeqR: scSeqR; a toolkit to analyze single cell sequencing data types (i.e scRNA-seq) and large numeric matrix files.

Pseudotime Tree

Description

This function takes an object of class scSeqR 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 scSeqR.
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", defult is "euclidean".
clust.method	Choose from "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median" or "centroid", defult is "complete".
label.offset	Space between names and tree, defult = 0.5.
type	Choose from "classic", "unrooted", "fan", "cladogram", "radial", defult = "classic".
cex	Text size, defult = 1.

Value

An object of class scSeqR.

Examples

## Not run: 
my.obj <- run.pca(my.obj, clust.method = "gene.model", gene.list = "my_model_genes.txt")

## End(Not run)

rezakj/scSeqR documentation built on March 28, 2022, 12:17 p.m.