cell.ordering.table: Ranking of cells according to backbone tree structure

In cellTree: Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure

Description

Produces a table of input cells ranked by their position in the backbone tree.

Usage

cell.ordering.table(b.tree, write.to.tex.file = NULL)

Arguments

b.tree	An igraph backbone tree, as returned by compute.backbone.tree.
write.to.tex.file	Boolean (optional). If not NULL, outputs LaTeX version of table to file write.to.tex.file.

Value

List of all cells, ranked by position in backbone tree, along with topic information.

Examples

# Load pre-computed LDA model for skeletal myoblast RNA-Seq data from HSMMSingleCell package:
data(HSMM_lda_model)

# Recover sampling time (in days) for each cell:
library(HSMMSingleCell)
data(HSMM_sample_sheet)
days.factor = HSMM_sample_sheet$Hours
days = as.numeric(levels(days.factor))[days.factor]

# Compute near-optimal backbone tree:
b.tree = compute.backbone.tree(HSMM_lda_model, days)
# Load pre-computed LDA model for skeletal myoblast RNA-Seq data from HSMMSingleCell package:
temp.output = tempfile()
cell.ordering.table(b.tree, write.to.tex.file = temp.output)

cellTree documentation built on Nov. 8, 2020, 5:05 p.m.