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

Description Usage Arguments Value Examples

View source: R/cellTree.R

Description

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

Usage

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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

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# 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 Oct. 31, 2019, 7:50 a.m.