cell.ordering.table {cellTree} | R Documentation

## Ranking of cells according to backbone 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)

[Package cellTree version 1.16.0 Index]