cell.ordering.table {cellTree} | R Documentation |
Produces a table of input cells ranked by their position in the backbone tree.
cell.ordering.table(b.tree, write.to.tex.file = NULL)
b.tree |
An igraph backbone tree, as returned by |
write.to.tex.file |
Boolean (optional). If not |
List of all cells, ranked by position in backbone tree, along with topic information.
# 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)