Produces a table of input cells ranked by their position in the backbone tree.
An igraph backbone tree, as returned by
Boolean (optional). If not
List of all cells, ranked by position in backbone tree, along with topic information.
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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)
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