Description Usage Arguments Details Value Examples
Builds a ‘backbone tree’ from a fitted LDA model.
1 2 3 4 
lda.results 
A fitted LDA model, as returned by 
grouping 
An (optional) vector of labels for each cell in the 
start.group.label 
If a 
absolute.width 
Numeric (optional). Distance threshold below which a cell vertex is considered to be attached to a backbone vertex (see paper for more details). By default, this threshold is computed dynamically, based on the distance distribution for each branch. 
width.scale.factor 
Numeric (optional). A scaling factor for the dynamicallycomputed distance threshold (ignored if 
outlier.tolerance.factor 
Numeric (optional). Proportion of vertices, out of the total number of vertices divided by the total number of branches, that can be left at the end of the backbone treebuilding algorithm. 
rooting.method 
String (optional). Method used to root the backbone tree. Must be either NULL or one of: ‘longest.path’, ‘center.start.group’ or ‘average.start.group’. ‘longest.path' picks one end of the longest shortestpath between two vertices. 'center.start.group’ picks the vertex in the starting group with lowest meansquaredistance to the others. ‘average.start.group’ creates a new artificial vertex, as the average of all cells in the starting group. If no value is provided, the best method is picked based on the type of grouping and start group information available. 
only.mst 
If 
grouping.colors 
(Optional) vector of RGB colors to be used for each grouping. 
merge.sequential.backbone 
(Optional) whether to merge sequential backbone vertices that are close enough. This will produce a more compact backbone tree, but at the cost of extra computing time. 
In order to easily visualise the structural and temporal relationship between cells, we introduced a special type of tree structure dubbed ‘backbone tree’, defined as such:
Considering a set of vertices V and a distance function over all pairs of vertices: d: V <c3><97> V > R+, we call backbone tree a graph, T with backbone B, such that:
T is a tree with set of vertices V and edges E.
B is a tree with set of vertices V_B in V and edges E_B in E.
All ‘vertebrae’ vertices of T: v in V \ V_B are connected by a single edge to the closest vertex in the set of backbone vertices v*_B in V_B. I.e: v*_B = argmin_{v_B in V_B} d(v_B, v).
For all vertices in V \ V_B are less than distance δ to a vertex in the backbone tree B: for all v in V \ V_B, there is a v_B in V_B such that d(v, v_b) < δ.
In this instance, we relax the last condition to cover only ‘most’ nonbackbone vertices, allowing for a variable proportion of outliers at distance > δ from any vertices in V_B.
We can then define the ‘optimal’ backbone tree to be a backbone tree such that the sum of weighted edges in the backbone subtree E_B is minimal. Finding such a tree can be easily shown to be NPComplete (by reduction to the Vertex Cover problem), but we developed a fast heuristic relying on Minimum Spanning Tree to produce a reasonable approximation.
The resulting quasioptimal backbone tree (simply referred to as ‘the’ backbone tree thereafter) gives a clear hierarchical representation of the cell relationship: the objective function puts pressure on finding a (small) group of prominent cells (the backbone) that are good representatives of major steps in the cell evolution (in time or space), while remaining cells are similar enough to their closest representative for their difference to be ignored. Such a tree provides a very clear visualisation of overall cell differentiation paths (including potential differentiation into subtypes).
A igraph object with either a minimum rooted spanningtree (if only.mst
is TRUE
) or a quasioptimal backbone tree connecting all input cells. Cell topic distribution, distances and branch order are added as vertex/edge/graph attributes.
1 2 3 4 5 6 7 8 9 10 11 12 13  # Load precomputed LDA model for skeletal myoblast RNASeq 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 nearoptimal backbone tree:
b.tree = compute.backbone.tree(HSMM_lda_model, days)
# Plot resulting tree with sampling time as a vertex group colour:
ct.plot.grouping(b.tree)

Loading required package: topGO
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: graph
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Attaching package: 'topGO'
The following object is masked from 'package:IRanges':
members
Loading required namespace: maptpx
Using start group: 0 (1)
Using rooting method: center.start.group
Using root vertex: 4
Adding branch #1:
[1] 65 53 45 2 55 47 57 48 44 7 19 25 69 66 9 63 18 62 51
[20] 56 16 70 136 133 143 89 78 140 94 100 177 194 141 199 201 181 161 204
[39] 225 236 255 247 246 233 229 259 258 146 235 159 185 191 216 166 149 83 168
[58] 158 8
Using branch width: 0.927 (width.scale.factor: 1.2)
Outliers: 1
Total number of branches: 1 (forks: 0)
Backbone fork merge (width: 0.927): 60 > 60
Ranking all cells...
Computing tree layout...
IGRAPH 6c9ebac DNW 271 270 
+ attr: grouping.colors (g/c), grouping.labels (g/n), ordered.branches
 (g/x), ratio (g/n), is.backbone (v/l), is.root (v/l), name (v/n),
 color (v/c), group.idx (v/n), grouping.label (v/n), pie (v/x), shape
 (v/c), cell.name (v/c), x (v/n), y (v/n), size (v/n), weight (e/n),
 arrow.mode (e/n)
+ edges from 6c9ebac (vertex names):
[1] 2> 20 2> 26 2> 50 2> 55 4> 1 4> 10 4> 13 4> 15 4> 24
[10] 4> 28 4> 30 4> 31 4> 34 4> 40 4> 41 4> 49 4> 58 4> 59
[19] 4> 60 4> 64 4> 65 4>150 4>196 4>234 4>242 4>266 4>267
[28] 7> 19 7> 73 7>211 8> 42 9> 27 9> 63 9> 68 16> 70 18> 22
+ ... omitted several edges
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.