destiny (version 2.0.4)

DPT: Diffusion Pseudo Time

Description

Create pseudotime ordering and assigns cell to one of three branches

Usage

DPT(dm, tips = random_root(dm), ..., w_width = 0.1)

Arguments

dm

A DiffusionMap object. Its transition probabilities will be used to calculate the DPT

tips

The cell index/indices from which to calculate the DPT(s) (integer of length 1-3)

...

All parameters after this have to be specified by name

w_width

Window width to use for deciding the branch cutoff

Value

A DPT object:

Slots

branch

matrix (of integer) recursive branch labels for each cell (row); NA for undeceided. Use branch_divide to modify this.

tips

matrix (of logical) indicating if a cell (row) is a tip of the corresponding banch level (col)

dm

DiffusionMap used to create this DPT object

Details

Treat it as a matrix of pseudotime by subsetting ([ dim nrow ncol as.matrix), and as a list of pseudodime, and expression vectors ($ [[ names as.data.frame).

Examples

data(guo_norm)
dm <- DiffusionMap(guo_norm)
dpt <- DPT(dm, branching = TRUE)
str(dpt)