Create pseudotime ordering and assigns cell to one of three branches

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)

...

Unused. All parameters to the right of the ... have to be specified by name (e.g. DPT(dm, w_width = 0.2))

w_width

Window width to use for deciding the branch cutoff

Value

A 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).

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

Examples

data(guo_norm) dm <- DiffusionMap(guo_norm) dpt <- DPT(dm) str(dpt)
#> Formal class 'DPT' [package "destiny"] with 3 slots #> ..@ branch: int [1:428, 1:7] 2 2 2 2 2 2 2 2 2 2 ... #> .. ..- attr(*, "dimnames")=List of 2 #> .. .. ..$ : chr [1:428] "10" "11" "12" "13" ... #> .. .. ..$ : chr [1:7] "Branch1" "Branch2" "Branch3" "Branch4" ... #> ..@ tips : logi [1:428, 1:7] FALSE FALSE FALSE FALSE FALSE FALSE ... #> .. ..- attr(*, "dimnames")=List of 2 #> .. .. ..$ : chr [1:428] "10" "11" "12" "13" ... #> .. .. ..$ : chr [1:7] "Tips1" "Tips2" "Tips3" "Tips4" ... #> ..@ dm :Formal class 'DiffusionMap' [package "destiny"] with 17 slots #> .. .. ..@ eigenvalues : Named num [1:20] 0.947 0.807 0.724 0.712 0.654 ... #> .. .. .. ..- attr(*, "names")= chr [1:20] "DC1" "DC2" "DC3" "DC4" ... #> .. .. ..@ eigenvectors : num [1:428, 1:20] -0.0483 -0.0468 -0.0401 -0.045 -0.0479 ... #> .. .. .. ..- attr(*, "dimnames")=List of 2 #> .. .. .. .. ..$ : chr [1:428] "10" "11" "12" "13" ... #> .. .. .. .. ..$ : chr [1:20] "DC1" "DC2" "DC3" "DC4" ... #> .. .. ..@ sigmas :Formal class 'Sigmas' [package "destiny"] with 5 slots #> .. .. .. .. ..@ log_sigmas : NULL #> .. .. .. .. ..@ dim_norms : NULL #> .. .. .. .. ..@ optimal_sigma: Named num [1:428] 9.72 9.28 10.9 9.69 9.52 ... #> .. .. .. .. .. ..- attr(*, "names")= chr [1:428] "10" "11" "12" "13" ... #> .. .. .. .. ..@ optimal_idx : NULL #> .. .. .. .. ..@ avrd_norms : NULL #> .. .. ..@ data_env :<environment: 0x55d5fb571658> #> .. .. ..@ eigenvec0 : Named num [1:428] 0.0546 0.0535 0.0513 0.0529 0.053 ... #> .. .. .. ..- attr(*, "names")= chr [1:428] "10" "11" "12" "13" ... #> .. .. ..@ transitions :Formal class 'dsCMatrix' [package "Matrix"] with 7 slots #> .. .. .. .. ..@ i : int [1:91378] 0 0 1 0 1 2 0 1 2 3 ... #> .. .. .. .. ..@ p : int [1:429] 0 0 1 3 6 10 15 21 28 36 ... #> .. .. .. .. ..@ Dim : int [1:2] 428 428 #> .. .. .. .. ..@ Dimnames:List of 2 #> .. .. .. .. .. ..$ : chr [1:428] "10" "11" "12" "13" ... #> .. .. .. .. .. ..$ : chr [1:428] "10" "11" "12" "13" ... #> .. .. .. .. ..@ x : num [1:91378] 0.1043 0.0445 0.0301 0.0413 0.039 ... #> .. .. .. .. ..@ uplo : chr "U" #> .. .. .. .. ..@ factors : list() #> .. .. ..@ d : num [1:428] 3.76 4.05 4.86 4.82 3.5 ... #> .. .. ..@ d_norm : num [1:428] 0.167 0.161 0.148 0.157 0.158 ... #> .. .. ..@ k : int 427 #> .. .. ..@ n_local : int [1:3] 5 6 7 #> .. .. ..@ density_norm : logi TRUE #> .. .. ..@ rotate : logi FALSE #> .. .. ..@ distance : chr "euclidean" #> .. .. ..@ censor_val : NULL #> .. .. ..@ censor_range : NULL #> .. .. ..@ missing_range: NULL #> .. .. ..@ vars : NULL