> Reference > > dynwrap :: Creating a trajectory > Constructs a trajectory using a graph between cells, by mapping cells onto a set of backbone cells.

Constructs a trajectory using a graph between cells, by mapping cells onto a set of backbone cells.

This function will generate the milestone_network and progressions.

add_cell_graph(dataset, cell_graph, to_keep,
  milestone_prefix = "milestone_", ...)

Arguments

dataset	A dataset created by `wrap_data()` or `wrap_expression()`
cell_graph	The edges between cells. Format: Data frame(from = character, to = character, length(optional) = numeric, directed(optional) = logical)
to_keep	A character vector with the identifiers of the backbone cells. Alternatively, a named boolean vector whether a cell is from the backbone
milestone_prefix	A prefix to add to the id of the cell ids when they are used as milestones, in order to avoid any naming conflicts,
...	extra information to be stored in the wrapper.

Value

The trajectory

Examples

library(tibble)
library(dplyr)
dataset <- wrap_data(cell_ids = letters)

backbone_cell_graph <- tibble(
  from = letters[1:10],
  to = letters[2:11],
  length = 1,
  directed = TRUE
)
leaves_cell_graph <- tibble(
  from = letters[12:26],
  to = sample(letters[1:11], 15, replace = TRUE),
  length = 1,
  directed = TRUE
)
cell_graph <- bind_rows(backbone_cell_graph, leaves_cell_graph)
cell_graph
#> # A tibble: 25 x 4
#>    from  to    length directed
#>    <chr> <chr>  <dbl> <lgl>   
#>  1 a     b          1 TRUE    
#>  2 b     c          1 TRUE    
#>  3 c     d          1 TRUE    
#>  4 d     e          1 TRUE    
#>  5 e     f          1 TRUE    
#>  6 f     g          1 TRUE    
#>  7 g     h          1 TRUE    
#>  8 h     i          1 TRUE    
#>  9 i     j          1 TRUE    
#> 10 j     k          1 TRUE    
#> # … with 15 more rows
to_keep <- letters[1:11]
to_keep
#>  [1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k"
trajectory <- add_cell_graph(dataset, cell_graph, to_keep)

# for plotting the result, install dynplot
dynplot::plot_graph(trajectory)
#> Coloring by milestone
#> Using milestone_percentages from trajectory