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Creating a TI method: Wrapping trajectories

Wouter Saelens

Robrecht Cannoodt

2023-07-18

Common trajectory model

dynwrap always represents trajectories in the same way, as illustrated here with a tree trajectory

## # A tibble: 5 × 4
##   from        to          length directed
##   <chr>       <chr>        <dbl> <lgl>   
## 1 Milestone_A Milestone_B    1   FALSE   
## 2 Milestone_B Milestone_C    2   FALSE   
## 3 Milestone_B Milestone_D    1   FALSE   
## 4 Milestone_C Milestone_E    1   FALSE   
## 5 Milestone_C Milestone_F    1.5 FALSE
## # A tibble: 10 × 3
##    cell_id milestone_id percentage
##    <chr>   <chr>             <dbl>
##  1 Cell_a  Milestone_B      0.679 
##  2 Cell_a  Milestone_C      0.321 
##  3 Cell_b  Milestone_B      0.248 
##  4 Cell_b  Milestone_D      0.752 
##  5 Cell_c  Milestone_C      0.607 
##  6 Cell_c  Milestone_F      0.393 
##  7 Cell_d  Milestone_B      0.708 
##  8 Cell_d  Milestone_C      0.292 
##  9 Cell_e  Milestone_B      0.971 
## 10 Cell_e  Milestone_C      0.0289
## # A tibble: 10 × 4
##    cell_id from        to          percentage
##    <chr>   <chr>       <chr>            <dbl>
##  1 Cell_a  Milestone_B Milestone_C     0.321 
##  2 Cell_b  Milestone_B Milestone_D     0.752 
##  3 Cell_c  Milestone_C Milestone_F     0.393 
##  4 Cell_d  Milestone_B Milestone_C     0.292 
##  5 Cell_e  Milestone_B Milestone_C     0.0289
##  6 Cell_f  Milestone_C Milestone_E     0.522 
##  7 Cell_g  Milestone_C Milestone_F     0.686 
##  8 Cell_h  Milestone_B Milestone_C     0.375 
##  9 Cell_i  Milestone_B Milestone_C     0.522 
## 10 Cell_j  Milestone_C Milestone_F     0.632
## # A tibble: 3 × 3
##   divergence_id milestone_id is_start
##   <chr>         <chr>        <lgl>   
## 1 Divergence_1  Milestone_B  TRUE    
## 2 Divergence_1  Milestone_C  FALSE   
## 3 Divergence_1  Milestone_D  FALSE

Direct wrapping

These three objects (with either milestone percentages or progressions) are enough to form a trajectory using add_trajectory.

trajectory <- wrap_data(cell_ids = cell_ids) %>% 
  add_trajectory(
    milestone_network = milestone_network, 
    milestone_percentages = milestone_percentages,
    divergence_regions = divergence_regions
  )

Indirect wrapping

Often, you don’t want to directly output the milestone network and percentages, but want to output an alternative representation that is converted by dynwrap to the common representation:

Check out the reference documentation for an overview and examples of the different wrappers

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.