add_linear_trajectory {dynwrap} | R Documentation |
Constructs a linear trajectory using pseudotime values
add_linear_trajectory(
dataset,
pseudotime,
directed = FALSE,
do_scale_minmax = TRUE,
...
)
dataset |
A dataset created by |
pseudotime |
A named vector of pseudo times. |
directed |
Whether the trajectory will be directed. |
do_scale_minmax |
Whether or not to scale the pseudotime between 0 and 1. Otherwise, will assume the values are already within that range. |
... |
extra information to be stored in the trajectory |
The dataset object with trajectory information, including:
milestone_ids: The names of the milestones, a character vector.
milestone_network: The network between the milestones, a dataframe with the from milestone, to milestone, length of the edge, and whether it is directed.
divergence_regions: The regions between three or more milestones where cells are diverging, a dataframe with the divergence id (divergence_id), the milestone id (milestone_id) and whether this milestone is the start of the divergence (is_start)
milestone_percentages: For each cell its closeness to a particular milestone, a dataframe with the cell id (cell_id), the milestone id (milestone_id), and its percentage (a number between 0 and 1 where higher values indicate that a cell is close to the milestone).
progressions: For each cell its progression along a particular edge of the milestone_network. Contains the same information as milestone_percentages. A dataframe with cell id (cell_id), from milestone, to milestone, and its percentage (a number between 0 and 1 where higher values indicate that a cell is close to the to milestone and far from the from milestone).
library(tibble)
dataset <- wrap_data(cell_ids = letters)
pseudotime <- tibble(
cell_id = dataset$cell_ids,
pseudotime = runif(length(dataset$cell_ids))
)
trajectory <- add_linear_trajectory(dataset, pseudotime)