dynwrap (version 1.2.1)

add_end_state_probabilities: Constructs a multifurcating trajectory using end state probabilities

Description

Constructs a multifurcating trajectory using the pseudotime values of each cell and their end state probabilities. If pseudotime values are not given, will use pseudotime already present in the dataset.

Usage

add_end_state_probabilities(
  dataset,
  end_state_probabilities,
  pseudotime = NULL,
  do_scale_minmax = TRUE,
  ...
)

Arguments

dataset

A dataset created by wrap_data() or wrap_expression()

end_state_probabilities

A dataframe containing the cell_id and additional numeric columns containing the probability for every end milestone. If the tibble contains only a cell_id column, the data will be processed using add_linear_trajectory

pseudotime

A named vector of pseudo times.

do_scale_minmax

Whether or not to scale the pseudotime between 0 and 1. Otherwise, will assume the values are already within that range.

...

Extras to be added to the trajectory

Value

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).

Examples

# NOT RUN {
dataset <- wrap_data(cell_ids = letters)

pseudotime <- runif(length(dataset$cell_ids))
names(pseudotime) <- dataset$cell_ids
pseudotime
end_state_probabilities <- tibble::tibble(
  cell_id = dataset$cell_ids,
  A = runif(length(dataset$cell_ids)),
  B = 1-A
)
end_state_probabilities
trajectory <- add_end_state_probabilities(dataset, end_state_probabilities, pseudotime)

# for plotting the result, install dynplot
#- dynplot::plot_graph(trajectory)
# }