add_dimred_projection {dynwrap}

R Documentation

Constructs a trajectory by projecting cells within a dimensionality reduction

Description

A dimensionality reduction of cells and milestones is used, along with the milestone network, to project cells onto the nearest edge. Optionally, a cell grouping can be given which will restrict the edges on which a cell can be projected.

Usage

add_dimred_projection(
  dataset,
  milestone_ids = NULL,
  milestone_network,
  dimred,
  dimred_milestones,
  grouping = NULL,
  ...
)

Arguments

dataset	A dataset created by wrap_data() or wrap_expression()
milestone_ids	The ids of the milestones in the trajectory. Type: Character vector.
milestone_network	The network of the milestones. Type: Data frame(from = character, to = character, length = numeric, directed = logical).
dimred	Can be A function which will perform the dimensionality reduction, see dyndimred::list_dimred_methods() A matrix with the dimensionality reduction, with cells in rows and dimensions (comp_1, comp_2, ...) in columns
dimred_milestones	An optional dimensionality reduction of the milestones. A matrix with milestones in rows and components (comp_1, comp_2, ...) in columns This will be automatically calculated if project_trajectory = TRUE
grouping	A grouping of the cells, can be a named vector or a dataframe with group_id and cell_id
...	extra information to be stored in the wrapper.

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

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

milestone_network <- tibble::tibble(
  from = c("A", "B", "B"),
  to = c("B", "C", "D"),
  directed = TRUE,
  length = 1
)
milestone_network
dimred <- matrix(
  runif(length(dataset$cell_ids) * 2),
  ncol = 2,
  dimnames = list(dataset$cell_ids, c("comp_1", "comp_2"))
)
dimred
dimred_milestones <- matrix(
  runif(2*4),
  ncol = 2,
  dimnames = list(c("A", "B", "C", "D"), c("comp_1", "comp_2"))
)
dimred_milestones
trajectory <- add_dimred_projection(
  dataset,
  milestone_network = milestone_network,
  dimred = dimred,
  dimred_milestones = dimred_milestones
)

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

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