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Order the cells by pseudotime

Source: R/pseudotime.R
custom_pseudotime_ordering.Rd

This function follows the logic of the order_cells function from the monocle3 package. The main difference consists in allowing the user to define both the start and the end points of the trajectory. In this case, the monocle object is subsetted.

Usage

custom_pseudotime_ordering(
  monocle_object,
  start_cells = NULL,
  end_cells = NULL
)

Arguments

monocle_object

A monocle object.

start_cells

A list of cells names that define the start of the ordering. If NULL, the end_cells must be provided. Defaults to NULL.

end_cells

A list of cells names that define the end of the ordering. If NULL, the start_cells must be provided. If end_cells is not NULL and start_cells is not NULL, subsetting is performed. If end_cells is not NULL and start_cells is NULL, the ordering will be reversed. Defaults to NULL.

Value

A named vector with the pseudotime values. In the case of subsetting, the cells that are not part of the inferred subtrajectory will be assigned the NA value.