Add or create a dimensionality reduction

Add or create a dimensionality reduction

add_dimred(dataset, dimred, dimred_milestones = NULL,
  dimred_segment_progressions = NULL, dimred_segment_points = NULL,
  connect_segments = FALSE, expression_source = "expression", ...)

is_wrapper_with_dimred(dataset)

get_dimred(dataset, dimred = NULL, expression_source = "expression")

Arguments

dataset

A dataset created by wrap_data() or wrap_expression()

dimred

The dimensionality reduction matrix (with cell_ids as rownames) or function which will run the dimensionality reduction

dimred_milestones

An optional dimensionality reduction of the milestones.

dimred_segment_progressions

An optional progression matrix of the trajectory segments. Format: tibble(from, to, percentage)

dimred_segment_points

An optional dimensionality reduction of the trajectory segments. Format: matrix(Comp1, Comp2, ...).

connect_segments

Whether to connect segments between edges

expression_source

The source of expression, can be "counts", "expression", an expression matrix, or another dataset which contains expression

...

extra information to be stored in the wrapper