Add a Representation to a SpatialMap or Region object

A user interface to create and add a Representation to a SpatialMap or Region object. If passing a SpatialMap object, expects named lists for feature.loadings, model, and misc (names should correspond to either the region names or a formal Analysis id).

Usage

addRepresentation(
  object,
  name,
  embeddings,
  col.names = NULL,
  feature.loadings = NULL,
  model = NULL,
  misc = NULL,
  ...,
  analyze = NULL
)

Arguments

object: A SpatialMap or Region object
name: The name of the representation. Must be unique in the SM
embeddings: The cell embeddings for the representation. Rownames should match the cells in analysis
col.names: The names of the embedding vectors. Will be automatically generated from the name if NULL.
feature.loadings: If features are involved, what are the feature loadings? For example, in PCA. If passing a matrix, expects the number of rows (and their names) to match those for features.
model: The model associated with the representation
misc: Miscellaneous information
...: Parameters passed to lapply, namely to FUN
analyze: What to analyze (and how). The options are "regions", NULL (activeAnalysis), the name of a currently existing formal analysis, or the name of a column in object's projectMetadata (an "informal" analysis).