Create Representation — createRepresentation • SpatialMap

A user interface to create an object of the Representation class

This class should be used to store spatial representations, dimension reductions, and similar structures pertaining to the visualization or representation of cells

Usage

createRepresentation(
  name,
  analysis,
  embeddings,
  col.names = NULL,
  feature.loadings = NULL,
  model = NULL,
  misc = NULL
)

Arguments

name: The name of the representation. Must be unique in the SM
analysis: An Analysis object, its name, or its constituent cells()
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