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Compute biMAP

biMAP.Rd

The function takes either a caclust or SingleCellExperimentas input and stores the biMAP in the "bimap" slot in the caclust object. If a SingleCellExperiment was provided the caclust object is stored in its metadata.

Usage

biMAP(obj, k = 30, rand_seed = 2358, method = "SNNdist", ...)

# S4 method for caclust
biMAP(obj, k = 30, rand_seed = 2358, method = "SNNdist", ...)

# S4 method for SingleCellExperiment
biMAP(
  obj,
  k = 30,
  rand_seed = 2358,
  method = "SNNdist",
  ...,
  caclust_meta_name = "caclust"
)

Arguments

obj

A caclust object or SingleCellExperiment object

k

integer. Number of nearest neighbours to use to compute UMAP.

rand_seed

integer. Random seed for UMAP.

method

Can be either "SNNdist" or "spectral".

...

Further arguments

caclust_meta_name

The name of caclust object stored in metadata (SingleCellExperiment object).

Value

A caclust object or SingleCellExperiment object.

Details

The biMAP cell and gene embeddings can be calculated via different methods as controlled by the parameter method:

  • 'SNNdist'(Default): run UMAP on the distance matrix of cell-gene SNN graph built up by caclust, which is '1-adj(SNN)'.

  • 'spectral': run UMAP on the selected eigenvectors of cell-gene graph laplacian (only eligiable when algorithm is set as 'spectral' in 'caclust' function)