ProFAST (version 1.4)

NCFM_fast: Cell-feature coembedding for SRT data

Description

Run cell-feature coembedding for SRT data based on FAST model.

Usage

NCFM_fast(
  object,
  Adj_sp,
  assay = NULL,
  slot = "data",
  nfeatures = 2000,
  q = 10,
  reduction.name = "fast",
  var.features = NULL,
  ...
)

Arguments

object

a Seurat object.

Adj_sp

a sparse matrix, specify the adjacency matrix among spots.

assay

an optional string, the name of assay used.

slot

an optional string, the name of slot used.

nfeatures

an optional postive integer, the number of features to select as top variable features. Default is 2000.

q

an optional positive integer, specify the dimension of low dimensional embeddings to compute and store. Default is 10.

reduction.name

an optional string, dimensional reduction name, `fast` by default.

var.features

an optional string vector, specify the variable features, used to calculate cell embedding.

...

Other argument passed to the FAST_run.

Examples

data(CosMx_subset)
pos <- as.matrix([e-mail][,c("x", "y")])
Adj_sp <- AddAdj(pos)
# Here, we set maxIter = 3 for fast computation and demonstration.
CosMx_subset <- NCFM_fast(CosMx_subset, Adj_sp = Adj_sp, maxIter=3)