Calculate gene<>gene spatial correlations — rs_hotspot_gene

This function implements the HotSpot gene <> gene local correlation functionality from HotSpot, see DeTomaso, et al.

Usage

rs_hotspot_gene_cor(
  f_path_genes,
  f_path_cells,
  embd,
  hotspot_params,
  cells_to_keep,
  genes_to_use,
  streaming,
  verbose,
  seed
)

f_path_genes: Path to the counts_genes.bin file.
f_path_cells: Path to the counts_cells.bin file.
embd: Numerical matrix. The embedding matrix from which to generate the kNN graph.
hotspot_params: List. The HotSpot parameter list.
cells_to_keep: Integer vector. 0-index vector indicating which cells to include in the analysis. Ensure that this is of same order/length as the embedding matrix.
genes_to_use: Integer vector. 0-index vector indicating which genes to include.
streaming: Boolean. Shall the data be streamed in chunks. Useful for large data sets.
verbose: Boolean. Controls verbosity of the function.
seed: Integer. Random seed for reproducibility.

A list with the following elements.

cor - A matrix of the N x N genes_to_use length with the auto- correlation coefficients.
z - A matrix of N x N genes_to_use length with the Z-scores of the local correlations between two genes.

DeTomaso, et al., Cell Systems, 2021