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Calculate the local pairwise gene-gene correlation

hotspot_gene_cor_sc.Rd

This method implements the HotSpot approach (see DeTomaso, et al.) to calculate the local gene-gene correlations and their Z-scores.

Usage

hotspot_gene_cor_sc(
  object,
  embd_to_use = "pca",
  use_knn = TRUE,
  hotspot_params = params_sc_hotspot(),
  no_embd_to_use = NULL,
  cells_to_take = NULL,
  genes_to_take = NULL,
  streaming = NULL,
  working_mem_gb = 4,
  random_seed = 42L,
  .verbose = TRUE
)

Arguments

object

SingleCells or MetaCells class.

embd_to_use

String. The embedding to use. Defaults to "pca".

use_knn

Boolean. Shall the internal kNN be used. If set to yes, you need to ensure consistency. If you provide cells_to_take, the function will regenerate the kNN graph with these cells.

hotspot_params

List with hotspot parameters, see params_sc_hotspot() with the following elements:

  • model - String. Which of the available models to use for the gene expression. Choices are one of c("danb", "normal", "bernoulli").

  • normalise - Boolean. Shall the data be normalised.

  • weighted_graph - Boolean. Shall the Gaussian kernel be applied to the neighbour distances. If FALSE, every retained edge weighs one.

  • neighborhood_factor - Float. Kernel width for weighted_graph.

  • knn - List of kNN parameters. See params_knn_defaults() for available parameters and their defaults.

no_embd_to_use

Optional integer. Number of embedding dimensions to use. If NULL all will be used.

cells_to_take

Optional string vector. If you want to only use selected cells. If NULL will default to all cells_to_keep in the class.

genes_to_take

Optional string vector. If you wish to limit the search to a subset of genes. If NULL will default to all genes in the class.

streaming

Optional Boolean. Shall the data be streamed in. Useful for larger data sets where you wish to avoid loading in the whole data. If NULL, will automatically detect. Ignored for MetaCells, which are held in memory.

working_mem_gb

Numeric. Approximate working memory (GB) the streaming pair path may use for resident gene panels. Ignored when streaming is FALSE. Larger values mean fewer disk re-reads. Note this excludes the two dense N_genes x N_genes output matrices, which scale with genes_to_use. Defaults to 4 (4 GB of memory allocated).

random_seed

Integer. Used for reproducibility.

.verbose

Boolean or integer. Controls verbosity and returns run times. FALSE -> quiet, TRUE or 1L -> normal verbosity, 2L -> detailed verbosity.

Value

A sc_hotspot class that can be used for subsequent analysis.

Details

Should a gene not be found in sufficient cells, the pairs with this gene will be set to 0. Please ensure prior to running the function that you are only calculating gene-gene auto-correlations that occur in sufficient cells.

Whether the neighbour distances need squaring before the kernel sees them follows from the metric. With use_knn = TRUE it is taken from the metric stored on the cached kNN graph, otherwise from ann_dist in hotspot_params.

Examples

# local gene-gene correlations over a subset of the genes
sc <- demo_single_cells()
res <- hotspot_gene_cor_sc(
  sc,
  genes_to_take = get_gene_names(sc)[1:20],
  .verbose = FALSE
)
res
#> Hotspot gene-gene local correlation results
#>   Genes: 20
#>   Cells: 500
#>   Modules: not yet computed (see generate_hotspot_membership)

unlink(sc@dir_data, recursive = TRUE, force = TRUE)