run_tucker_ica {scITD}

Run the Tucker decomposition and rotate the factors

Description

Run the Tucker decomposition and rotate the factors

Usage

run_tucker_ica(
  container,
  ranks,
  tucker_type = "regular",
  rotation_type = "hybrid"
)

Arguments

container

environment Project container that stores sub-containers for each cell type as well as results and plots from all analyses

ranks

numeric The number of donor factors and gene factors, respectively, to decompose the data into. Since we rearrange the standard output of the Tucker decomposition to be 'donor centric', the number of donor factors will also be the total number of main factors that can be used for downstream analysis. The number of gene factors will only impact the quality of the decomposition.

tucker_type

character The 'regular' type is the only one currently implemented

rotation_type

character Set to 'hybrid' to optimize loadings via our hybrid method (see paper for details). Set to 'ica_dsc' to perform ICA rotation on resulting donor factor matrix. Set to 'ica_lds' to optimize loadings by the ICA rotation. (default='hybrid')

Value

The project container with results of the decomposition in container$tucker_results. The results object is a list with the donor scores matrix in the first element and the unfolded loadings matrix in the second element.

Examples

test_container <- run_tucker_ica(test_container,ranks=c(2,4))