get_subtype_prop_associations: Compute and plot associations between factor scores and cell...

In scITD: Single-Cell Interpretable Tensor Decomposition

Compute and plot associations between factor scores and cell subtype composition for various clustering resolution parameters

Description

Compute and plot associations between factor scores and cell subtype composition for various clustering resolution parameters

Usage

get_subtype_prop_associations(
  container,
  max_res,
  stat_type,
  integration_var = NULL,
  min_cells_group = 50,
  use_existing_subc = FALSE,
  alt_ct_names = NULL,
  n_col = 2
)

Arguments

container	environment Project container that stores sub-containers for each cell type as well as results and plots from all analyses
max_res	numeric The maximum clustering resolution to use. Minimum is 0.5.
stat_type	character Either "fstat" to get F-Statistics, "adj_rsq" to get adjusted R-squared values, or "adj_pval" to get adjusted pvalues.
integration_var	character The meta data variable to use for creating the joint embedding with Conos if not already provided in container$embedding (default=NULL)
min_cells_group	numeric The minimum allowable size for cell subpopulations (default=50)
use_existing_subc	logical Set to TRUE to use existing subcluster annotations (default=FALSE)
alt_ct_names	character Cell type names used in clustering if different from those used in the main analysis. Should match the order of container$experiment_params$ctypes_use. (default=NULL)
n_col	numeric The number of columns to organize the plots into (default=2)

Value

The project container with a cowplot figure of cell subtype proportion-factor association results plots in container$plots$subtype_prop_factor_associations.

scITD documentation built on Sept. 8, 2023, 5:11 p.m.