Annotate Milo Neighborhoods with Cell Types — annotate

Annotates Milo neighborhoods with cell type information and filters neighborhoods based on abundance threshold.

Usage

annotate_nhood(
  sce_milo,
  da_results,
  celltype_var,
  abundance_thresh = 0.7,
  plot = TRUE
)

Arguments

sce_milo: A list containing a Milo object and a design matrix.
da_results: A data frame of differential abundance results for the neighborhoods.
celltype_var: Character string specifying the column in metadata containing cell type annotations.
abundance_thresh: Numeric value specifying the minimum fraction threshold for a cell type to be considered dominant in a neighborhood. Default is 0.7.
plot: Logical indicating whether to generate diagnostic plots. Default is TRUE.

Value

A list containing:

milo: The updated Milo object.
da_results: The annotated differential abundance results.
design: The design matrix used for differential testing.

Details

This function annotates neighborhoods with cell type information, filters neighborhoods based on an abundance threshold, and optionally generates plots.

Examples

# Example usage:
# result <- annotate_nhood(sce_milo, da_results, celltype_var = "cell_type")