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Add neighbourhood info on majority cell type

add_nhoods_info.Rd

This function adds cell type composition information to the nhoods_info slot within the miloR object. For each neighbourhood, it calculates the proportion of the majority cell type and identifies which cell type is most abundant. This is useful for annotating differential abundance results with the cellular composition of each neighbourhood.

Usage

add_nhoods_info(x, cell_info)

# S3 method for class 'miloR'
add_nhoods_info(x, cell_info)

Arguments

x

miloR object on which to tag on additional neighbourhood information.

cell_info

Character vector. Represents the cell type annotations you wish to add to the different neighbourhoods. Must be the same length as the number of cells (rows) in the nhoods matrix.

Value

Modified miloR object with updated nhoods_info containing majority_celltype and majority_prop columns.

Examples

# tag each neighbourhood with its majority cell type
sc <- demo_single_cells(
  syn_data_params = params_sc_synthetic_data(
    n_cells = 500L,
    n_genes = 50L,
    n_samples = 6L,
    sample_bias = "even"
  )
)
milo <- get_miloR_abundances_sc(
  sc,
  sample_id_col = "sample_id",
  miloR_params = params_sc_miloR(k_refine = 10L),
  .verbose = FALSE
)
design_df <- data.frame(
  grp = rep(c("a", "b"), each = 3),
  row.names = sprintf("sample_%i", 1:6)
)
milo <- test_nhoods(milo, design = ~grp, design_df = design_df)
milo <- add_nhoods_info(milo, cell_info = get_sc_obs(sc)$cell_grp)
head(get_differential_abundance_res(milo))
#>    Nhood        logFC   logCPM            F    PValue       FDR SpatialFDR
#>    <int>        <num>    <num>        <num>     <num>     <num>      <num>
#> 1:     1  0.696761445 14.32139 8.523319e-01 0.3565560 0.8319639  0.8269572
#> 2:     2  0.340283155 14.32108 2.207650e-01 0.6387624 0.8455142  0.8402161
#> 3:     3 -1.087351007 14.31886 2.594503e+00 0.1267721 0.8163203  0.8108069
#> 4:     4 -0.005885377 14.31889 8.100235e-05 0.9931983 0.9945522  0.9945522
#> 5:     5  0.696752491 14.30611 3.770292e-01 0.5396130 0.8455142  0.8402161
#> 6:     6 -0.351990673 14.32160 2.136750e-01 0.6442013 0.8455142  0.8402161
#>    majority_celltype majority_prop
#>               <char>         <num>
#> 1:       cell_type_1        1.0000
#> 2:       cell_type_3        1.0000
#> 3:       cell_type_1        0.6875
#> 4:       cell_type_2        0.9375
#> 5:       cell_type_2        1.0000
#> 6:       cell_type_1        1.0000

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