Find rank bias

Usage

assess_rank_bias(
  avg_mat,
  ref_mat,
  query_genes = NULL,
  res,
  organism,
  plot_name = NULL,
  rds_name = NULL,
  expand_unassigned = FALSE
)

Arguments

avg_mat: average expression matrix
ref_mat: reference expression matrix
query_genes: original vector of genes used to clustify
res: dataframe of idents, such as output of cor_to_call
organism: for GO term analysis, organism name: human - 'hsapiens', mouse - 'mmusculus'
plot_name: name for saved pdf, if NULL then no file is written (default)
rds_name: name for saved rds of rank_diff, if NULL then no file is written (default)
expand_unassigned: test all ref clusters for unassigned results

Value

pdf of ggplot object

Examples

if (FALSE) { # \dontrun{
avg <- average_clusters(
    pbmc_matrix_small,
    pbmc_meta$seurat_clusters
)
res <- clustify(
    input = pbmc_matrix_small,
    metadata = pbmc_meta,
    ref_mat = cbmc_ref,
    query_genes = pbmc_vargenes,
    cluster_col = "seurat_clusters"
)
top_call <- cor_to_call(
    res,
    metadata = pbmc_meta,
    cluster_col = "seurat_clusters",
    collapse_to_cluster = FALSE,
    threshold = 0.8
)
res_rank <- assess_rank_bias(
    avg,
    cbmc_ref,
    res = top_call
)
} # }