Annotate a post-merge SingleCellExperiment with plots

Annotate a post-merge SingleCellExperiment with plots

annotate_merged_sce(
  sce,
  plot_vars = c("total_features_by_counts", "total_counts", "pc_mito", "pc_ribo"),
  unique_id_var = "manifest",
  facet_vars = NULL,
  outlier_vars = c("total_features_by_counts", "total_counts")
)

Arguments

sce

a SingleCellExperiment object

plot_vars

the colData variable(s) to generate plots for

unique_id_var

the colData variable identifying unique samples

facet_vars

the colData variable(s) to facet/subset by

outlier_vars

the colData variable(s) to apply adaptive thresholding

Value

sce a annotated SingleCellExperiment object

See also

Other annotation functions: .preprocess_seurat_object(), annotate_celltype_metrics(), annotate_integrated_sce(), annotate_sce(), annotate_sce_cells(), annotate_sce_genes(), filter_sce(), find_cells(), find_singlets(), generate_sce(), map_ensembl_gene_id(), merge_sce(), read_metadata(), report_celltype_metrics(), report_celltype_model(), report_merged_sce(), report_qc_sce(), run_doubletfinder(), sce_to_seu()