annotate_merged_sce: Annotate a post-merge SingleCellExperiment with plots

In combiz/scFlow: A Single-Cell/Nuclei Analysis Toolkit

Annotate a post-merge SingleCellExperiment with plots

Description

Annotate a post-merge SingleCellExperiment with plots

Usage

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()

combiz/scFlow documentation built on Feb. 25, 2024, 10:25 a.m.