Obtain a map of cell types for each dataset

The ontomap function provides a mapping of all the cell names across the all the data sets or for a specified data set.

Usage

ontomap(dataset = c("scNMT", "scMultiome", "SCoPE2", "CITEseq", "seqFISH"))

Arguments

dataset

character() One of the existing functions within the package. If missing, a map of all cell types in each function will be provided.

Value

A data.frame of metadata with cell types and ontologies

Details

Note that CITEseq does not have any cell annotations; therefore, no entries are present in the ontomap.

Examples

ontomap(dataset = "scNMT")
#>              DataType function_name original_column_name original_cell_name
#> 3  mouse_gastrulation         scNMT              lineage           Epiblast
#> 4  mouse_gastrulation         scNMT              lineage           Mesoderm
#> 5  mouse_gastrulation         scNMT              lineage   Primitive_Streak
#> 6  mouse_gastrulation         scNMT              lineage           Ectoderm
#> 7  mouse_gastrulation         scNMT              lineage           Endoderm
#> 8  mouse_gastrulation         scNMT              lineage       ExE_ectoderm
#> 9  mouse_gastrulation         scNMT              lineage  Visceral_endoderm
#> 10 mouse_gastrulation         scNMT              lineage Primitive_endoderm
#>       ontology_ID ontology_cell_name
#> 3     NCIT:C34164           Epiblast
#> 4     NCIT:C12750           Mesoderm
#> 5     NCIT:C28402   Primitive_Streak
#> 6     NCIT:C12703           Ectoderm
#> 7     NCIT:C12706           Endoderm
#> 8     NCIT:C12703           Ectoderm
#> 9  UBERON:0004877  visceral endoderm
#> 10    BTO:0002123 primitive endoderm