plotMatchedOntoTree: Plot a ontology tree with matched ontology from ontoMatch

In scOntoMatch: Aligning Ontology Annotation Across Single Cell Datasets with 'scOntoMatch'

Plot a ontology tree with matched ontology from ontoMatch

Description

Plot a ontology tree with matched ontology from ontoMatch

Usage

plotMatchedOntoTree(
  obj_list,
  ont,
  anno_col = "cell_ontology_mapped",
  onto_id_col,
  roots = c("CL:0000548"),
  ...
)

Arguments

obj_list	a list of seurat obj files as the output of ontoMatch
ont	ontology object
anno_col	the cell ontology text annotation column name
onto_id_col	if also have ontology id column for direct mapping
roots	root ontology in tree to plot, default "animal cells" in cell ontology
...	additional parameters for ontologyPlot::onto_plot

Value

a lit of matched ontology tree plot

Examples

## Not run: 
plotMatchedOntoTree(seurat_obj_list, ont, 'cell_ontology_mapped', 'ontology_id')

## End(Not run)

scOntoMatch documentation built on Nov. 2, 2023, 5:20 p.m.