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scOntoMatch

scOntoMatch is an R package which unifies ontology annotation of scRNA-seq datasets to make them comparable across studies.

Author&Maintainer: Yuyao Song ysong@ebi.ac.uk

Large-scale single cell atlases often have curated annotations using a standard ontology system. This package aims to match ontology labels between different datasets to make them comparable across studies.

Installation

## from source

install.packages("devtools")
devtools::install_github("Papatheodorou-Group/scOntoMatch")
library(scOntoMatch)
library(ontologyIndex)

Usage

First download the ontology .obo file from the OBO foundry. Common ontologies include:

• Cell ontology
• Uberon multi-species anatomy ontology
• Drosophila gross anatomy (FBbt)
• Zebrafish anatomy and development ontology (ZFA)

Refer to vignette for detailed usage.

Get input ready

adatas = getAdatas(metadata = metadata, sep = "\t")
ont = ontologyIndex::get_OBO(oboFile, propagate_relationships = c('is_a', 'part_of'), )

Trim ontology tree to remove redundant terms

adatas_minimal = ontoMultiMinimal(adatas, ont = ont, anno_col = "cell_ontology_type", onto_id_col = "cell_ontology_id")

Match ontology cross datasets by direct mapping and mapping descendants to ancestor terms.

adatas_matched = ontoMultiMatch(adatas_minimal, ont = ont, anno_col = "cell_ontology_base")

This package also provides convenient plotting functions to help comprehend the hierarchy of cell types in any single cell dataset.

Plot a ontology tree per dataset

plotOntoTree(ont, onts, plot_ancestors=TRUE, ont_query, fontsize = 20)

Plot a matched ontology tree for all datasets

# use 'animal cells' as root
plts = plotMatchedOntoTree(ont = ont, adatas = adatas, anno_col = "cell_ontology_mapped", roots = 'CL:0000548', fontsize=25)

The Single Cell Expression Atlas hosted at EBI provides uniformly analysed and annotated scRNA-Seq data across multiple species. Datasets with curated ontology labels are all great inputs to this package. scRNA-seq data stored as h5ad files can be downloaded via the ftp site. Files that has extension .project.h5ad can be pass to ontoMatch with anno_col = 'authors_cell_type_-_ontology_labels'.

This package imports functions from ontologyIndex, ontologyPlot and anndata

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.