| Type: | Package |
| Title: | Aligning Ontology Annotation Across Single Cell Datasets with 'scOntoMatch' |
| Version: | 0.1.1 |
| Maintainer: | Yuyao Song <ysong@ebi.ac.uk> |
| Description: | Unequal granularity of cell type annotation makes it difficult to compare scRNA-seq datasets at scale. Leveraging the ontology system for defining cell type hierarchy, 'scOntoMatch' aims to align cell type annotations to make them comparable across studies. The alignment involves two core steps: first is to trim the cell type tree within each dataset so each cell type does not have descendants, and then map cell type labels cross-studies by direct matching and mapping descendants to ancestors. Various functions for plotting cell type trees and manipulating ontology terms are also provided. In the Single Cell Expression Atlas hosted at EBI, a compendium of datasets with curated ontology labels are great inputs to this package. |
| Imports: | ontologyIndex, ontologyPlot, purrr |
| URL: | https://github.com/Papatheodorou-Group/scOntoMatch |
| BugReports: | https://github.com/Papatheodorou-Group/scOntoMatch/issues |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.3 |
| Depends: | R(≥ 3.5) |
| Suggests: | knitr, devtools, SeuratObject |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2023-10-27 12:33:09 UTC; ysong |
| Author: | Yuyao Song [aut, cre, ctb], Irene Papatheodorou [aut, ths] |
| Repository: | CRAN |
| Date/Publication: | 2023-10-27 12:50:02 UTC |
make sure ontology names are all translated to ontology ids while warning, consider manual reannotation
Description
make sure ontology names are all translated to ontology ids while warning, consider manual reannotation
Usage
check_ontology_translate(obj, onts, ont, anno_col)
Arguments
obj |
seurat rds object |
onts |
ontology ids from translate |
ont |
ontologyIndex object |
anno_col |
annotation column in obj@meta.data that is translated to onts ids |
Value
do not return a value but output messages
Get a names list of ontology and id by id
Description
Get a names list of ontology and id by id
Usage
fill_query(all, query)
Arguments
all |
all ontology id to plot tree |
query |
query ontology id to fill |
Value
a color object to fill query in onto_plot
Examples
## Not run:
fill_query(all = c("CL0000548", "CL:0000066", "CL:0000082"), query = c("CL:0000082"))
## End(Not run)
match ontology terms by direct mapping and mapping descendants to ancestors
Description
match ontology terms by direct mapping and mapping descendants to ancestors
Usage
getOntoMapping(ont, onts1, onts2)
Arguments
ont |
the ontology object from get_OBO |
onts1 |
a character vector of ontology id |
onts2 |
a character vector of ontology id |
Value
a named list for ontology id mapping looks like ontology_id:ontology_id
Examples
## Not run:
getOntoMapping(ont = ont, onts1 = "CL:0000548", onts2 = c("CL0000548", "CL:0000066"))
## End(Not run)
match descendant terms to ancestor terms within a dataset
Description
match descendant terms to ancestor terms within a dataset
Usage
getOntoMinimal(ont, onts)
Arguments
ont |
the ontology object from get_OBO |
onts |
a character vector of ontology id |
Value
a named list for ontology id mapping looks like ontology_id:ontology_id
Examples
## Not run:
getOntoMinimal(ont = ont, onts = c("CL0000548", "CL:0000066", "CL:0000082"))
## End(Not run)
Match descendants to ancestors in multiple ontology id lists
Description
Match descendants to ancestors in multiple ontology id lists
Usage
getOntoMultiMapping(ont, onts)
Arguments
ont |
ontologyIndex object |
onts |
named list of ontology ids |
Value
a named character of mapping from:mapping to
Examples
## Not run:
getOntoMultiMapping(ont = ont, onts = c("CL0000548", "CL:0000066", "CL:0000082"))
## End(Not run)
Get a names list of ontology and id by name
Description
Get a names list of ontology and id by name
Usage
getOntologyId(ont, onto_name)
Arguments
ont |
ontology object |
onto_name |
character vector of ontology names |
Value
a named list mapping ontology id and ontology name
Examples
## Not run:
getOntologyId(onto_name = "epithelial cell of lung", ont = ont)
## End(Not run)
Get a names list of ontology and id by id
Description
Get a names list of ontology and id by id
Usage
getOntologyName(ont, onto_id)
Arguments
ont |
ontology object |
onto_id |
character vector of ontology ids |
Value
a named list mapping ontology id and ontology name
Examples
## Not run:
getOntologyName(onto_id = "epithelial cell of lung", ont = ont)
## End(Not run)
read in seurat object .rds files as a named list of seurat object
Description
read in seurat object .rds files as a named list of seurat object
Usage
getSeuratRds(metadata, sep)
Arguments
metadata |
a metadata file indicating name, path to 'seurat' rds file |
sep |
sep of the metadata file |
Value
a named list contains data name and the corresponding 'seurat' object
Examples
## Not run:
getSeuratRds(metadata = 'metadata.tsv', sep = '\t')
## End(Not run)
get the minimal ontology tree of a dataset by reducing descendant terms to ancestor terms return obj meta.data[["cell_ontology_base"]] storing the reduced ontology annotation
Description
get the minimal ontology tree of a dataset by reducing descendant terms to ancestor terms return obj meta.data[["cell_ontology_base"]] storing the reduced ontology annotation
Usage
ontoMinimal(obj, ont, anno_col, onto_id_col)
Arguments
obj |
the seurat object |
ont |
ontologyIndex object |
anno_col |
the cell ontology text annotation column name |
onto_id_col |
if also have ontology id column for direct mapping |
Value
an seurat object with meta.data[["cell_ontology_base"]]
Examples
## Not run:
ontoMinimal(obj = seurat_obj, ont = ont, anno_col = 'ontology_name', onto_id_col = 'ontology_id')
## End(Not run)
Core function of scOntoMatch Match the ontology annotation of multiple seurat objects
Description
Core function of scOntoMatch Match the ontology annotation of multiple seurat objects
Usage
ontoMultiMatch(obj_list, anno_col, onto_id_col, ont)
Arguments
obj_list |
a namesd list of seurat objects to match |
anno_col |
the cell ontology text annotation column name |
onto_id_col |
if also have ontology id column for direct mapping |
ont |
ontologyIndex object |
Value
a list of seurat objects with annotation ontology mapped to each-other in obs[['cell_ontology_mapped']]
Examples
## Not run:
ontoMultiMatch(seurat_obj_list, ont, "ontology_name", 'ontology_id')
## End(Not run)
get the minimal ontology tree of a list of seurat objects by reducing descendant terms to ancestor terms return a named list of seurat objects with meta.data[["cell_ontology_base"]] storing the reduced ontology annotation
Description
get the minimal ontology tree of a list of seurat objects by reducing descendant terms to ancestor terms return a named list of seurat objects with meta.data[["cell_ontology_base"]] storing the reduced ontology annotation
Usage
ontoMultiMinimal(obj_list, ont, anno_col = "cell_ontology_base", onto_id_col)
Arguments
obj_list |
a named list of seurat objects |
ont |
ontologyIndex object |
anno_col |
the cell ontology text annotation column name |
onto_id_col |
if also have ontology id column for direct mapping |
Value
a named list of seurat objects with meta.data[["cell_ontology_base"]]
Examples
## Not run:
ontoMultiMinimal(seurat_obj_list, ont, "cell_ontology_base", 'ontology_id')
## End(Not run)
translate named list of obj_list to named list of cell ontology ids per obj
Description
translate named list of obj_list to named list of cell ontology ids per obj
Usage
ontoTranslate(obj_list, ont, onto_id_col, anno_col)
Arguments
obj_list |
a named list of seurat object |
ont |
ontologyIndex object |
onto_id_col |
if also have ontology id column for direct mapping |
anno_col |
the cell ontology text annotation column name |
Value
a named list of cell ontology ids
Examples
## Not run:
ontoTranslate(seurat_obj_list, ont, 'ontology_name', 'ontology_id')
## End(Not run)
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)
Plot a tree representation of ontology terms
Description
Plot a tree representation of ontology terms
Usage
plotOntoTree(
ont,
onts,
plot_ancestors = TRUE,
ont_query = NULL,
roots = c("CL:0000548"),
...
)
Arguments
ont |
ontology object |
onts |
ontology ids to plot |
plot_ancestors |
if plot ancestors or not |
ont_query |
query ontology to highlight in the tree |
roots |
root ontology in tree, default "animal cells" in cell ontology |
... |
additional parameters for ontologyPlot::onto_plot |
Value
an ontology tree plot
Examples
## Not run:
plotOntoTree(ont = ont, onts = c("CL:0000066", "CL:0000082"), ont_query = c("CL:0000082"))
## End(Not run)