Package 'HCATonsilData'

Annotation dictionary to keep track of annotations changes and versions

Description

Annotations are opinionated and dynamic by nature. They are subjected to change as more experts look into the data and more evidence is published. HCATonsilData has been designed to account for that. We timestamp annotations and plan to include additional annotations if users propose them and we validate them.

Format

A list of named vectors with the correspondence between time-stamped annotations

Source

This file was created with the script in "inst/scripts/make-annotation-dictionary.R

---

Color palettes

Description

Color palettes used in the paper for all cell types

Format

A list with the HEX color codes for each cell type

Source

This file was created with the script in "inst/scripts/make-annotation-colors.R

---

Donor metadata

Description

Data frame that contains all metadata information for the 17 donors included in the tonsil atlas.

Format

A dataframe with 17 observations and 8 variables

Source

Check the tonsil atlas publication

---

Access the Tonsil Atlas data (RNA, ATAC, Multiome, CITE, Spatial)

Description

The data was downloaded from Zenodo https://zenodo.org/record/8373756

Usage

HCATonsilData(
  assayType = c("RNA", "ATAC", "CITE", "Spatial"),
  cellType = "All",
  version = "2.0",
  processedCounts = TRUE
)

Arguments

assayType	One of 'RNA', 'ATAC', 'Multiome', 'CITE' or 'Spatial'.
cellType	A character vector of length 1 with the desired cell type. A list of available cell types can be obtained using listCellTypes(assay_type).
version	Version of the tonsil atlas data to retrieve: "1.0" (preprint) or "2.0" (publication, default)
processedCounts	Logical scalar. If TRUE, include the processed (normalized) counts in addition to the raw counts in the SingleCellExperiment object.

Value

A SingleCellExperiment object for the cellType requested. For scATAC-seq, Multiome and CITE we provide the instructions for downloading the Seurat objects in Zenodo (see vignette)

Author(s)

Ramon Massoni-Badosa

Examples

# retrieve the epithelial scRNA-seq dataset
sce_epithelial <- HCATonsilData(
  assayType = "RNA",
  cellType = "epithelial"
)
sce_epithelial

---

List available cell types for a dataset of the tonsil cell atlas

Description

List available cell types for a dataset of the tonsil cell atlas

Usage

listCellTypes(
  assayType = c("RNA", "ATAC", "Multiome", "CITE", "Spatial"),
  version = "2.0"
)

Arguments

assayType	Either 'RNA', 'ATAC', 'Multiome', 'CITE', or 'Spatial'
version	Version of the tonsil atlas data: '1.0' (preprint) or '2.0' or '2.0' (publication, default). Note that, for version 2.0, CD8-T and ILC-NK are combined in a single 'Cytotoxic' object.

Value

A character vector with the available cell types for the indicated dataset.

Examples

listCellTypes(assayType = "RNA", version = "2.0")

---

Annotation dictionary for naive and memory B cells (NBC-MBC)

Description

In version 1 of the atlas, we changed the clusters and annotation for NBC-MBC prior to publishing the preprint. Since, there is not a 1:1 mapping between clusters, here we provide the correspondence between the annotations in February 2022 and the preprint (June 2022) for each NBC-MBC cell barcode.

Format

A dataframe with 112478 NBC-MBC and 5 variables

barcode

cell barcode

names_level_5_clusters_eta

Cell annotation given by the B-cell annotation team in February 2022

annotation_20220619

Cell annotation given by the B-cell annotation team June 2022 (preprint)

UMAP_1

UMAP1 coordinates

UMAP_2

UMAP2 coordinates

Details

This data is used by the updateAnnotation function in B cells.

Source

https://zenodo.org/record/8373756

---

TonsilData_cellinfo

Description

Query the glossary to traceback the rationale for each annotation of the tonsil atlas

Usage

TonsilData_cellinfo(cellType = NULL)

Arguments

cellType

String character, used to define the cell type for which the information will be displayed. Defaults to NULL - if left unspecified, the function returns a list of the possible options

Value

Invisible NULL - the information is displayed as a message in the console.

Examples

TonsilData_cellinfo()

TonsilData_cellinfo("PDC")

---

TonsilData_cellinfo_html

Description

TonsilData_cellinfo_html

Usage

TonsilData_cellinfo_html(
  cellType = NULL,
  display_plot = TRUE,
  output_to = c("single_page", "html_to_embed")
)

Arguments

cellType	String character, used to define the cell type for which the information will be displayed. Defaults to NULL - if left unspecified, the function returns a list of the possible options
display_plot	Logical value, defines whether to include or not a plot for the UMAP of the selected cell type
output_to	Character value, one of "single_page" or "html_to_embed". Defines in which form the information is returned, either as an individual page or simply as HTML code to directly embed into other documents.

Value

Either the HTML code generated to be embedded, or a standalone HTML page is created - and the location to this temp file is returned as a character (default).

Examples

TonsilData_cellinfo_html("PDC")
TonsilData_cellinfo_html("preB")
TonsilData_cellinfo_html("preT")
TonsilData_cellinfo_html("preT", output_to = "html_to_embed")

---

TonsilData_glossary

Description

Convenience function to read directly in the file provided as extdata

Usage

TonsilData_glossary()

Value

Data frame containing the info on the cell types included in the TonsilDataAtlas

Examples

glossary_df <- TonsilData_glossary()
head(glossary_df)

---

Update cell type annotation

Description

Annotations are dynamic by nature. As more experts look into the data and newer literature comes out, we expect annotations to be refined over time. We have accommodated this by allowing us and users to add new annotations to the SingleCellExperiment objects. If you want to propose a new annotation based on your experience or new evidence, please open an issue at https://github.com/massonix/HCATonsilData/issues.

Usage

updateAnnotation(sce, refAnnotation = "20220215", newAnnotation = "20220619")

Arguments

sce	A SingleCellExperiment object obtained using HCATonsilData function.
refAnnotation	string specifying the date of the annotation to use as reference.
newAnnotation	string specifying the suffix to add to the new column (annotation_*).

Value

A SingleCellExperiment object with additional an additional column (annotation_*) that contains more annotations.

Examples

# update the annotation from preprint (version 1.0) to publication (version 2.0)
## Not run: 
sce <- updateAnnotation(
  sce,
  refAnnotation = "20220619",
  newAnnotation = "20230508"
)

## End(Not run)

---