Merge pull request #147 from myushen/master

add reference to exported functions

Author: stemangiola

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: CuratedAtlasQueryR
 Title: Queries the Human Cell Atlas
-Version: 1.3.5
+Version: 1.3.6
 Authors@R: c(
     person(
         "Stefano",

R/counts.R

@@ -37,6 +37,11 @@ pseudobulk_url <- single_line_str(
 #' @inheritDotParams get_single_cell_experiment
 #' @importFrom cli cli_alert_warning
 #' @export
+#' @references Mangiola, S., M. Milton, N. Ranathunga, C. S. N. Li-Wai-Suen, 
+#'   A. Odainic, E. Yang, W. Hutchison et al. "A multi-organ map of the human 
+#'   immune system across age, sex and ethnicity." bioRxiv (2023): 2023-06.
+#'   doi:10.1101/2023.06.08.542671.
+#' @source [Mangiola et al.,2023](https://www.biorxiv.org/content/10.1101/2023.06.08.542671v3)
 get_SingleCellExperiment <- function(...){
   single_line_str("This function name is deprecated. 
                     Please use `get_single_cell_experiment()` instead") |>
@@ -55,6 +60,11 @@ get_SingleCellExperiment <- function(...){
 #' meta <- get_metadata() |> head(2)
 #' sce <- get_single_cell_experiment(meta)
 #' @export
+#' @references Mangiola, S., M. Milton, N. Ranathunga, C. S. N. Li-Wai-Suen, 
+#'   A. Odainic, E. Yang, W. Hutchison et al. "A multi-organ map of the human 
+#'   immune system across age, sex and ethnicity." bioRxiv (2023): 2023-06.
+#'   doi:10.1101/2023.06.08.542671.
+#' @source [Mangiola et al.,2023](https://www.biorxiv.org/content/10.1101/2023.06.08.542671v3)
 get_single_cell_experiment <- function(data, ...){
   raw_data <- collect(data)
   assert_that(
@@ -77,6 +87,11 @@ get_single_cell_experiment <- function(data, ...){
 #' pseudobulk <- meta |> get_pseudobulk()
 #' }
 #' @export
+#' @references Mangiola, S., M. Milton, N. Ranathunga, C. S. N. Li-Wai-Suen, 
+#'   A. Odainic, E. Yang, W. Hutchison et al. "A multi-organ map of the human 
+#'   immune system across age, sex and ethnicity." bioRxiv (2023): 2023-06.
+#'   doi:10.1101/2023.06.08.542671.
+#' @source [Mangiola et al.,2023](https://www.biorxiv.org/content/10.1101/2023.06.08.542671v3)
 get_pseudobulk <- function(data, ...) {
   raw_data <- collect(data)
   assert_that(
@@ -118,6 +133,11 @@ get_pseudobulk <- function(data, ...) {
 #' @importFrom cli cli_alert_success cli_alert_info
 #' @importFrom rlang .data
 #' @importFrom S4Vectors DataFrame
+#' @references Mangiola, S., M. Milton, N. Ranathunga, C. S. N. Li-Wai-Suen, 
+#'   A. Odainic, E. Yang, W. Hutchison et al. "A multi-organ map of the human 
+#'   immune system across age, sex and ethnicity." bioRxiv (2023): 2023-06.
+#'   doi:10.1101/2023.06.08.542671.
+#' @source [Mangiola et al.,2023](https://www.biorxiv.org/content/10.1101/2023.06.08.542671v3)
 get_data_container <- function(
     data,
     assays = "counts",

R/data.R

@@ -5,4 +5,10 @@
 #' @format An object of class \code{SingleCellExperiment}
 #' @source HeOrganAtlasData Liver 
 #' @keywords datasets
+#' @docType data
+#' @references Mangiola, S., M. Milton, N. Ranathunga, C. S. N. Li-Wai-Suen, 
+#'   A. Odainic, E. Yang, W. Hutchison et al. "A multi-organ map of the human 
+#'   immune system across age, sex and ethnicity." bioRxiv (2023): 2023-06.
+#'   doi:10.1101/2023.06.08.542671.
+#' @source [Mangiola et al.,2023](https://www.biorxiv.org/content/10.1101/2023.06.08.542671v3)
 "sample_sce_obj"

R/import_metadata_and_counts.R

@@ -20,6 +20,11 @@
 #' data(sample_sce_obj)
 #' import_one_sce(sample_sce_obj,
 #'                cache_dir = get_default_cache_dir())
+#' @references Mangiola, S., M. Milton, N. Ranathunga, C. S. N. Li-Wai-Suen, 
+#'   A. Odainic, E. Yang, W. Hutchison et al. "A multi-organ map of the human 
+#'   immune system across age, sex and ethnicity." bioRxiv (2023): 2023-06.
+#'   doi:10.1101/2023.06.08.542671.
+#' @source [Mangiola et al.,2023](https://www.biorxiv.org/content/10.1101/2023.06.08.542671v3)
 import_one_sce <- function(
     sce_obj,  
     cache_dir = get_default_cache_dir()

R/metadata.R

@@ -15,6 +15,11 @@ cache <- rlang::env(
 #' @return A character vector of URLs to parquet files to download
 #' @examples
 #' get_database_url("metadata.0.2.3.parquet")
+#' @references Mangiola, S., M. Milton, N. Ranathunga, C. S. N. Li-Wai-Suen, 
+#'   A. Odainic, E. Yang, W. Hutchison et al. "A multi-organ map of the human 
+#'   immune system across age, sex and ethnicity." bioRxiv (2023): 2023-06.
+#'   doi:10.1101/2023.06.08.542671.
+#' @source [Mangiola et al.,2023](https://www.biorxiv.org/content/10.1101/2023.06.08.542671v3)
 get_database_url <- function(databases = c("metadata.0.2.3.parquet", "fibrosis.0.2.3.parquet")) {
   glue::glue(
     "https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/metadata/{databases}")
@@ -26,6 +31,11 @@ get_database_url <- function(databases = c("metadata.0.2.3.parquet", "fibrosis.0
 #' @return A character scalar consisting of the URL
 #' @examples
 #' get_metadata(remote_url = SAMPLE_DATABASE_URL, cache_directory = tempdir())
+#' @references Mangiola, S., M. Milton, N. Ranathunga, C. S. N. Li-Wai-Suen, 
+#'   A. Odainic, E. Yang, W. Hutchison et al. "A multi-organ map of the human 
+#'   immune system across age, sex and ethnicity." bioRxiv (2023): 2023-06.
+#'   doi:10.1101/2023.06.08.542671.
+#' @source [Mangiola et al.,2023](https://www.biorxiv.org/content/10.1101/2023.06.08.542671v3)
 SAMPLE_DATABASE_URL <- single_line_str(
   "https://object-store.rc.nectar.org.au/v1/
     AUTH_06d6e008e3e642da99d806ba3ea629c5/metadata/
@@ -142,6 +152,12 @@ SAMPLE_DATABASE_URL <- single_line_str(
 #' ```R
 #' get_metadata(cache_directory = path.expand('~'))
 #' ```
+#' 
+#' @references Mangiola, S., M. Milton, N. Ranathunga, C. S. N. Li-Wai-Suen, 
+#'   A. Odainic, E. Yang, W. Hutchison et al. "A multi-organ map of the human 
+#'   immune system across age, sex and ethnicity." bioRxiv (2023): 2023-06.
+#'   doi:10.1101/2023.06.08.542671.
+#' @source [Mangiola et al.,2023](https://www.biorxiv.org/content/10.1101/2023.06.08.542671v3)
 get_metadata <- function(
     remote_url = get_database_url(),
     cache_directory = get_default_cache_dir(),

R/seurat.R

@@ -21,7 +21,11 @@ as.sparse.DelayedMatrix <- function(x, ...) {
 #' @examples
 #' meta <- get_metadata() |> head(2)
 #' seurat <- get_seurat(meta)
-#'
+#' @references Mangiola, S., M. Milton, N. Ranathunga, C. S. N. Li-Wai-Suen, 
+#'   A. Odainic, E. Yang, W. Hutchison et al. "A multi-organ map of the human 
+#'   immune system across age, sex and ethnicity." bioRxiv (2023): 2023-06.
+#'   doi:10.1101/2023.06.08.542671.
+#' @source [Mangiola et al.,2023](https://www.biorxiv.org/content/10.1101/2023.06.08.542671v3)
 get_seurat <- function(...) {
     get_single_cell_experiment(...) |> as.Seurat(data = NULL)
 }

R/unharmonised.R

@@ -45,6 +45,11 @@ UNHARMONISED_URL <- single_line_str(
 #' unharmonised_tbl <- dplyr::collect(unharmonised_meta[[dataset]])
 #' dplyr::left_join(harmonised_meta, unharmonised_tbl, by=c("file_id", "cell_"))
 #' }
+#' @references Mangiola, S., M. Milton, N. Ranathunga, C. S. N. Li-Wai-Suen, 
+#'   A. Odainic, E. Yang, W. Hutchison et al. "A multi-organ map of the human 
+#'   immune system across age, sex and ethnicity." bioRxiv (2023): 2023-06.
+#'   doi:10.1101/2023.06.08.542671.
+#' @source [Mangiola et al.,2023](https://www.biorxiv.org/content/10.1101/2023.06.08.542671v3)
 get_unharmonised_dataset <- function(
     dataset_id,
     cells = NULL,
@@ -85,6 +90,11 @@ get_unharmonised_dataset <- function(
 #' @examples
 #' harmonised <- dplyr::filter(get_metadata(), tissue == "kidney blood vessel")
 #' unharmonised <- get_unharmonised_metadata(harmonised)
+#' @references Mangiola, S., M. Milton, N. Ranathunga, C. S. N. Li-Wai-Suen, 
+#'   A. Odainic, E. Yang, W. Hutchison et al. "A multi-organ map of the human 
+#'   immune system across age, sex and ethnicity." bioRxiv (2023): 2023-06.
+#'   doi:10.1101/2023.06.08.542671.
+#' @source [Mangiola et al.,2023](https://www.biorxiv.org/content/10.1101/2023.06.08.542671v3)
 get_unharmonised_metadata <- function(metadata, ...){
     args <- list(...)
     metadata |>

R/utils.R

@@ -48,6 +48,11 @@ single_line_str <- function(text){
 #' @importFrom utils packageName
 #' @examples
 #' get_metadata(cache_directory = get_default_cache_dir())
+#' @references Mangiola, S., M. Milton, N. Ranathunga, C. S. N. Li-Wai-Suen, 
+#'   A. Odainic, E. Yang, W. Hutchison et al. "A multi-organ map of the human 
+#'   immune system across age, sex and ethnicity." bioRxiv (2023): 2023-06.
+#'   doi:10.1101/2023.06.08.542671.
+#' @source [Mangiola et al.,2023](https://www.biorxiv.org/content/10.1101/2023.06.08.542671v3)
 get_default_cache_dir <- function() {
     packageName() |>
         R_user_dir(