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This repository was archived by the owner on Oct 14, 2025. It is now read-only.
#' @param remote_url Optional character vector of length 1. An HTTP URL pointing
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#' to the location of the parquet database.
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#' @param cache_directory Optional character vector of length 1. A file path on
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#' your local system to a directory (not a file) that will be used to store
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#' metadata.parquet
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#' @param use_cache Optional logical scalar. If `TRUE` (the default), and this
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#' function has been called before with the same parameters, then a cached
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#' reference to the table will be returned. If `FALSE`, a new connection will
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#' be created no matter what.
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#' function has been called before with the same parameters, then a cached
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#' reference to the table will be returned. If `FALSE`, a new connection will
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#' be created no matter what.
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#' @return A lazy data.frame subclass containing the metadata. You can interact
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#' with this object using most standard dplyr functions. For string matching,
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#' it is recommended that you use `stringr::str_like` to filter character
@@ -39,63 +48,87 @@ cache = rlang::env(
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#' @importFrom duckdb duckdb
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#' @importFrom dplyr tbl
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#' @importFrom httr progress
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#' @importFrom cli cli_alert_info
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#'
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#' @details
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#'
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#' The metadata was collected from the Bioconductor package `cellxgenedp`. it's vignette `using_cellxgenedp` provides an overview of the columns in the metadata.
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#' The data for which the column `organism_name` included "Homo sapiens" was collected collected from `cellxgenedp`.
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#'
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#' The columns `dataset_id` and `file_id` link the datasets explorable through `CuratedAtlasQueryR` and `cellxgenedp`to the CELLxGENE portal.
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#'
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#' Our representation, harmonises the metadata at dataset, sample and cell levels, in a unique coherent database table.
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#'
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#' @importFrom cli cli_alert_info hash_sha256
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#'
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#' @details
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#'
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#' The metadata was collected from the Bioconductor package `cellxgenedp`. it's
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#' vignette `using_cellxgenedp` provides an overview of the columns in the
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#' metadata. The data for which the column `organism_name` included "Homo
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#' sapiens" was collected collected from `cellxgenedp`.
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#'
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#' The columns `dataset_id` and `file_id` link the datasets explorable through
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#' `CuratedAtlasQueryR` and `cellxgenedp`to the CELLxGENE portal.
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#'
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#' Our representation, harmonises the metadata at dataset, sample and cell
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#' levels, in a unique coherent database table.
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#'
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#' Dataset-specific columns (definitions available at cellxgene.cziscience.com)
#' Through harmonisation and curation we introduced custom column, not present
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#' in the original CELLxGENE metadata
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#'
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#' - `tissue_harmonised`: a coarser tissue name for better filtering
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#' - `age_days`: the number of days corresponding to the age
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#' - `cell_type_harmonised`: the consensus call identity (for immune cells) using the original and three novel annotations using Seurat Azimuth and SingleR
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#' - `confidence_class`: an ordinal class of how confident `cell_type_harmonised` is. 1 is complete consensus, 2 is 3 out of four and so on.
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#' - `cell_type_harmonised`: the consensus call identity (for immune cells)
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#' using the original and three novel annotations using Seurat Azimuth and
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#' SingleR
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#' - `confidence_class`: an ordinal class of how confident
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#' `cell_type_harmonised` is. 1 is complete consensus, 2 is 3 out of four and
#' - `cell_annotation_blueprint_singler`: SingleR cell annotation using Blueprint reference
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#' - `cell_annotation_blueprint_monaco`: SingleR cell annotation using Monaco reference
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#' - `cell_annotation_blueprint_singler`: SingleR cell annotation using
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#' Blueprint reference
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#' - `cell_annotation_blueprint_monaco`: SingleR cell annotation using Monaco
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#' reference
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#' - `sample_id_db`: Sample subdivision for internal use
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#' - `file_id_db`: File subdivision for internal use
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#' - `sample_`: Sample ID
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#' - `.sample_name`: How samples were defined
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#'
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#'
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#'
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#'
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#' **Possible cache path issues**
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#'
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#' If your default R cache path includes non-standard characters (e.g. dash because of your user or organisation name), the following error can manifest
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#'
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#' Error in `db_query_fields.DBIConnection()`:
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#' ! Can't query fields.
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#' Caused by error:
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#' ! Parser Error: syntax error at or near "/"
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#' LINE 2: FROM /Users/bob/Library/Cach...
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#'
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#'
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#' If your default R cache path includes non-standard characters (e.g. dash
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#' because of your user or organisation name), the following error can manifest
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#'
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#' Error in `db_query_fields.DBIConnection()`: ! Can't query fields. Caused by
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#' error: ! Parser Error: syntax error at or near "/" LINE 2: FROM
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#' /Users/bob/Library/Cach...
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#'
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#' The solution is to choose a different cache, for example
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