Join Census metadata to an existing data frame

Downloads and joins the Census metadata with cellNexus metadata. This function creates indexed tables for efficient joining and returns a data frame.

Usage

join_census_table(
  tbl,
  cloud_metadata = get_metadata_url("census_cell_metadata.2.2.0.parquet"),
  cache_directory = get_default_cache_dir(),
  join_keys = c("sample_id", "dataset_id", "observation_joinid")
)

Arguments

tbl

A tbl_sql object (from get_metadata) or a database connection.

cloud_metadata

HTTP URL/URLs pointing to the census parquet database name and location.

cache_directory

A character string specifying the local cache directory where remote parquet files will be stored. Defaults to get_default_cache_dir().

join_keys

A character vector of column names used for the join. Defaults to c("sample_id", "dataset_id", "observation_joinid").

Value

A lazy SQL table with Census metadata joined to the cellNexus metadata.

Examples

library(dplyr)
get_metadata(cloud_metadata = SAMPLE_DATABASE_URL) |> head(2) |>
  # You do not need to specify anything in cloud_metadata
  join_census_table(
    cloud_metadata = SAMPLE_DATABASE_URL,
    cache_directory = tempdir()
  )
#> ℹ Downloading 1 file, totalling 0 GB
#> ℹ Downloading https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/cellNexus-metadata/census_sample_metadata.2.2.0.parquet to /tmp/RtmpQWE1lc/census_sample_metadata.2.2.0.parquet
#> # Source:   SQL [?? x 143]
#> # Database: DuckDB 1.5.2 [unknown@Linux 6.17.0-1010-azure:R 4.7.0/:memory:]
#>   cell_id.x observation_joinid dataset_id       sample_id sample_.x cell_count.x
#>       <dbl> <chr>              <chr>            <chr>     <chr>            <int>
#> 1        15 TjgA2vJ1;{         842c6f5d-4a94-4… 1119f482… 1119f482…       714331
#> 2        19 lNmuO5xs~3         842c6f5d-4a94-4… 1119f482… 1119f482…       714331
#> 3        15 TjgA2vJ1;{         842c6f5d-4a94-4… 1119f482… 1119f482…       714331
#> 4        19 lNmuO5xs~3         842c6f5d-4a94-4… 1119f482… 1119f482…       714331
#> # ℹ 137 more variables: citation.x <chr>, collection_id.x <chr>,
#> #   dataset_version_id.x <chr>, default_embedding.x <chr>,
#> #   experiment___.x <chr>, explorer_url.x <chr>, feature_count.x <int>,
#> #   filesize.x <dbl>, filetype.x <chr>, mean_genes_per_cell.x <dbl>,
#> #   primary_cell_count.x <chr>, published_at.x <chr>,
#> #   raw_data_location.x <chr>, revised_at.x <chr>, run_from_cell_id.x <chr>,
#> #   sample_heuristic.x <chr>, schema_version.x <chr>, …