Load an ImmunData object from disk¶

Description¶

Continue an analysis later by reopening an ImmunData dataset saved on disk. Use read_immundata() after restarting R, in another script, or when another person gives you a dataset created by write_immundata() or read_repertoires(). It is that simple, just don’t forget to save the ImmunData object first!

The unit restored retains all information: chain rows, cell and receptor identifiers, repertoire and stratum definitions, and provenance. The function does not change these biological units or the saved files. It returns a new ImmunData object.

Usage¶

read_immundata(
  path,
  tag = NULL,
  version = NULL,
  prudence = "stingy",
  verbose = getOption("immundata.verbose", TRUE)
)

Arguments¶

path A character string. Path to a saved dataset directory. The directory must contain annotations.parquet and metadata.json. When tag is supplied, use the project home directory that contains the snapshots directory. Read more about snapshots on the website.

tag A character string or NULL. Snapshot tag to read from path/snapshots/\/vNNN. If NULL, the default, path itself is read.

version A non-negative integer or NULL. Snapshot version within tag. For example, 1 reads v001. If NULL, the default, the latest available version for the tag is read. version can only be used with tag.

prudence A character string. Memory protection used while reading the Parquet data. This controls whether duckplyr may convert an intermediate result from DuckDB-managed memory to an R data frame: “stingy”, the default here, never permits conversion; “thrifty” permits up to 1 million table cells (rows multiplied by columns); and “lavish” permits conversion regardless of size. Here, "table cells" does not mean biological cells. Passed to duckplyr::read_parquet_duckdb().

verbose A logical value. Whether to print progress and summary messages. Defaults to getOption(“immundata.verbose”, TRUE).

Details¶

Read either a dataset directory directly or a versioned snapshot within its project home.

Value¶

A new, disk-backed ImmunData object representing the selected saved state. Its provenance records the directory that was read.

Choose the saved state¶

To reopen a dataset saved directly in a folder, supply that folder as path and leave tag and version as NULL.

To reopen a managed snapshot, supply the project home as path and its tag. By default, the latest version for that tag is read. Supply version when you need an exact earlier state.

Backend and serialized data¶

annotations.parquet stores the retained chain-level annotation table. It is reopened as a lazy duckplyr table, so the complete table does not need to be loaded into R memory. metadata.json stores the format and package versions, receptor, repertoire, and stratum schemas, the repertoire table, the snapshot identifier, lineage events, and provenance paths.

Receptor and stratum views are reconstructed from this serialized state; they are not stored as separate files. Please also mind, that the saved files is an ImmunData-specific serialization, not an RDS file.

Examples¶

library("immundata")

library(immundata)
library(dplyr)

options(immundata.verbose = FALSE)

# Create a project home and save a filtered biological state as a snapshot
idata <- get_test_idata()
project_dir <- tempfile("immundata-project-")

project_idata <- write_immundata(
  idata,
  output_folder = project_dir,
  rehome = TRUE
)

fr_response <- project_idata |>
  filter(Response == "FR")

write_immundata(fr_response, tag = "fr-response")

# Read the exact first version of this snapshot
continued_fr <- read_immundata(
  project_dir,
  tag = "fr-response",
  version = 1
)

continued_fr |>
  collect() |>
  summarise(
    n_chains = n(),
    n_receptors = n_distinct(imd_receptor_id)
  )

#> # A tibble: 1 × 2
#>   n_chains n_receptors
#> *    <int>       <dbl>
#> 1      955         871

# Expected result: the snapshot contains the 955 chain rows and 871
# receptors from the FR response group.
#   n_chains n_receptors
#        955         871

list.files(file.path(project_dir, "snapshots", "fr-response"))

#> [1] "v001"

# Expected result: "v001"

unlink(project_dir, recursive = TRUE)