Reconstructs an ImmunData object from files previously saved to a directory
by write_immundata() or the internal saving step of read_repertoires().
It reads the annotations.parquet file for the main data and metadata.json
to retrieve the necessary receptor and repertoire schemas.
read_immundata(path, prudence = "stingy", verbose = TRUE)Character(1). Path to the directory containing the saved
ImmunData files (annotations.parquet and metadata.json).
Character(1). Controls strictness of type inference when
reading the Parquet file, passed to duckplyr::read_parquet_duckdb().
Default "stingy" likely implies stricter type checking or safer inference.
Logical(1). If TRUE (default), prints informative messages
using cli during loading. Set to FALSE for quiet operation.
A new ImmunData object reconstructed from the saved files. If
repertoire information was saved, it will be recalculated and included.
This function expects a directory structure created by write_immundata(),
containing at least:
annotations.parquet: The main annotation data table.
metadata.json: Contains package version, receptor schema, and optionally
repertoire schema.
The loading process involves:
Checking that the specified path is a directory and contains the
required annotations.parquet and metadata.json files.
Reading metadata.json using jsonlite::read_json().
Reading annotations.parquet using duckplyr::read_parquet_duckdb() with
the specified prudence level.
Extracting the receptor_schema and repertoire_schema from the loaded
metadata.
Instantiating a new ImmunData object using the loaded annotations data
and the receptor_schema.
If a non-empty repertoire_schema was found in the metadata, it calls
agg_repertoires() on the newly created object to recalculate and
attach repertoire-level information based on that schema.
write_immundata() for saving ImmunData objects,
read_repertoires() for the primary data loading pipeline, ImmunData class,
agg_repertoires() for repertoire definition.
if (FALSE) { # \dontrun{
# Assume 'my_idata' is an ImmunData object created previously
# my_idata <- read_repertoires(...)
# Define a temporary directory for saving
save_dir <- tempfile("saved_immundata_")
# Save the ImmunData object
write_immundata(my_idata, save_dir)
# --- Later, in a new session or script ---
# Load the ImmunData object back from the directory
loaded_idata <- read_immundata(save_dir)
# Verify the loaded object
print(loaded_idata)
# compare_methods(my_idata$annotations, loaded_idata$annotations) # If available
# Clean up
unlink(save_dir, recursive = TRUE)
} # }