The single_cell_experiment format provides an on-disk representation of a single cell experiment.
It is based on the SingleCellExperiment class from the SingleCellExperiment bioconductor package.
The OBJECT file should contain a single_cell_experiment property, which is itself a JSON object with the following properties:
version, a string specifying the version of thesingle_cell_experimentformat. This should be set to "1.0".- (optional)
main_experiment_name, a string containing the name of the main experiment. If provided, this should not overlap with any names of the alternative experiments in thealternative_experimentssubdirectory.
In addition, the OBJECT file should contain all properties expected for the ranged_summarized_experiment format, i.e., a ranged_summarized_experiment property.
This transitively includes the properties that are expected of the summarized_experiment format.
The directory should contain all files expected of a ranged_summarized_experiment format.
This includes the transitive expectations of files that should be present in a summarized_experiment format.
The dimensions of the single cell experiment are determined from the summarized_experiment-based files.
The directory may contain a reduced_dimensions subdirectory.
The subdirectory should contain a names.json file, which contains a JSON-formatted array of strings.
Each string is the name of a dimensionality reduction result and should be non-empty and unique.
The reduced_dimensions subdirectory should contain one subdirectory for each dimensionality reduction result,
named after the result's positional index in the JSON array, e.g., 0 for the first result, 1 for the second result, and so on.
Each subdirectory of reduced_dimensions should be a child object that has some concept of dimensions,
where the extent of the first dimension is equal to the number of columns of the single cell experiment.
If no reduced_dimensions subdirectory is present, it is assumed that the single cell experiment contains no reduced dimensions.
The directory may contain an alternative_experiments subdirectory.
The subdirectory should contain a names.json file, which contains a JSON-formatted array of strings.
Each string is the name of an alternative experiment and should be non-empty and unique.
The alternative_experiments subdirectory should contain one subdirectory for each alternative experiment,
named after the experiment's positional index in the JSON array, e.g., 0 for the first experiment, 1 for the second experiment, and so on.
Each subdirectory of alternative_experiments should be a child object that satisfies the SUMMARIZED_EXPERIMENT interface,
with number of columns equal to the number of columns of the single cell experiment.
If no alternative_experiments subdirectory is present, it is assumed that the single cell experiment contains no alternative experiments.
Note that any names in the reduced_dimensions or alternative_experiments should not be used as the column names of the ranged summarized experiment,
as this is determined from the summarized_experiment-based files instead.
The height of the single_cell_experiment is defined in the same manner as that of the underlying summarized_experiment.
The dimensions of the single_cell_experiment is defined in the same manner as that of the summarized_experiment.
The single_cell_experiment satisfies the SUMMARIZED_EXPERIMENT interface.