AbstractArtifactdbResult

AbstractArtifactdbResult

Pre-computed analysis results stored as a SummarizedExperiment object (or one of its subclasses) in the ArtifactDB format. This is intended as a virtual base class; applications should define subclasses that are tied to a specific ArtifactdbProjectNavigator class.

Constructor

new AbstractArtifactdbResult(path, navigator)

Source:
Parameters:
Name Type Description
path string

Path to the SummarizedExperiment in the ArtifactDB project directory.
navigator ArtifactdbProjectNavigator

A navigator object that describes how to obtain the various assets from the project directory containing path.

Classes

AbstractArtifactdbResult

Methods

clear()

Description:

  • Destroy caches if present, releasing the associated memory. This may be called at any time but only has an effect if cache = true in load or summary.

Source:

(async) load(optionsopt) → {object}

Source:
Parameters:
Name Type Attributes Default Description
options object <optional>
 {}

Optional parameters.

Properties
Name Type Attributes Default Description
cache boolean <optional>
 false

Whether to cache the results for re-use in subsequent calls to this method or summary. If true, users should consider calling clear to release the memory once this dataset instance is no longer needed.
Returns:

Object containing the per-feature and per-cell annotations. This has the following properties:

  • features: an object where each key is a modality name and each value is a DataFrame of per-feature annotations for that modality.
  • cells: a DataFrame containing per-cell annotations.
  • matrix: a MultiMatrix containing one ScranMatrix per modality.
  • reduced_dimensions: an object containing the dimensionality reduction results. Each value is an array of arrays, where each inner array contains the coordinates for one dimension.
  • other_metadata: an object containing other metadata.
Type
object

options() → {object}

Source:
Returns:

Object containing all options used for loading.

Type
object

setOptions(options)

Source:
Parameters:
Name Type Description
options object

Optional parameters that affect load (but not summary.

Properties
Name Type Attributes Description
primaryAssay object | string | number <optional>

Assay containing the relevant data for each modality.

  • If a string, this is used as the name of the assay across all modalities.
  • If a number, this is used as the index of the assay across all modalities.
  • If any object, the key should be the name of a modality and the value may be either a string or number specifying the assay to use for that modality. Modalities absent from this object will not be loaded.
isPrimaryNormalized object | boolean <optional>

Whether or not the assay for a particular modality has already been normalized.

  • If a boolean, this is used to indicate normalization status of assays across all modalities. If false, that modality's assay is assumed to contain count data and is subjected to library size normalization.
  • If any object, the key should be the name of a modality and the value should be a boolean indicating whether that modality's assay has been normalized. Modalities absent from this object are assumed to have been normalized.
reducedDimensionNames Array <optional>
<nullable>

Array of names of the reduced dimensions to load. If null, all reduced dimensions found in the file are loaded.

(async) summary(optionsopt) → {object}

Source:
Parameters:
Name Type Attributes Default Description
options object <optional>
 {}

Optional parameters.

Properties
Name Type Attributes Default Description
cache boolean <optional>
 false

Whether to cache the results for re-use in subsequent calls to this method or load. If true, users should consider calling clear to release the memory once this dataset instance is no longer needed.
Returns:

Object containing the per-feature and per-cell annotations. This has the following properties:

  • modality_features: an object where each key is a modality name and each value is a DataFrame of per-feature annotations for that modality.
  • cells: a DataFrame of per-cell annotations.
  • modality_assay_names: an object where each key is a modality name and each value is an Array containing the names of available assays for that modality. Unnamed assays are represented as null names.
  • reduced_dimension_names: an Array of strings containing names of dimensionality reduction results.
  • other_metadata: an object containing other metadata.
Type
object

(static) defaults() → {object}

Source:
Returns:

Default options, see setOptions for more details.

Type
object