Dataset workflows

The dataset processing pipeline uses dataset loaders to create raw dataset files (Figure 1). The raw dataset files are then processed to generate common dataset files. Common dataset files are used in one or more tasks.

graph LR
  normalization:::group
  dataset_processors:::group
  raw_dataset["Raw dataset"]:::anndata
  common_dataset[Common<br/>dataset]:::anndata
  test_dataset[Test<br/>dataset]:::anndata
  dataset_loader[/Dataset<br/>loader/]:::component
  subgraph normalization [Normalization methods]
    log_cp10k[/"Log CP10k"/]:::component
    l1_sqrt[/"L1 sqrt"/]:::component
    log_scran_pooling[/"Log scran<br/>pooling"/]:::component
    sqrt_cp10k[/Sqrt CP10k/]:::component
  end
  subgraph dataset_processors[Dataset processors]
    pca[/PCA/]:::component
    hvg[/HVG/]:::component
    knn[/KNN/]:::component
  end
  dataset_loader --> raw_dataset --> log_cp10k & l1_sqrt & log_scran_pooling & sqrt_cp10k --> pca --> hvg --> knn --> common_dataset
  subset[/Subset/]:::component
  common_dataset --> subset --> test_dataset

Figure 1: Overview of the dataset processing workflow. Legend: Grey rectangles are AnnData .h5ad files, purple rhomboids are Viash components.

Directory structure

• Dataset file and component formats (src/datasets/api): This folder contains specifications for dataset file formats and component interfaces. This documentation page was generated mostly by reading in these files.

• Dataset loader (src/datasets/loaders): This folder contains components to load and format datasets for various sources.

• Dataset normalization (src/datasets/normalization): This folder contains various dataset normalization methods.

• Dataset processors (src/datasets/processors): This folder contains components for processing datasets, such as computing a KNN, PCA, HVG or subsetting.

• Resource generation scripts (src/common/resources_scripts): This folder contains scripts for generating the datasets using the dataset loaders, normalization methods and processors.

• Test resource generation scripts (src/common/resources_test_scripts): This folder contains scripts for generating test resources.

Component type: Dataset loader

Path: src/datasets/loaders

A component which generates a “Common dataset”.

Arguments:

Name	Type	Description
--output	file	(Output) An unprocessed dataset as output by a dataset loader.

Warning: Unknown or uninitialised column: `file_type`.

File format: Raw dataset

An unprocessed dataset as output by a dataset loader.

Example file: resources_test/common/pancreas/raw.h5ad

Description:

This dataset contains raw counts and metadata as output by a dataset loader.

The format of this file is derived from the CELLxGENE schema v4.0.0.

Format:

AnnData object
 obs: 'dataset_id', 'assay', 'assay_ontology_term_id', 'cell_type', 'cell_type_ontology_term_id', 'development_stage', 'development_stage_ontology_term_id', 'disease', 'disease_ontology_term_id', 'donor_id', 'is_primary_data', 'organism', 'organism_ontology_term_id', 'self_reported_ethnicity', 'self_reported_ethnicity_ontology_term_id', 'sex', 'sex_ontology_term_id', 'suspension_type', 'tissue', 'tissue_ontology_term_id', 'tissue_general', 'tissue_general_ontology_term_id', 'batch', 'soma_joinid'
 var: 'feature_id', 'feature_name', 'soma_joinid'
 layers: 'counts'
 uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism'

Slot description:

Slot	Type	Description
obs["dataset_id"]	string	(Optional) Identifier for the dataset from which the cell data is derived, useful for tracking and referencing purposes.
obs["assay"]	string	(Optional) Type of assay used to generate the cell data, indicating the methodology or technique employed.
obs["assay_ontology_term_id"]	string	(Optional) Experimental Factor Ontology (EFO:) term identifier for the assay, providing a standardized reference to the assay type.
obs["cell_type"]	string	(Optional) Classification of the cell type based on its characteristics and function within the tissue or organism.
obs["cell_type_ontology_term_id"]	string	(Optional) Cell Ontology (CL:) term identifier for the cell type, offering a standardized reference to the specific cell classification.
obs["development_stage"]	string	(Optional) Stage of development of the organism or tissue from which the cell is derived, indicating its maturity or developmental phase.
obs["development_stage_ontology_term_id"]	string	(Optional) Ontology term identifier for the developmental stage, providing a standardized reference to the organism’s developmental phase. If the organism is human (organism_ontology_term_id == 'NCBITaxon:9606'), then the Human Developmental Stages (HsapDv:) ontology is used. If the organism is mouse (organism_ontology_term_id == 'NCBITaxon:10090'), then the Mouse Developmental Stages (MmusDv:) ontology is used. Otherwise, the Uberon (UBERON:) ontology is used.
obs["disease"]	string	(Optional) Information on any disease or pathological condition associated with the cell or donor.
obs["disease_ontology_term_id"]	string	(Optional) Ontology term identifier for the disease, enabling standardized disease classification and referencing. Must be a term from the Mondo Disease Ontology (MONDO:) ontology term, or PATO:0000461 from the Phenotype And Trait Ontology (PATO:).
obs["donor_id"]	string	(Optional) Identifier for the donor from whom the cell sample is obtained.
obs["is_primary_data"]	boolean	(Optional) Indicates whether the data is primary (directly obtained from experiments) or has been computationally derived from other primary data.
obs["organism"]	string	(Optional) Organism from which the cell sample is obtained.
obs["organism_ontology_term_id"]	string	(Optional) Ontology term identifier for the organism, providing a standardized reference for the organism. Must be a term from the NCBI Taxonomy Ontology (NCBITaxon:) which is a child of NCBITaxon:33208.
obs["self_reported_ethnicity"]	string	(Optional) Ethnicity of the donor as self-reported, relevant for studies considering genetic diversity and population-specific traits.
obs["self_reported_ethnicity_ontology_term_id"]	string	(Optional) Ontology term identifier for the self-reported ethnicity, providing a standardized reference for ethnic classifications. If the organism is human (organism_ontology_term_id == 'NCBITaxon:9606'), then the Human Ancestry Ontology (HANCESTRO:) is used.
obs["sex"]	string	(Optional) Biological sex of the donor or source organism, crucial for studies involving sex-specific traits or conditions.
obs["sex_ontology_term_id"]	string	(Optional) Ontology term identifier for the biological sex, ensuring standardized classification of sex. Only PATO:0000383, PATO:0000384 and PATO:0001340 are allowed.
obs["suspension_type"]	string	(Optional) Type of suspension or medium in which the cells were stored or processed, important for understanding cell handling and conditions.
obs["tissue"]	string	(Optional) Specific tissue from which the cells were derived, key for context and specificity in cell studies.
obs["tissue_ontology_term_id"]	string	(Optional) Ontology term identifier for the tissue, providing a standardized reference for the tissue type. For organoid or tissue samples, the Uber-anatomy ontology (UBERON:) is used. The term ids must be a child term of UBERON:0001062 (anatomical entity). For cell cultures, the Cell Ontology (CL:) is used. The term ids cannot be CL:0000255, CL:0000257 or CL:0000548.
obs["tissue_general"]	string	(Optional) General category or classification of the tissue, useful for broader grouping and comparison of cell data.
obs["tissue_general_ontology_term_id"]	string	(Optional) Ontology term identifier for the general tissue category, aiding in standardizing and grouping tissue types. For organoid or tissue samples, the Uber-anatomy ontology (UBERON:) is used. The term ids must be a child term of UBERON:0001062 (anatomical entity). For cell cultures, the Cell Ontology (CL:) is used. The term ids cannot be CL:0000255, CL:0000257 or CL:0000548.
obs["batch"]	string	(Optional) A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc.
obs["soma_joinid"]	integer	(Optional) If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the cell.
var["feature_id"]	string	(Optional) Unique identifier for the feature, usually a ENSEMBL gene id.
var["feature_name"]	string	A human-readable name for the feature, usually a gene symbol.
var["soma_joinid"]	integer	(Optional) If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the feature.
layers["counts"]	integer	Raw counts.
uns["dataset_id"]	string	A unique identifier for the dataset. This is different from the obs.dataset_id field, which is the identifier for the dataset from which the cell data is derived.
uns["dataset_name"]	string	A human-readable name for the dataset.
uns["dataset_url"]	string	(Optional) Link to the original source of the dataset.
uns["dataset_reference"]	string	(Optional) Bibtex reference of the paper in which the dataset was published.
uns["dataset_summary"]	string	Short description of the dataset.
uns["dataset_description"]	string	Long description of the dataset.
uns["dataset_organism"]	string	(Optional) The organism of the sample in the dataset.

Component type: Dataset normalization

Path: src/datasets/normalization

A normalization method which processes the raw counts into a normalized dataset.

Arguments:

Name	Type	Description
--input	file	An unprocessed dataset as output by a dataset loader.
--output	file	(Output) A normalized dataset.
--normalization_id	string	(Optional) The normalization id to store in the dataset metadata. If not specified, the functionality name will be used.
--layer_output	string	(Optional) The name of the layer in which to store the normalized data. Default: normalized.
--obs_size_factors	string	(Optional) In which .obs slot to store the size factors (if any). Default: size_factors.

Warning: Unknown or uninitialised column: `file_type`.

File format: Normalized dataset

A normalized dataset

Example file: resources_test/common/pancreas/normalized.h5ad

Description:

This dataset contains raw counts and metadata as output by a dataset loader.

The format of this file is derived from the CELLxGENE schema v4.0.0.

Format:

AnnData object
 obs: 'dataset_id', 'assay', 'assay_ontology_term_id', 'cell_type', 'cell_type_ontology_term_id', 'development_stage', 'development_stage_ontology_term_id', 'disease', 'disease_ontology_term_id', 'donor_id', 'is_primary_data', 'organism', 'organism_ontology_term_id', 'self_reported_ethnicity', 'self_reported_ethnicity_ontology_term_id', 'sex', 'sex_ontology_term_id', 'suspension_type', 'tissue', 'tissue_ontology_term_id', 'tissue_general', 'tissue_general_ontology_term_id', 'batch', 'soma_joinid', 'size_factors'
 var: 'feature_id', 'feature_name', 'soma_joinid'
 layers: 'counts', 'normalized'
 uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'normalization_id'

Slot description:

Slot	Type	Description
obs["dataset_id"]	string	(Optional) Identifier for the dataset from which the cell data is derived, useful for tracking and referencing purposes.
obs["assay"]	string	(Optional) Type of assay used to generate the cell data, indicating the methodology or technique employed.
obs["assay_ontology_term_id"]	string	(Optional) Experimental Factor Ontology (EFO:) term identifier for the assay, providing a standardized reference to the assay type.
obs["cell_type"]	string	(Optional) Classification of the cell type based on its characteristics and function within the tissue or organism.
obs["cell_type_ontology_term_id"]	string	(Optional) Cell Ontology (CL:) term identifier for the cell type, offering a standardized reference to the specific cell classification.
obs["development_stage"]	string	(Optional) Stage of development of the organism or tissue from which the cell is derived, indicating its maturity or developmental phase.
obs["development_stage_ontology_term_id"]	string	(Optional) Ontology term identifier for the developmental stage, providing a standardized reference to the organism’s developmental phase. If the organism is human (organism_ontology_term_id == 'NCBITaxon:9606'), then the Human Developmental Stages (HsapDv:) ontology is used. If the organism is mouse (organism_ontology_term_id == 'NCBITaxon:10090'), then the Mouse Developmental Stages (MmusDv:) ontology is used. Otherwise, the Uberon (UBERON:) ontology is used.
obs["disease"]	string	(Optional) Information on any disease or pathological condition associated with the cell or donor.
obs["disease_ontology_term_id"]	string	(Optional) Ontology term identifier for the disease, enabling standardized disease classification and referencing. Must be a term from the Mondo Disease Ontology (MONDO:) ontology term, or PATO:0000461 from the Phenotype And Trait Ontology (PATO:).
obs["donor_id"]	string	(Optional) Identifier for the donor from whom the cell sample is obtained.
obs["is_primary_data"]	boolean	(Optional) Indicates whether the data is primary (directly obtained from experiments) or has been computationally derived from other primary data.
obs["organism"]	string	(Optional) Organism from which the cell sample is obtained.
obs["organism_ontology_term_id"]	string	(Optional) Ontology term identifier for the organism, providing a standardized reference for the organism. Must be a term from the NCBI Taxonomy Ontology (NCBITaxon:) which is a child of NCBITaxon:33208.
obs["self_reported_ethnicity"]	string	(Optional) Ethnicity of the donor as self-reported, relevant for studies considering genetic diversity and population-specific traits.
obs["self_reported_ethnicity_ontology_term_id"]	string	(Optional) Ontology term identifier for the self-reported ethnicity, providing a standardized reference for ethnic classifications. If the organism is human (organism_ontology_term_id == 'NCBITaxon:9606'), then the Human Ancestry Ontology (HANCESTRO:) is used.
obs["sex"]	string	(Optional) Biological sex of the donor or source organism, crucial for studies involving sex-specific traits or conditions.
obs["sex_ontology_term_id"]	string	(Optional) Ontology term identifier for the biological sex, ensuring standardized classification of sex. Only PATO:0000383, PATO:0000384 and PATO:0001340 are allowed.
obs["suspension_type"]	string	(Optional) Type of suspension or medium in which the cells were stored or processed, important for understanding cell handling and conditions.
obs["tissue"]	string	(Optional) Specific tissue from which the cells were derived, key for context and specificity in cell studies.
obs["tissue_ontology_term_id"]	string	(Optional) Ontology term identifier for the tissue, providing a standardized reference for the tissue type. For organoid or tissue samples, the Uber-anatomy ontology (UBERON:) is used. The term ids must be a child term of UBERON:0001062 (anatomical entity). For cell cultures, the Cell Ontology (CL:) is used. The term ids cannot be CL:0000255, CL:0000257 or CL:0000548.
obs["tissue_general"]	string	(Optional) General category or classification of the tissue, useful for broader grouping and comparison of cell data.
obs["tissue_general_ontology_term_id"]	string	(Optional) Ontology term identifier for the general tissue category, aiding in standardizing and grouping tissue types. For organoid or tissue samples, the Uber-anatomy ontology (UBERON:) is used. The term ids must be a child term of UBERON:0001062 (anatomical entity). For cell cultures, the Cell Ontology (CL:) is used. The term ids cannot be CL:0000255, CL:0000257 or CL:0000548.
obs["batch"]	string	(Optional) A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc.
obs["soma_joinid"]	integer	(Optional) If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the cell.
obs["size_factors"]	double	(Optional) The size factors created by the normalisation method, if any.
var["feature_id"]	string	(Optional) Unique identifier for the feature, usually a ENSEMBL gene id.
var["feature_name"]	string	A human-readable name for the feature, usually a gene symbol.
var["soma_joinid"]	integer	(Optional) If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the feature.
layers["counts"]	integer	Raw counts.
layers["normalized"]	double	Normalised expression values.
uns["dataset_id"]	string	A unique identifier for the dataset. This is different from the obs.dataset_id field, which is the identifier for the dataset from which the cell data is derived.
uns["dataset_name"]	string	A human-readable name for the dataset.
uns["dataset_url"]	string	(Optional) Link to the original source of the dataset.
uns["dataset_reference"]	string	(Optional) Bibtex reference of the paper in which the dataset was published.
uns["dataset_summary"]	string	Short description of the dataset.
uns["dataset_description"]	string	Long description of the dataset.
uns["dataset_organism"]	string	(Optional) The organism of the sample in the dataset.
uns["normalization_id"]	string	Which normalization was used.

Component type: PCA

Path: src/datasets/processors

Computes a PCA embedding of the normalized data.

Arguments:

Name	Type	Description
--input	file	A normalised dataset with a PCA embedding and HVG selection.
--input_layer	string	(Optional) Which layer to use as input. Default: normalized.
--input_var_features	string	(Optional) Column name in .var matrix that will be used to select which genes to run the PCA on. Default: hvg.
--output	file	(Output) A normalised dataset with a PCA embedding.
--obsm_embedding	string	(Optional) In which .obsm slot to store the resulting embedding. Default: X_pca.
--varm_loadings	string	(Optional) In which .varm slot to store the resulting loadings matrix. Default: pca_loadings.
--uns_variance	string	(Optional) In which .uns slot to store the resulting variance objects. Default: pca_variance.
--num_components	integer	(Optional) Number of principal components to compute. Defaults to 50, or 1 - minimum dimension size of selected representation.

Component type: HVG

Path: src/datasets/processors

Computes the highly variable genes scores.

Arguments:

Name	Type	Description
--input	file	A normalized dataset.
--input_layer	string	(Optional) Which layer to use as input. Default: normalized.
--output	file	(Output) A normalised dataset with a PCA embedding and HVG selection.
--var_hvg	string	(Optional) In which .var slot to store whether a feature is considered to be hvg. Default: hvg.
--var_hvg_score	string	(Optional) In which .var slot to store the gene variance score (normalized dispersion). Default: hvg_score.
--num_features	integer	(Optional) The number of HVG to select. Default: 1000.

Component type: KNN

Path: src/datasets/processors

Computes the k-nearest-neighbours for each cell.

Arguments:

Name	Type	Description
--input	file	A normalised dataset with a PCA embedding.
--input_layer	string	(Optional) Which layer to use as input. Default: normalized.
--output	file	(Output) A normalised data with a PCA embedding, HVG selection and a kNN graph.
--key_added	string	(Optional) The neighbors data is added to .uns[key_added], distances are stored in .obsp[key_added+'_distances'] and connectivities in .obsp[key_added+'_connectivities']. Default: knn.
--num_neighbors	integer	(Optional) The size of local neighborhood (in terms of number of neighboring data points) used for manifold approximation. Default: 15.

Warning: Unknown or uninitialised column: `file_type`.

File format: Common dataset

A dataset processed by the common dataset processing pipeline.

Example file: resources_test/common/pancreas/dataset.h5ad

Description:

This dataset contains both raw counts and normalized data matrices, as well as a PCA embedding, HVG selection and a kNN graph.

Format:

AnnData object
 obs: 'dataset_id', 'assay', 'assay_ontology_term_id', 'cell_type', 'cell_type_ontology_term_id', 'development_stage', 'development_stage_ontology_term_id', 'disease', 'disease_ontology_term_id', 'donor_id', 'is_primary_data', 'organism', 'organism_ontology_term_id', 'self_reported_ethnicity', 'self_reported_ethnicity_ontology_term_id', 'sex', 'sex_ontology_term_id', 'suspension_type', 'tissue', 'tissue_ontology_term_id', 'tissue_general', 'tissue_general_ontology_term_id', 'batch', 'soma_joinid', 'size_factors'
 var: 'feature_id', 'feature_name', 'soma_joinid', 'hvg', 'hvg_score'
 obsm: 'X_pca'
 obsp: 'knn_distances', 'knn_connectivities'
 varm: 'pca_loadings'
 layers: 'counts', 'normalized'
 uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'normalization_id', 'pca_variance', 'knn'

Slot description:

Slot	Type	Description
obs["dataset_id"]	string	(Optional) Identifier for the dataset from which the cell data is derived, useful for tracking and referencing purposes.
obs["assay"]	string	(Optional) Type of assay used to generate the cell data, indicating the methodology or technique employed.
obs["assay_ontology_term_id"]	string	(Optional) Experimental Factor Ontology (EFO:) term identifier for the assay, providing a standardized reference to the assay type.
obs["cell_type"]	string	(Optional) Classification of the cell type based on its characteristics and function within the tissue or organism.
obs["cell_type_ontology_term_id"]	string	(Optional) Cell Ontology (CL:) term identifier for the cell type, offering a standardized reference to the specific cell classification.
obs["development_stage"]	string	(Optional) Stage of development of the organism or tissue from which the cell is derived, indicating its maturity or developmental phase.
obs["development_stage_ontology_term_id"]	string	(Optional) Ontology term identifier for the developmental stage, providing a standardized reference to the organism’s developmental phase. If the organism is human (organism_ontology_term_id == 'NCBITaxon:9606'), then the Human Developmental Stages (HsapDv:) ontology is used. If the organism is mouse (organism_ontology_term_id == 'NCBITaxon:10090'), then the Mouse Developmental Stages (MmusDv:) ontology is used. Otherwise, the Uberon (UBERON:) ontology is used.
obs["disease"]	string	(Optional) Information on any disease or pathological condition associated with the cell or donor.
obs["disease_ontology_term_id"]	string	(Optional) Ontology term identifier for the disease, enabling standardized disease classification and referencing. Must be a term from the Mondo Disease Ontology (MONDO:) ontology term, or PATO:0000461 from the Phenotype And Trait Ontology (PATO:).
obs["donor_id"]	string	(Optional) Identifier for the donor from whom the cell sample is obtained.
obs["is_primary_data"]	boolean	(Optional) Indicates whether the data is primary (directly obtained from experiments) or has been computationally derived from other primary data.
obs["organism"]	string	(Optional) Organism from which the cell sample is obtained.
obs["organism_ontology_term_id"]	string	(Optional) Ontology term identifier for the organism, providing a standardized reference for the organism. Must be a term from the NCBI Taxonomy Ontology (NCBITaxon:) which is a child of NCBITaxon:33208.
obs["self_reported_ethnicity"]	string	(Optional) Ethnicity of the donor as self-reported, relevant for studies considering genetic diversity and population-specific traits.
obs["self_reported_ethnicity_ontology_term_id"]	string	(Optional) Ontology term identifier for the self-reported ethnicity, providing a standardized reference for ethnic classifications. If the organism is human (organism_ontology_term_id == 'NCBITaxon:9606'), then the Human Ancestry Ontology (HANCESTRO:) is used.
obs["sex"]	string	(Optional) Biological sex of the donor or source organism, crucial for studies involving sex-specific traits or conditions.
obs["sex_ontology_term_id"]	string	(Optional) Ontology term identifier for the biological sex, ensuring standardized classification of sex. Only PATO:0000383, PATO:0000384 and PATO:0001340 are allowed.
obs["suspension_type"]	string	(Optional) Type of suspension or medium in which the cells were stored or processed, important for understanding cell handling and conditions.
obs["tissue"]	string	(Optional) Specific tissue from which the cells were derived, key for context and specificity in cell studies.
obs["tissue_ontology_term_id"]	string	(Optional) Ontology term identifier for the tissue, providing a standardized reference for the tissue type. For organoid or tissue samples, the Uber-anatomy ontology (UBERON:) is used. The term ids must be a child term of UBERON:0001062 (anatomical entity). For cell cultures, the Cell Ontology (CL:) is used. The term ids cannot be CL:0000255, CL:0000257 or CL:0000548.
obs["tissue_general"]	string	(Optional) General category or classification of the tissue, useful for broader grouping and comparison of cell data.
obs["tissue_general_ontology_term_id"]	string	(Optional) Ontology term identifier for the general tissue category, aiding in standardizing and grouping tissue types. For organoid or tissue samples, the Uber-anatomy ontology (UBERON:) is used. The term ids must be a child term of UBERON:0001062 (anatomical entity). For cell cultures, the Cell Ontology (CL:) is used. The term ids cannot be CL:0000255, CL:0000257 or CL:0000548.
obs["batch"]	string	(Optional) A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc.
obs["soma_joinid"]	integer	(Optional) If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the cell.
obs["size_factors"]	double	(Optional) The size factors created by the normalisation method, if any.
var["feature_id"]	string	(Optional) Unique identifier for the feature, usually a ENSEMBL gene id.
var["feature_name"]	string	A human-readable name for the feature, usually a gene symbol.
var["soma_joinid"]	integer	(Optional) If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the feature.
var["hvg"]	boolean	Whether or not the feature is considered to be a ‘highly variable gene’.
var["hvg_score"]	double	A score for the feature indicating how highly variable it is.
obsm["X_pca"]	double	The resulting PCA embedding.
obsp["knn_distances"]	double	K nearest neighbors distance matrix.
obsp["knn_connectivities"]	double	K nearest neighbors connectivities matrix.
varm["pca_loadings"]	double	The PCA loadings matrix.
layers["counts"]	integer	Raw counts.
layers["normalized"]	double	Normalised expression values.
uns["dataset_id"]	string	A unique identifier for the dataset. This is different from the obs.dataset_id field, which is the identifier for the dataset from which the cell data is derived.
uns["dataset_name"]	string	A human-readable name for the dataset.
uns["dataset_url"]	string	(Optional) Link to the original source of the dataset.
uns["dataset_reference"]	string	(Optional) Bibtex reference of the paper in which the dataset was published.
uns["dataset_summary"]	string	Short description of the dataset.
uns["dataset_description"]	string	Long description of the dataset.
uns["dataset_organism"]	string	(Optional) The organism of the sample in the dataset.
uns["normalization_id"]	string	Which normalization was used.
uns["pca_variance"]	double	The PCA variance objects.
uns["knn"]	object	Supplementary K nearest neighbors data.

Component type: Subset

Path: src/datasets/processors

Sample cells and genes randomly.

Arguments:

Name	Type	Description
--input	file	A dataset processed by the common dataset processing pipeline.
--input_mod2	file	(Optional) A dataset processed by the common dataset processing pipeline.
--output	file	(Output) A dataset processed by the common dataset processing pipeline.
--output_mod2	file	(Optional, Output) A dataset processed by the common dataset processing pipeline.