AnnDataWrapper: AnnDataWrapper Class
In vitessce/vitessceR: Create Interactive Single-cell Visualizations with the 'Vitessce' JavaScript Library
AnnDataWrapper R Documentation
AnnDataWrapper Class
Description
Class representing an AnnData object (saved to a Zarr store) in a Vitessce dataset.
Details
AnnData object wrapper class
Super class
vitessceR::AbstractWrapper -> AnnDataWrapper
Public fields
adata_pathThe object to wrap.
adata_urlThe object to wrap.
local_dir_uidThe path to the local zarr store.
obs_feature_matrix_pathThe path to the observation-by-feature matrix within the Zarr store.
feature_filter_pathThe path to the a column of adata.var within the Zarr store.
Use this if obs_feature_matrix_path points to a subset of adata.X (relative to the full adata.var).
initial_feature_filter_pathThe path to the a column of adata.var within the Zarr store.
Use this to load a subset of the matrix at obs_feature_matrix_path initially.
obs_set_pathsA list of paths to the observation sets within the Zarr store.
obs_set_namesA list of names for the observation sets.
obs_locations_pathThe path to the observation locations within the Zarr store.
obs_segmentations_pathThe path to the observation segmentations within the Zarr store.
obs_embedding_pathsA list of paths to the observation embeddings within the Zarr store.
obs_embedding_namesA list of names for the observation embeddings.
obs_embedding_dimsA list of dimensions for the observation embeddings.
feature_labels_pathThe path to the feature labels within the Zarr store.
obs_labels_pathThe path to the observation labels within the Zarr store.
obs_labels_pathsA list of paths to the observation labels within the Zarr store.
obs_labels_namesA list of names for the observation labels.
coordination_valuesA list of coordination values for the file definition.
request_initA list of requestInit options for the Zarr store.
Methods
Public methods
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Inherited methods
vitessceR::AbstractWrapper$auto_view_config()vitessceR::AbstractWrapper$get_file_defs()vitessceR::AbstractWrapper$get_local_dir_route()vitessceR::AbstractWrapper$get_local_dir_url()vitessceR::AbstractWrapper$get_local_file_route()vitessceR::AbstractWrapper$get_local_file_url()vitessceR::AbstractWrapper$get_out_dir()vitessceR::AbstractWrapper$get_out_dir_route()vitessceR::AbstractWrapper$get_route_str()vitessceR::AbstractWrapper$get_routes()vitessceR::AbstractWrapper$get_url()vitessceR::AbstractWrapper$get_url_simple()
Method new()
Create a wrapper around an AnnData object saved to a Zarr store.
Usage
AnnDataWrapper$new(
adata_path = NA,
adata_url = NA,
obs_feature_matrix_path = NA,
feature_filter_path = NA,
initial_feature_filter_path = NA,
obs_set_paths = NA,
obs_set_names = NA,
obs_locations_path = NA,
obs_segmentations_path = NA,
obs_embedding_paths = NA,
obs_embedding_names = NA,
obs_embedding_dims = NA,
request_init = NA,
feature_labels_path = NA,
coordination_values = NA,
obs_labels_paths = NA,
obs_labels_names = NA,
...
)
Arguments
adata_pathThe path to a local Zarr store.
adata_urlThe URL to a remote Zarr store.
obs_feature_matrix_pathThe path to the observation-by-feature matrix within the Zarr store.
feature_filter_pathThe path to the a column of adata.var within the Zarr store. Use this if obs_feature_matrix_path points to a subset of adata.X (relative to the full adata.var).
initial_feature_filter_pathThe path to the a column of adata.var within the Zarr store. Use this to load a subset of the matrix at obs_feature_matrix_path initially.
obs_set_pathsA list of paths to the observation sets within the Zarr store.
obs_set_namesA list of names for the observation sets.
obs_locations_pathThe path to the observation locations within the Zarr store.
obs_segmentations_pathThe path to the observation segmentations within the Zarr store.
obs_embedding_pathsA list of paths to the observation embeddings within the Zarr store.
obs_embedding_namesA list of names for the observation embeddings.
obs_embedding_dimsA list of dimensions for the observation embeddings.
request_initA list of requestInit options for the Zarr store.
feature_labels_pathThe path to the feature labels within the Zarr store.
coordination_valuesA list of coordination values for the file definition.
obs_labels_pathsA list of paths to the observation labels within the Zarr store.
obs_labels_namesA list of names for the observation labels.
...Parameters inherited from AbstractWrapper.
Returns
A new AnnDataWrapper object.
Method convert_and_save()
Create the JSON output files, web server routes, and file definition creators.
Usage
AnnDataWrapper$convert_and_save(dataset_uid, obj_i, base_dir = NA)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
base_dirA base directory for local data.
Method make_routes()
Get a list of server route objects.
Usage
AnnDataWrapper$make_routes(dataset_uid, obj_i)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
Method get_zarr_url()
Get the URL to the Zarr store, to fill in the file URL in the file definitions.
Usage
AnnDataWrapper$get_zarr_url(base_url, dataset_uid, obj_i)
Arguments
base_urlThe base URL, on which the route will be served.
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
Returns
A URL as a string.
Method make_file_def_creator()
Make the file definition creator function for the cells data type.
Usage
AnnDataWrapper$make_file_def_creator(dataset_uid, obj_i)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
Returns
A file definition creator function which takes a base_url parameter.
Method clone()
The objects of this class are cloneable with this method.
Usage
AnnDataWrapper$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
vitessce/vitessceR documentation built on Oct. 12, 2024, 12:24 a.m.
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| AnnDataWrapper | R Documentation |
AnnDataWrapper Class
Description
Class representing an AnnData object (saved to a Zarr store) in a Vitessce dataset.
Details
AnnData object wrapper class
Super class
vitessceR::AbstractWrapper -> AnnDataWrapper
Public fields
adata_pathThe object to wrap.
adata_urlThe object to wrap.
local_dir_uidThe path to the local zarr store.
obs_feature_matrix_pathThe path to the observation-by-feature matrix within the Zarr store.
feature_filter_pathThe path to the a column of adata.var within the Zarr store. Use this if obs_feature_matrix_path points to a subset of adata.X (relative to the full adata.var).
initial_feature_filter_pathThe path to the a column of adata.var within the Zarr store. Use this to load a subset of the matrix at obs_feature_matrix_path initially.
obs_set_pathsA list of paths to the observation sets within the Zarr store.
obs_set_namesA list of names for the observation sets.
obs_locations_pathThe path to the observation locations within the Zarr store.
obs_segmentations_pathThe path to the observation segmentations within the Zarr store.
obs_embedding_pathsA list of paths to the observation embeddings within the Zarr store.
obs_embedding_namesA list of names for the observation embeddings.
obs_embedding_dimsA list of dimensions for the observation embeddings.
feature_labels_pathThe path to the feature labels within the Zarr store.
obs_labels_pathThe path to the observation labels within the Zarr store.
obs_labels_pathsA list of paths to the observation labels within the Zarr store.
obs_labels_namesA list of names for the observation labels.
coordination_valuesA list of coordination values for the file definition.
request_initA list of requestInit options for the Zarr store.
Methods
Public methods
Inherited methods
vitessceR::AbstractWrapper$auto_view_config()vitessceR::AbstractWrapper$get_file_defs()vitessceR::AbstractWrapper$get_local_dir_route()vitessceR::AbstractWrapper$get_local_dir_url()vitessceR::AbstractWrapper$get_local_file_route()vitessceR::AbstractWrapper$get_local_file_url()vitessceR::AbstractWrapper$get_out_dir()vitessceR::AbstractWrapper$get_out_dir_route()vitessceR::AbstractWrapper$get_route_str()vitessceR::AbstractWrapper$get_routes()vitessceR::AbstractWrapper$get_url()vitessceR::AbstractWrapper$get_url_simple()
Method new()
Create a wrapper around an AnnData object saved to a Zarr store.
Usage
AnnDataWrapper$new( adata_path = NA, adata_url = NA, obs_feature_matrix_path = NA, feature_filter_path = NA, initial_feature_filter_path = NA, obs_set_paths = NA, obs_set_names = NA, obs_locations_path = NA, obs_segmentations_path = NA, obs_embedding_paths = NA, obs_embedding_names = NA, obs_embedding_dims = NA, request_init = NA, feature_labels_path = NA, coordination_values = NA, obs_labels_paths = NA, obs_labels_names = NA, ... )
Arguments
adata_pathThe path to a local Zarr store.
adata_urlThe URL to a remote Zarr store.
obs_feature_matrix_pathThe path to the observation-by-feature matrix within the Zarr store.
feature_filter_pathThe path to the a column of adata.var within the Zarr store. Use this if obs_feature_matrix_path points to a subset of adata.X (relative to the full adata.var).
initial_feature_filter_pathThe path to the a column of adata.var within the Zarr store. Use this to load a subset of the matrix at obs_feature_matrix_path initially.
obs_set_pathsA list of paths to the observation sets within the Zarr store.
obs_set_namesA list of names for the observation sets.
obs_locations_pathThe path to the observation locations within the Zarr store.
obs_segmentations_pathThe path to the observation segmentations within the Zarr store.
obs_embedding_pathsA list of paths to the observation embeddings within the Zarr store.
obs_embedding_namesA list of names for the observation embeddings.
obs_embedding_dimsA list of dimensions for the observation embeddings.
request_initA list of requestInit options for the Zarr store.
feature_labels_pathThe path to the feature labels within the Zarr store.
coordination_valuesA list of coordination values for the file definition.
obs_labels_pathsA list of paths to the observation labels within the Zarr store.
obs_labels_namesA list of names for the observation labels.
...Parameters inherited from
AbstractWrapper.
Returns
A new AnnDataWrapper object.
Method convert_and_save()
Create the JSON output files, web server routes, and file definition creators.
Usage
AnnDataWrapper$convert_and_save(dataset_uid, obj_i, base_dir = NA)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
base_dirA base directory for local data.
Method make_routes()
Get a list of server route objects.
Usage
AnnDataWrapper$make_routes(dataset_uid, obj_i)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
Method get_zarr_url()
Get the URL to the Zarr store, to fill in the file URL in the file definitions.
Usage
AnnDataWrapper$get_zarr_url(base_url, dataset_uid, obj_i)
Arguments
base_urlThe base URL, on which the route will be served.
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
Returns
A URL as a string.
Method make_file_def_creator()
Make the file definition creator function for the cells data type.
Usage
AnnDataWrapper$make_file_def_creator(dataset_uid, obj_i)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
Returns
A file definition creator function which takes a base_url parameter.
Method clone()
The objects of this class are cloneable with this method.
Usage
AnnDataWrapper$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
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