AbstractWrapper: AbstractWrapper Class
In vitessce/vitessce-r: Create Interactive Single-cell Visualizations with the 'Vitessce' JavaScript Library
AbstractWrapper R Documentation
AbstractWrapper Class
Description
Abstract class representing a local dataset object in a Vitessce dataset.
Details
Abstract dataset object wrapper class
Public fields
out_dirThe directory for processed output files.
use_cacheIf converted output files already exist, should they be used?
is_remoteIs the data object fully remote?
routesA list of VitessceConfigServerRoute objects.
file_def_creatorsA list of file definition creator functions.
base_dirThe base directory for local data.
Methods
Public methods
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Method new()
Create an abstract wrapper around a data object.
Usage
AbstractWrapper$new(out_dir = NA, use_cache = FALSE)
Arguments
out_dirThe directory for processed output files.
use_cacheIf converted output files already exist, should they be used? By default, FALSE.
Returns
A new AbstractWrapper object.
Method convert_and_save()
Fill in the file_def_creators array.
Each function added to this list should take in a base URL and generate a Vitessce file definition.
If this wrapper is wrapping local data, then create routes and fill in the routes array.
This method is void, should not return anything.
Usage
AbstractWrapper$convert_and_save(dataset_uid, obj_i, base_dir = NA)
Arguments
dataset_uidA unique identifier for this dataset.
obj_iWithin the dataset, the index of this data wrapper object.
base_dirPath to a base directory.
Method get_routes()
Obtain the routes that have been created for this wrapper class.
Usage
AbstractWrapper$get_routes()
Returns
A list of server routes.
Method get_file_defs()
Obtain the file definitions for this wrapper class.
Usage
AbstractWrapper$get_file_defs(base_url)
Arguments
base_urlA base URL to prepend to relative URLs.
Returns
A list of server routes.
Method get_out_dir_route()
Create a web server route for this object.
Usage
AbstractWrapper$get_out_dir_route(dataset_uid, obj_i)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
Returns
A new VitessceConfigServerStaticRoute instance.
Method get_local_dir_url()
Construct a URL to a local directory.
Usage
AbstractWrapper$get_local_dir_url(
base_url,
dataset_uid,
obj_i,
local_dir_path,
local_dir_uid
)
Arguments
base_urlThe base URL on which the web server is serving.
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
local_dir_pathThe path to the local directory.
local_dir_uidA unique identifier for this local directory in this dataset.
Returns
A string for the URL.
Method get_local_file_url()
Construct a URL to a local file.
Usage
AbstractWrapper$get_local_file_url(
base_url,
dataset_uid,
obj_i,
local_file_path,
local_file_uid
)
Arguments
base_urlThe base URL on which the web server is serving.
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
local_file_pathThe path to the local file.
local_file_uidA unique identifier for this local file in this dataset.
Returns
A string for the URL.
Method get_local_dir_route()
Create a web server route for this object.
Usage
AbstractWrapper$get_local_dir_route(
dataset_uid,
obj_i,
local_dir_path,
local_dir_uid
)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
local_dir_pathThe path to the local directory.
local_dir_uidA unique identifier for this local directory in this dataset.
Returns
A new VitessceConfigServerStaticRoute instance.
Method get_local_file_route()
Create a web server route for this object.
Usage
AbstractWrapper$get_local_file_route(
dataset_uid,
obj_i,
local_file_path,
local_file_uid
)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
local_file_pathThe path to the local file.
local_file_uidA unique identifier for this local file in this dataset.
Returns
A new VitessceConfigServerFileRoute instance.
Method get_url()
Create a local web server URL for a dataset object.
Usage
AbstractWrapper$get_url(base_url, dataset_uid, obj_i, ...)
Arguments
base_urlThe base URL on which the web server is serving.
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
...Passes extra arguments to get_route_str
Returns
A URL as a string.
Method get_url_simple()
Construct a URL.
Usage
AbstractWrapper$get_url_simple(base_url, suffix)
Arguments
base_urlThe base URL on which the web server is serving.
suffixThe suffix to append to the base URL.
Returns
A URL as a string like base_url/suffix
Method get_route_str()
Create a string representing a web server route path (the part following the base URL).
Usage
AbstractWrapper$get_route_str(dataset_uid, obj_i, ...)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
...Pastes extra arguments together after obj_i, separated by slash.
Returns
A path as a string.
Method get_out_dir()
Create a directory path to a dataset within the base output directory.
Usage
AbstractWrapper$get_out_dir(dataset_uid, obj_i, ...)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
...Passes extra arguments to file.path
Returns
A path as a string.
Method auto_view_config()
Automatically configure views for a particular dataset.
Usage
AbstractWrapper$auto_view_config(vc)
Arguments
vcA VitessceConfig instance to configure.
Method clone()
The objects of this class are cloneable with this method.
Usage
AbstractWrapper$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
vitessce/vitessce-r documentation built on Oct. 12, 2024, 11:47 p.m.
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| AbstractWrapper | R Documentation |
AbstractWrapper Class
Description
Abstract class representing a local dataset object in a Vitessce dataset.
Details
Abstract dataset object wrapper class
Public fields
out_dirThe directory for processed output files.
use_cacheIf converted output files already exist, should they be used?
is_remoteIs the data object fully remote?
routesA list of
VitessceConfigServerRouteobjects.file_def_creatorsA list of file definition creator functions.
base_dirThe base directory for local data.
Methods
Public methods
Method new()
Create an abstract wrapper around a data object.
Usage
AbstractWrapper$new(out_dir = NA, use_cache = FALSE)
Arguments
out_dirThe directory for processed output files.
use_cacheIf converted output files already exist, should they be used? By default, FALSE.
Returns
A new AbstractWrapper object.
Method convert_and_save()
Fill in the file_def_creators array. Each function added to this list should take in a base URL and generate a Vitessce file definition. If this wrapper is wrapping local data, then create routes and fill in the routes array. This method is void, should not return anything.
Usage
AbstractWrapper$convert_and_save(dataset_uid, obj_i, base_dir = NA)
Arguments
dataset_uidA unique identifier for this dataset.
obj_iWithin the dataset, the index of this data wrapper object.
base_dirPath to a base directory.
Method get_routes()
Obtain the routes that have been created for this wrapper class.
Usage
AbstractWrapper$get_routes()
Returns
A list of server routes.
Method get_file_defs()
Obtain the file definitions for this wrapper class.
Usage
AbstractWrapper$get_file_defs(base_url)
Arguments
base_urlA base URL to prepend to relative URLs.
Returns
A list of server routes.
Method get_out_dir_route()
Create a web server route for this object.
Usage
AbstractWrapper$get_out_dir_route(dataset_uid, obj_i)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
Returns
A new VitessceConfigServerStaticRoute instance.
Method get_local_dir_url()
Construct a URL to a local directory.
Usage
AbstractWrapper$get_local_dir_url( base_url, dataset_uid, obj_i, local_dir_path, local_dir_uid )
Arguments
base_urlThe base URL on which the web server is serving.
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
local_dir_pathThe path to the local directory.
local_dir_uidA unique identifier for this local directory in this dataset.
Returns
A string for the URL.
Method get_local_file_url()
Construct a URL to a local file.
Usage
AbstractWrapper$get_local_file_url( base_url, dataset_uid, obj_i, local_file_path, local_file_uid )
Arguments
base_urlThe base URL on which the web server is serving.
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
local_file_pathThe path to the local file.
local_file_uidA unique identifier for this local file in this dataset.
Returns
A string for the URL.
Method get_local_dir_route()
Create a web server route for this object.
Usage
AbstractWrapper$get_local_dir_route( dataset_uid, obj_i, local_dir_path, local_dir_uid )
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
local_dir_pathThe path to the local directory.
local_dir_uidA unique identifier for this local directory in this dataset.
Returns
A new VitessceConfigServerStaticRoute instance.
Method get_local_file_route()
Create a web server route for this object.
Usage
AbstractWrapper$get_local_file_route( dataset_uid, obj_i, local_file_path, local_file_uid )
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
local_file_pathThe path to the local file.
local_file_uidA unique identifier for this local file in this dataset.
Returns
A new VitessceConfigServerFileRoute instance.
Method get_url()
Create a local web server URL for a dataset object.
Usage
AbstractWrapper$get_url(base_url, dataset_uid, obj_i, ...)
Arguments
base_urlThe base URL on which the web server is serving.
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
...Passes extra arguments to
get_route_str
Returns
A URL as a string.
Method get_url_simple()
Construct a URL.
Usage
AbstractWrapper$get_url_simple(base_url, suffix)
Arguments
base_urlThe base URL on which the web server is serving.
suffixThe suffix to append to the base URL.
Returns
A URL as a string like base_url/suffix
Method get_route_str()
Create a string representing a web server route path (the part following the base URL).
Usage
AbstractWrapper$get_route_str(dataset_uid, obj_i, ...)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
...Pastes extra arguments together after
obj_i, separated by slash.
Returns
A path as a string.
Method get_out_dir()
Create a directory path to a dataset within the base output directory.
Usage
AbstractWrapper$get_out_dir(dataset_uid, obj_i, ...)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
...Passes extra arguments to
file.path
Returns
A path as a string.
Method auto_view_config()
Automatically configure views for a particular dataset.
Usage
AbstractWrapper$auto_view_config(vc)
Arguments
vcA
VitessceConfiginstance to configure.
Method clone()
The objects of this class are cloneable with this method.
Usage
AbstractWrapper$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
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