FilterStates R6 class

FilteredDataset is a class which renders/controls FilterStates(s) Each FilteredDataset contains filter_states field - a list which contains one (data.frame) or multiple (MultiAssayExperiment) FilterStates objects. Each FilterStates is responsible for one filter/subset expression applied for specific components of the dataset.

Methods

Method `new()`

Initializes this FilteredDataset object

Usage

FilteredDataset$new(
  dataset,
  dataname,
  keys = character(0),
  label = attr(dataset, "label"),
  metadata = NULL
)

Arguments

dataset: (data.frame or MultiAssayExperiment)
single dataset for which filters are rendered
dataname: (character(1))
A given name for the dataset it may not contain spaces
keys: optional, (character)
Vector with primary keys
label: (character(1))
Label to describe the dataset
metadata: (named list or NULL)
Field containing metadata about the dataset. Each element of the list should be atomic and length one.

Method `get_formatted_filter_state()`

Returns a string representation of the filter state in this FilteredDataset.

Usage

FilteredDataset$get_formatted_filter_state()

Returns

character(1) the formatted string representing the filter state

Method `queues_empty()`

Removes all active filter items applied to this dataset

Usage

FilteredDataset$queues_empty()

Returns

NULL

Method `get_call()`

Gets a filter expression

This functions returns filter calls equivalent to selected items within each of filter_states. Configuration of the calls is constant and depends on filter_states type and order which are set during initialization.

Usage

FilteredDataset$get_call()

Returns

filter call or list of filter calls Gets the reactive values from the active FilterState objects.

Get all active filters from this dataset in form of the nested list. The output list is a compatible input to self$set_filter_state.

Method `get_filter_state()`

Usage

FilteredDataset$get_filter_state()

Returns

list with named elements corresponding to FilterStates objects with active filters.

Method `get_filter_states()`

Gets the active FilterStates objects.

Usage

FilteredDataset$get_filter_states(id = character(0))

Arguments

id: (character(1), character(0))
the id of the private$filter_states list element where FilterStates is kept.

Returns

FilterStates or list of FilterStates objects.

Method `get_dataname()`

Get name of the dataset

Usage

FilteredDataset$get_dataname()

Returns

character(1) as a name of this dataset

Method `get_dataset()`

Gets the dataset object in this FilteredDataset

Usage

FilteredDataset$get_dataset()

Returns

data.frame or MultiAssayExperiment

Method `get_metadata()`

Gets the metadata for the dataset in this FilteredDataset

Usage

FilteredDataset$get_metadata()

Returns

named list or NULL

Method `get_filter_overview_info()`

Get filter overview rows of a dataset The output shows the comparison between filtered_dataset function parameter and the dataset inside self

Usage

FilteredDataset$get_filter_overview_info(filtered_dataset = self$get_dataset())

Arguments

filtered_dataset: comparison object, of the same class as self$get_dataset(), if NULL then self$get_dataset() is used.

Returns

(matrix) matrix of observations and subjects

Method `get_hash()`

Returns the hash of the dataset

Usage

FilteredDataset$get_hash()

Returns

(character(1)) the hash

Method `get_keys()`

Gets the keys for the dataset of this FilteredDataset

Usage

FilteredDataset$get_keys()

Returns

(character) the keys of dataset

Method `get_varlabels()`

Gets labels of variables in the data

Variables are the column names of the data. Either, all labels must have been provided for all variables in set_data or NULL.

Usage

FilteredDataset$get_varlabels(variables = NULL)

Arguments

variables: (character vector) variables to get labels for; if NULL, for all variables in data

Returns

(character or NULL) variable labels, NULL if column_labels attribute does not exist for the data

Method `get_dataset_label()`

Gets the dataset label

Usage

FilteredDataset$get_dataset_label()

Returns

(character) the dataset label

Method `get_varnames()`

Gets variable names from dataset

Usage

FilteredDataset$get_varnames()

Returns

character the variable names

Method `get_filtered_dataname()`

Gets the suffixed dataname Used when filtering the data to get <dataname>_FILTERED, <dataname>_FILTERED_ALONE or any other name.

Usage

FilteredDataset$get_filtered_dataname(
  dataname = self$get_dataname(),
  suffix = "_FILTERED"
)

Arguments

dataname: (character(1)) dataname
suffix: (character(1)) string to be putted after dataname

Returns

character(1)

Method `get_filterable_varnames()`

Gets variable names for the filtering.

Usage

FilteredDataset$get_filterable_varnames()

Returns

(character vector) of variable names

Method `ui()`

UI module for dataset active filters

UI module containing dataset active filters along with title and remove button.

Usage

FilteredDataset$ui(id)

Arguments

id: (character(1))
identifier of the element - preferably containing dataset name

Returns

function - shiny UI module

Method `server()`

Server module for a dataset active filters

Server module managing a active filters.

Usage

FilteredDataset$server(id)

Arguments

id: (character(1))
an ID string that corresponds with the ID used to call the module's UI function.

Returns

moduleServer function which returns NULL

Method `ui_add_filter_state()`

UI module to add filter variable for this dataset

Usage

FilteredDataset$ui_add_filter_state(id)

Arguments

id: (character(1))
identifier of the element - preferably containing dataset name

Returns

function - shiny UI module

Method `srv_add_filter_state()`

Server module to add filter variable for this dataset

Usage

FilteredDataset$srv_add_filter_state(id, ...)

Arguments

id: (character(1))
an ID string that corresponds with the ID used to call the module's UI function.
...: ignored

Returns

moduleServer function.

Method `clone()`

The objects of this class are cloneable with this method.

Usage

FilteredDataset$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Methods

Public methods

Method new()

Usage

Arguments

Method get_formatted_filter_state()

Usage

Returns

Method queues_empty()

Usage

Returns

Method get_call()

Usage

Returns

Method get_filter_state()

Usage

Returns

Method get_filter_states()

Usage

Arguments

Returns

Method get_dataname()

Usage

Returns

Method get_dataset()

Usage

Returns

Method get_metadata()

Usage

Returns

Method get_filter_overview_info()

Usage

Arguments

Returns

Method get_hash()

Usage

Returns

Method get_keys()

Usage

Returns

Method get_varlabels()

Usage

Arguments

Returns

Method get_dataset_label()

Usage

Returns

Method get_varnames()

Usage

Returns

Method get_filtered_dataname()

Usage

Arguments

Returns

Method get_filterable_varnames()

Usage

Returns

Method ui()

Usage

Arguments

Returns

Method server()

Usage

Arguments

Returns

Method ui_add_filter_state()

Usage

Arguments

Returns

Method srv_add_filter_state()

Usage

Arguments

Returns

Method clone()

Usage

Arguments

`FilterStates` R6 class

Method `new()`

Method `get_formatted_filter_state()`

Method `queues_empty()`

Method `get_call()`

Method `get_filter_state()`

Method `get_filter_states()`

Method `get_dataname()`

Method `get_dataset()`

Method `get_metadata()`

Method `get_filter_overview_info()`

Method `get_hash()`

Method `get_keys()`

Method `get_varlabels()`

Method `get_dataset_label()`

Method `get_varnames()`

Method `get_filtered_dataname()`

Method `get_filterable_varnames()`

Method `ui()`

Method `server()`

Method `ui_add_filter_state()`

Method `srv_add_filter_state()`

Method `clone()`