FilterStates: 'FilterStates' 'R6' class
In teal.slice: Filter Module for 'teal' Applications
FilterStates R Documentation
FilterStates R6 class
Description
Abstract class that manages adding and removing FilterState objects
and builds a subset expression.
A FilterStates object tracks all condition calls
(logical predicates that limit observations) associated with a given dataset
and composes them into a single reproducible R expression
that will assign a subset of the original data to a new variable.
This expression is hereafter referred to as subset expression.
The subset expression is constructed differently for different
classes of the underlying data object and FilterStates sub-classes.
Currently implemented for data.frame, matrix,
SummarizedExperiment, and MultiAssayExperiment.
Methods
Public methods
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Method new()
Initializes FilterStates object by setting
dataname, and datalabel.
Usage
FilterStates$new(
data,
data_reactive = function(sid = "") NULL,
dataname,
datalabel = NULL
)
Arguments
data(data.frame or MultiAssayExperiment or SummarizedExperiment or matrix)
the R object which subset function is applied on.
data_reactive(function(sid))
should return an object of the same type as data object or NULL.
This object is needed for the FilterState counts being updated
on a change in filters. If function returns NULL then filtered counts are not shown.
Function has to have sid argument being a character.
dataname(character(1))
name of the dataset, used in the subset expression.
Passed to the function argument attached to this FilterStates.
datalabel(character(1)) optional
text label.
Returns
Object of class FilterStates, invisibly.
Method format()
Returns a formatted string representing this FilterStates object.
Usage
FilterStates$format(show_all = FALSE, trim_lines = TRUE)
Arguments
show_all(logical(1)) passed to format.teal_slices
trim_lines(logical(1)) passed to format.teal_slices
Returns
character(1) the formatted string
Method get_call()
Filter call
Builds subset expression from condition calls generated by FilterState.
The lhs of the expression is a dataname_prefixed, where word prefixed refers to
situation when call is evaluated on elements of the original data, for example dataname[[x]].
By default dataname_prefixed = dataname and it's not alterable through class methods.
Customization of private$dataname_prefixed is done through inheriting classes.
The rhs is a call to private$fun with following arguments:
-
dataname_prefixed
list of logical expressions generated by FilterState objects
stored in private$state_list. Each logical predicate is combined with & operator.
Variables in these logical expressions by default are not prefixed but this can be changed
by setting private$extract_type (change in the similar way as dataname_prefixed)
Possible call outputs depending on a custom fields/options:
# default
dataname <- subset(dataname, col == "x")
# fun = dplyr::filter
dataname <- dplyr::filter(dataname, col == "x")
# fun = MultiAssayExperiment::subsetByColData; extract_type = "list"
dataname <- MultiAssayExperiment::subsetByColData(dataname, dataname$col == "x")
# teal_slice objects having `arg = "subset"` and `arg = "select"`
dataname <- subset(dataname, subset = row_col == "x", select = col_col == "x")
# dataname = dataname[[element]]
dataname[[element]] <- subset(dataname[[element]], subset = col == "x")
If no filters are applied, NULL is returned to avoid no-op calls such as dataname <- dataname.
Usage
FilterStates$get_call(sid = "")
Arguments
sid(character)
when specified then method returns code containing condition calls (logical predicates) of
FilterState objects which "sid" attribute is different than this sid argument.
Returns
call or NULL
Method print()
Prints this FilterStates object.
Usage
FilterStates$print(...)
Arguments
...additional arguments passed to format.
Method remove_filter_state()
Remove one or more FilterStates from the state_list along with their UI elements.
Usage
FilterStates$remove_filter_state(state)
Arguments
state(teal_slices)
specifying FilterState objects to remove;
teal_slices may contain only dataname and varname, other elements are ignored
Returns
NULL, invisibly.
Method get_filter_state()
Gets reactive values from active FilterState objects.
Get active filter state from FilterState objects stored in state_list(s).
The output is a list compatible with input to self$set_filter_state.
Usage
FilterStates$get_filter_state()
Returns
Object of class teal_slices.
Method set_filter_state()
Sets active FilterState objects.
Usage
FilterStates$set_filter_state(state)
Arguments
state(teal_slices)
Returns
Function that raises an error.
Method clear_filter_states()
Remove all FilterState objects from this FilterStates object.
Usage
FilterStates$clear_filter_states(force = FALSE)
Arguments
force(logical(1))
flag specifying whether to include anchored filter states.
Returns
NULL, invisibly.
Method ui_active()
shiny UI definition that stores FilterState UI elements.
Populated with elements created with renderUI in the module server.
Usage
FilterStates$ui_active(id)
Arguments
id(character(1))
shiny module instance id.
Returns
shiny.tag
Method srv_active()
shiny server module.
Usage
FilterStates$srv_active(id)
Arguments
id(character(1))
shiny module instance id.
Returns
NULL.
Method ui_add()
shiny UI module to add filter variable.
Usage
FilterStates$ui_add(id)
Arguments
id(character(1))
shiny module instance id.
Returns
shiny.tag
Method srv_add()
shiny server module to add filter variable.
This module controls available choices to select as a filter variable.
Once selected, a variable is removed from available choices.
Removing a filter variable adds it back to available choices.
Usage
FilterStates$srv_add(id)
Arguments
id(character(1))
shiny module instance id.
Returns
NULL.
Method clone()
The objects of this class are cloneable with this method.
Usage
FilterStates$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
teal.slice documentation built on May 29, 2024, 1:39 a.m.
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| FilterStates | R Documentation |
FilterStates R6 class
Description
Abstract class that manages adding and removing FilterState objects
and builds a subset expression.
A FilterStates object tracks all condition calls
(logical predicates that limit observations) associated with a given dataset
and composes them into a single reproducible R expression
that will assign a subset of the original data to a new variable.
This expression is hereafter referred to as subset expression.
The subset expression is constructed differently for different
classes of the underlying data object and FilterStates sub-classes.
Currently implemented for data.frame, matrix,
SummarizedExperiment, and MultiAssayExperiment.
Methods
Public methods
Method new()
Initializes FilterStates object by setting
dataname, and datalabel.
Usage
FilterStates$new( data, data_reactive = function(sid = "") NULL, dataname, datalabel = NULL )
Arguments
data(
data.frameorMultiAssayExperimentorSummarizedExperimentormatrix) theRobject whichsubsetfunction is applied on.data_reactive(
function(sid)) should return an object of the same type asdataobject orNULL. This object is needed for theFilterStatecounts being updated on a change in filters. If function returnsNULLthen filtered counts are not shown. Function has to havesidargument being a character.dataname(
character(1)) name of the dataset, used in the subset expression. Passed to the function argument attached to thisFilterStates.datalabel(
character(1)) optional text label.
Returns
Object of class FilterStates, invisibly.
Method format()
Returns a formatted string representing this FilterStates object.
Usage
FilterStates$format(show_all = FALSE, trim_lines = TRUE)
Arguments
show_all(
logical(1)) passed toformat.teal_slicestrim_lines(
logical(1)) passed toformat.teal_slices
Returns
character(1) the formatted string
Method get_call()
Filter call
Builds subset expression from condition calls generated by FilterState.
The lhs of the expression is a dataname_prefixed, where word prefixed refers to
situation when call is evaluated on elements of the original data, for example dataname[[x]].
By default dataname_prefixed = dataname and it's not alterable through class methods.
Customization of private$dataname_prefixed is done through inheriting classes.
The rhs is a call to private$fun with following arguments:
-
dataname_prefixed list of logical expressions generated by
FilterStateobjects stored inprivate$state_list. Each logical predicate is combined with&operator. Variables in these logical expressions by default are not prefixed but this can be changed by settingprivate$extract_type(change in the similar way asdataname_prefixed) Possible call outputs depending on a custom fields/options:
# default dataname <- subset(dataname, col == "x") # fun = dplyr::filter dataname <- dplyr::filter(dataname, col == "x") # fun = MultiAssayExperiment::subsetByColData; extract_type = "list" dataname <- MultiAssayExperiment::subsetByColData(dataname, dataname$col == "x") # teal_slice objects having `arg = "subset"` and `arg = "select"` dataname <- subset(dataname, subset = row_col == "x", select = col_col == "x") # dataname = dataname[[element]] dataname[[element]] <- subset(dataname[[element]], subset = col == "x")
If no filters are applied, NULL is returned to avoid no-op calls such as dataname <- dataname.
Usage
FilterStates$get_call(sid = "")
Arguments
sid(
character) when specified then method returns code containing condition calls (logical predicates) ofFilterStateobjects which"sid"attribute is different than thissidargument.
Returns
call or NULL
Method print()
Prints this FilterStates object.
Usage
FilterStates$print(...)
Arguments
...additional arguments passed to
format.
Method remove_filter_state()
Remove one or more FilterStates from the state_list along with their UI elements.
Usage
FilterStates$remove_filter_state(state)
Arguments
state(
teal_slices) specifyingFilterStateobjects to remove;teal_slices may contain onlydatanameandvarname, other elements are ignored
Returns
NULL, invisibly.
Method get_filter_state()
Gets reactive values from active FilterState objects.
Get active filter state from FilterState objects stored in state_list(s).
The output is a list compatible with input to self$set_filter_state.
Usage
FilterStates$get_filter_state()
Returns
Object of class teal_slices.
Method set_filter_state()
Sets active FilterState objects.
Usage
FilterStates$set_filter_state(state)
Arguments
state(
teal_slices)
Returns
Function that raises an error.
Method clear_filter_states()
Remove all FilterState objects from this FilterStates object.
Usage
FilterStates$clear_filter_states(force = FALSE)
Arguments
force(
logical(1)) flag specifying whether to include anchored filter states.
Returns
NULL, invisibly.
Method ui_active()
shiny UI definition that stores FilterState UI elements.
Populated with elements created with renderUI in the module server.
Usage
FilterStates$ui_active(id)
Arguments
id(
character(1))shinymodule instance id.
Returns
shiny.tag
Method srv_active()
shiny server module.
Usage
FilterStates$srv_active(id)
Arguments
id(
character(1))shinymodule instance id.
Returns
NULL.
Method ui_add()
shiny UI module to add filter variable.
Usage
FilterStates$ui_add(id)
Arguments
id(
character(1))shinymodule instance id.
Returns
shiny.tag
Method srv_add()
shiny server module to add filter variable.
This module controls available choices to select as a filter variable. Once selected, a variable is removed from available choices. Removing a filter variable adds it back to available choices.
Usage
FilterStates$srv_add(id)
Arguments
id(
character(1))shinymodule instance id.
Returns
NULL.
Method clone()
The objects of this class are cloneable with this method.
Usage
FilterStates$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
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