JavaScript
-
Value
-
+
Value
A shiny.tag.list.
-
Details
-
+
Details
Simply add include_teal_css_js() as one of the UI elements.
part of 
+
@@ -116,311 +74,239 @@ Package index
-
Core teal functions
-
+
Core teal functions
Main functions needed to build a teal app
-
+
-
+
Helper Functions
Helper functions for teal
-
+
-
-
+
-
-
+
-
-
+
-
-
Functions for module developers
-
+
+
Functions for module developers
-
+
-
-
Validation functions
-
+
+
+
-
+
-
+
+
+
-
-
diff --git a/main/reference/init.html b/main/reference/init.html
index 109499a69e..b10bcbd243 100644
--- a/main/reference/init.html
+++ b/main/reference/init.html
@@ -1,25 +1,9 @@
-
-
-
-
-
-
-Create the server and UI function for the shiny app — init • teal
-
-
-
-
-
-Create the server and UI function for the shiny app — init • teal
-
-
-
-
-
+teal app that is composed of teal modules.">
Skip to contents
@@ -27,7 +11,7 @@
teal
- 0.15.2.9079
+ 0.15.2.9080
part of
+
@@ -130,8 +86,7 @@ Create the server and UI function for the shiny app
-
Usage
-
+
Usage
init(
data,
modules,
@@ -145,20 +100,16 @@ Usage
-
Arguments
-
+
Arguments
-
-- data
-
+- data
(teal_data or teal_data_module)
For constructing the data object, refer to teal_data() and teal_data_module().
If datanames are not set for the teal_data object, defaults from the teal_data environment will be used.
- modules
-
+- modules
(list or teal_modules or teal_module)
Nested list of teal_modules or teal_module objects or a single
teal_modules or teal_module object. These are the specific output modules which
@@ -166,55 +117,46 @@
Argumentsfilter
-
+- filter
(teal_slices) Optionally,
specifies the initial filter using teal_slices().
- title
-
+- title
(shiny.tag or character(1)) Optionally,
the browser window title. Defaults to a title "teal app" with the icon of NEST.
Can be created using the build_app_title() or
by passing a valid shiny.tag which is a head tag with title and link tag.
(shiny.tag or character(1)) Optionally,
the header of the app.
(shiny.tag or character(1)) Optionally,
the footer of the app.
- id
-
+- id
(character) Optionally,
a string specifying the shiny module id in cases it is used as a shiny module
rather than a standalone shiny app. This is a legacy feature.
- landing_popup
-
+- landing_popup
(teal_module_landing) Optionally,
a landing_popup_module to show up as soon as the teal app is initialized.
-
+
-
Value
-
+
Value
Named list containing server and UI functions.
-
Examples
-
+
Examples
+
part of
+
@@ -114,8 +70,7 @@
@@ -125,48 +80,39 @@ Does the object make use of the arg
-
Usage
-
+
Usage
is_arg_used(modules, arg)
-
Arguments
-
+
Arguments
-
-- modules
-
+- modules
(teal_module or teal_modules) object
- arg
-
+- arg
(character(1)) names of the arguments to be checked against formals of teal modules.
-
-
Value
-
+
Value
logical whether the object makes use of arg.
part of
+
@@ -130,8 +86,7 @@ Landing popup module
-
Usage
-
+
Usage
landing_popup_module(
label = "Landing Popup",
title = NULL,
@@ -141,42 +96,33 @@ Usage
-
Arguments
-
+
Arguments
-
-- label
-
+- label
(character(1)) Label of the module.
- title
-
+- title
(character(1)) Text to be displayed as popup title.
- content
-
+- content
(character(1), shiny.tag or shiny.tag.list) with the content of the popup.
Passed to ... of shiny::modalDialog. See examples.
- buttons
-
+- buttons
(shiny.tag or shiny.tag.list) Typically a modalButton or actionButton. See examples.
-
+
-
Value
-
+
Value
A teal_module (extended with teal_landing_module class) to be used in teal applications.
-
Examples
-
+
Examples
+
part of
+
@@ -127,8 +83,7 @@ App state management.
-
Usage
-
+
Usage
ui_bookmark_panel(id, modules)
srv_bookmark_panel(id, modules)
@@ -139,36 +94,29 @@ Usage
-
Arguments
-
+
Arguments
-
-- id
-
+- id
(character) Optionally,
a string specifying the shiny module id in cases it is used as a shiny module
rather than a standalone shiny app. This is a legacy feature.
- modules
-
+- modules
(list or teal_modules or teal_module)
Nested list of teal_modules or teal_module objects or a single
teal_modules or teal_module object. These are the specific output modules which
will be displayed in the teal application. See modules() and module() for
more details.
-
+
-
Value
-
+
Value
Invisible NULL.
-
Details
-
+
Details
This module introduces bookmarks into teal apps: the shiny bookmarking mechanism becomes enabled
and server-side bookmarks can be created.
The bookmark manager presents a button with the bookmark icon and is placed in the tab-bar.
@@ -180,8 +128,7 @@
-
Server logic
-
+
Server logic
A bookmark is a URL that contains the app address with a /?_state_id_=<bookmark_dir> suffix.
@@ -189,31 +136,25 @@
part of
+
@@ -124,8 +80,7 @@ Data summary
-
Usage
-
+
Usage
ui_data_summary(id)
srv_data_summary(id, teal_data)
@@ -140,76 +95,60 @@ Usage
-
Arguments
-
+
Arguments
-
-- id
-
+- id
(character(1)) shiny module instance id.
- teal_data
-
+- teal_data
(reactive returning teal_data)
- current_data
-
+- current_data
(object) current object (after filtering and transforming).
- initial_data
-
+- initial_data
(object) initial object.
- dataname
-
+- dataname
(character(1))
- subject_keys
-
+- subject_keys
(character) names of the columns which determine a single unique subjects
-
+
-
Details
-
+
Details
Handling different data classes:
-get_filter_overview() is a pseudo S3 method which has variants for:
-
-array (data.frame, DataFrame, array, Matrix and SummarizedExperiment): Method variant
+get_filter_overview() is a pseudo S3 method which has variants for:
array (data.frame, DataFrame, array, Matrix and SummarizedExperiment): Method variant
can be applied to any two-dimensional objects on which ncol() can be used.
MultiAssayExperiment: for which summary contains counts for colData and all experiments.
For other data types module displays data name with warning icon and no more details.
-Module includes also "Show/Hide unsupported" button to toggle rows of the summary table
+
Module includes also "Show/Hide unsupported" button to toggle rows of the summary table
containing datasets where number of observations are not calculated.
part of
+
@@ -136,8 +92,7 @@ Filter panel module in teal
-
Usage
-
+
Usage
ui_filter_data(id)
srv_filter_data(id, datasets, active_datanames, data_rv, is_active)
@@ -150,70 +105,56 @@ Usage
-
Arguments
-
+
Arguments
-
-- id
-
+- id
(character) Optionally,
a string specifying the shiny module id in cases it is used as a shiny module
rather than a standalone shiny app. This is a legacy feature.
- datasets
-
+- datasets
(reactive returning FilteredData or NULL)
When datasets is passed from the parent module (srv_teal) then dataset is a singleton
which implies in filter-panel to be "global". When NULL then filter-panel is "module-specific".
- active_datanames
-
+- active_datanames
(reactive returning character) this module's data names
- data_rv
-
+- data_rv
(reactive returning teal_data)
- modules
-
+- modules
(list or teal_modules or teal_module)
Nested list of teal_modules or teal_module objects or a single
teal_modules or teal_module object. These are the specific output modules which
will be displayed in the teal application. See modules() and module() for
more details.
-
+
-
Value
-
+
Value
A eventReactive containing teal_data containing filtered objects and filter code.
-eventReactive triggers only if all conditions are met:
-
part of
+
@@ -124,8 +80,7 @@ Manage multiple FilteredData objects
-
Usage
-
+
Usage
ui_filter_manager_panel(id)
srv_filter_manager_panel(id, slices_global)
@@ -138,95 +93,71 @@ Usage
-
Arguments
-
+
Arguments
-
-- id
-
+- id
(character(1))
shiny module instance id.
- slices_global
-
+- slices_global
(reactiveVal)
containing teal_slices.
- module_fd
-
+- module_fd
(FilteredData)
Object containing the data to be filtered in a single teal module.
-
+
-
Value
-
+
Value
Module returns a slices_global (reactiveVal) containing a teal_slices object with mapping.
-
Slices global
-
+
Slices global
The key role in maintaining the module-specific filter states is played by the .slicesGlobal
-object. It is a reference class that holds the following fields:
-
-all_slices (reactiveVal) - reactive value containing all filters registered in an app.
all_slices (reactiveVal) - reactive value containing all filters registered in an app.
module_slices_api (reactiveValues) - reactive field containing references to each modules'
FilteredData object methods. At this moment it is used only in srv_filter_manager to display
the filter states in a table combining informations from all_slices and from
FilteredData$get_available_teal_slices().
-During a session only new filters are added to all_slices unless module_snapshot_manager is
+
During a session only new filters are added to all_slices unless module_snapshot_manager is
used to restore previous state. Filters from all_slices can be activated or deactivated in a
-module which is linked (both ways) by attr(, "mapping") so that:
-
-
Filter manager
-
+
Filter manager
-
Filter-manager is split into two parts:
-
-ui/srv_filter_manager_panel - Called once for the whole app. This module observes changes in
+
Filter-manager is split into two parts:
ui/srv_filter_manager_panel - Called once for the whole app. This module observes changes in
the filters in slices_global and displays them in a table utilizing information from mapping:
-
(TRUE) - filter is active in the module
(FALSE) - filter is inactive in the module
(NA) - filter is not available in the module
-
-ui/srv_module_filter_manager - Called once for each teal_module. Handling filter states
+
ui/srv_module_filter_manager - Called once for each teal_module. Handling filter states
for of single module and keeping module FilteredData consistent with slices_global, so that
local filters are always reflected in the slices_global and its mapping and vice versa.
-
part of
+
@@ -131,66 +87,51 @@ Data Module for teal
This module manages the data argument for srv_teal. The teal framework uses teal_data(),
-which can be provided in various ways:
-
-Directly as a teal.data::teal_data() object. This will automatically convert it into a reactive teal_data.
Directly as a teal.data::teal_data() object. This will automatically convert it into a reactive teal_data.
As a reactive object that returns a teal.data::teal_data() object.
-
+
-
Usage
-
+
Usage
ui_init_data(id)
srv_init_data(id, data)
-
Arguments
-
+
Arguments
-
-- id
-
+- id
(character) Optionally,
a string specifying the shiny module id in cases it is used as a shiny module
rather than a standalone shiny app. This is a legacy feature.
- data
-
+- data
(teal_data, teal_data_module, or reactive returning teal_data)
The data which application will depend on.
-
-
Value
-
+
Value
A reactive object that returns:
Output of the data. If data fails then returned error is handled (after tryCatch()) so that
rest of the application can respond to this respectively.
-
Details
-
+
Details
-
Reactive teal_data:
-
+
Reactive teal_data:
The data in the application can be reactively updated, prompting srv_teal() to rebuild the
-content accordingly. There are two methods for creating interactive teal_data:
-
-Using a reactive object provided from outside the teal application. In this scenario,
+content accordingly. There are two methods for creating interactive teal_data:
Using a reactive object provided from outside the teal application. In this scenario,
reactivity is controlled by an external module, and srv_teal responds to changes.
Using teal_data_module(), which is embedded within the teal application, allowing data to
be resubmitted by the user as needed.
-Since the server of teal_data_module() must return a reactive teal_data object, both
+
Since the server of teal_data_module() must return a reactive teal_data object, both
methods (1 and 2) produce the same reactive behavior within a teal application. The distinction
lies in data control: the first method involves external control, while the second method
involves control from a custom module within the app.
@@ -200,19 +141,17 @@
+
part of
+
@@ -114,8 +70,7 @@
@@ -125,44 +80,36 @@ Retrieve labels from teal_modules
-
Arguments
-
+
Arguments
-
-- modules
-
+- modules
(teal_modules)
-
-
Value
-
+
Value
A list containing the labels of the modules. If the modules are nested,
the function returns a nested list of labels.
part of
+
@@ -124,55 +80,44 @@ Extract/Remove module(s) of specific class
-
Usage
-
+
Usage
extract_module(modules, class)
drop_module(modules, class)
-
Arguments
-
+
Arguments
-
-- modules
-
+- modules
(teal_modules)
- class
-
+- class
The class name of teal_module to be extracted or dropped.
-
-
Value
-
+
Value
-
teal_modules
part of
+
@@ -124,8 +80,7 @@ Filter state snapshot management
-
Usage
-
+
Usage
ui_snapshot_manager_panel(id)
srv_snapshot_manager_panel(id, slices_global)
@@ -136,31 +91,24 @@ Usage
-
Arguments
-
+
Arguments
-
-- id
-
+- id
(character(1)) shiny module instance id.
- slices_global
-
+- slices_global
(reactiveVal) that contains a teal_slices object
containing all teal_slices existing in the app, both active and inactive.
-
+
-
Value
-
+
Value
list containing the snapshot history, where each element is an unlisted teal_slices object.
-
Details
-
+
Details
This module introduces snapshots: stored descriptions of the filter state of the entire application.
Snapshots allow the user to save the current filter state of the application for later use in the session,
as well as to save it to file in order to share it with an app developer or other users,
@@ -172,8 +120,7 @@
Details
-
Bookmarks
-
+
Bookmarks
An onBookmark callback creates a snapshot of the current filter state.
@@ -240,25 +184,22 @@
part of
+
@@ -120,8 +76,7 @@
@@ -134,8 +89,7 @@
-
Usage
-
+
Usage
ui_teal(
id,
modules,
@@ -148,20 +102,16 @@ Usage
-
Arguments
-
+
Arguments
-
-- id
-
+- id
(character) Optionally,
a string specifying the shiny module id in cases it is used as a shiny module
rather than a standalone shiny app. This is a legacy feature.
- modules
-
+- modules
(list or teal_modules or teal_module)
Nested list of teal_modules or teal_module objects or a single
teal_modules or teal_module object. These are the specific output modules which
@@ -169,69 +119,55 @@
Argumentstitle
-
+- title
(shiny.tag or character(1)) Optionally,
the browser window title. Defaults to a title "teal app" with the icon of NEST.
Can be created using the build_app_title() or
by passing a valid shiny.tag which is a head tag with title and link tag.
(shiny.tag or character(1)) Optionally,
the header of the app.
(shiny.tag or character(1)) Optionally,
the footer of the app.
- data
-
+- data
(teal_data, teal_data_module, or reactive returning teal_data)
The data which application will depend on.
- filter
-
+- filter
(teal_slices) Optionally,
specifies the initial filter using teal_slices().
-
+
-
Value
-
+
Value
NULL invisibly
-
Details
-
+
Details
Module is responsible for creating the main shiny app layout and initializing all the necessary
components. This module establishes reactive connection between the input data and every other
component in the app. Reactive change of the data passed as an argument, reloads the app and
-possibly keeps all input settings the same so the user can continue where one left off.
-
-
data flow in teal application
-
+possibly keeps all input settings the same so the user can continue where one left off.
+
data flow in teal application
This module supports multiple data inputs but eventually, they are all converted to reactive
returning teal_data in this module. On this reactive teal_data object several actions are
-performed:
-
+
-
Fallback on failure
-
+
Fallback on failure
teal is designed in such way that app will never crash if the error is introduced in any
@@ -243,19 +179,17 @@
+
part of
+
@@ -120,8 +76,7 @@
@@ -134,8 +89,7 @@ Execute and validate teal_data_module
-
Usage
-
+
Usage
ui_teal_data(id, data_module = function(id) NULL)
srv_teal_data(
@@ -158,84 +112,68 @@ Usage
-
Arguments
-
+
Arguments
-
-- id
-
+- id
(character(1)) Module id
- data_module
-
+- data_module
(teal_data_module)
- modules
-
+- modules
(teal_modules or teal_module) For datanames validation purpose
- validate_shiny_silent_error
-
+- validate_shiny_silent_error
(logical) If TRUE, then shiny.silent.error is validated and
- is_transformer_failed
-
+- is_transformer_failed
(reactiveValues) contains logical flags named after each transformer.
Help to determine if any previous transformer failed, so that following transformers can be disabled
and display a generic failure message.
- data
-
+- data
(reactive teal_data)
-
+
-
Value
-
+
Value
reactive teal_data
-
data validation
-
+
data validation
Executed teal_data_module() is validated and output is validated for consistency.
-Output data is invalid if:
-
-teal_data_module() is invalid if server doesn't return reactive. Immediately crashes an app!
data is invalid if:teal_data_module() is invalid if server doesn't return reactive. Immediately crashes an app!
reactive throws a shiny.error - happens when module creating teal_data() fails.
reactive returns qenv.error - happens when teal_data() evaluates a failing code.
reactive object doesn't return teal_data().
teal_data() object lacks any datanames specified in the modules argument.
-teal (observers in srv_teal) always waits to render an app until reactive teal_data is
+
teal (observers in srv_teal) always waits to render an app until reactive teal_data is
returned. If error 2-4 occurs, relevant error message is displayed to the app user. Once the issue is
resolved, the app will continue to run. teal guarantees that errors in data don't crash the app
(except error 1).
part of
+
@@ -124,8 +80,7 @@ Generate lockfile for application's environment reproducibility
-
Usage
-
+
Usage
ui_teal_lockfile(id)
srv_teal_lockfile(id)
@@ -140,30 +95,22 @@ Usage
-
Arguments
-
+
Arguments
-
-- lockfile_path
-
+- lockfile_path
(character) path to the lockfile.
-
+
-
Different ways of creating lockfile
-
+
Different ways of creating lockfile
-
teal leverages renv::snapshot(), which offers multiple methods for lockfile creation.
-
-Working directory lockfile: teal, by default, will create an implicit type lockfile that uses
+
teal leverages renv::snapshot(), which offers multiple methods for lockfile creation.
Working directory lockfile: teal, by default, will create an implicit type lockfile that uses
renv::dependencies() to detect all R packages in the current project's working directory.
DESCRIPTION-based lockfile: To generate a lockfile based on a DESCRIPTION file in your working
directory, set renv::settings$snapshot.type("explicit"). The naming convention for type follows
@@ -171,35 +118,30 @@
Different ways of creating lockfile
DESCRIPTION fields included in the lockfile.
Custom files-based lockfile: To specify custom files as the basis for the lockfile, set
renv::settings$snapshot.type("custom") and configure the renv.snapshot.filter option.
-
-
lockfile usage
-
+
lockfile usage
After creating the lockfile, you can restore the application's environment using renv::restore().
part of
+
@@ -118,8 +74,7 @@
@@ -131,8 +86,7 @@ Calls all modules
-
Usage
-
+
Usage
ui_teal_module(id, modules, depth = 0L)
# Default S3 method
@@ -193,20 +147,16 @@ Usage
-
Arguments
-
+
Arguments
-
-- id
-
+- id
(character) Optionally,
a string specifying the shiny module id in cases it is used as a shiny module
rather than a standalone shiny app. This is a legacy feature.
- modules
-
+- modules
(list or teal_modules or teal_module)
Nested list of teal_modules or teal_module objects or a single
teal_modules or teal_module object. These are the specific output modules which
@@ -214,69 +164,53 @@
Argumentsdepth
-
+- depth
(integer(1))
number which helps to determine depth of the modules nesting.
- data_rv
-
+- data_rv
(reactive returning teal_data)
- datasets
-
+- datasets
(reactive returning FilteredData or NULL)
When datasets is passed from the parent module (srv_teal) then dataset is a singleton
which implies in filter-panel to be "global". When NULL then filter-panel is "module-specific".
- slices_global
-
+- slices_global
(reactiveVal returning modules_teal_slices)
see module_filter_manager
- data_load_status
-
--
-
(reactive returning character)
-Determines action dependent on a data loading status:
-
-
-
+
-
Value
-
-
output of currently active module.
-
-srv_teal_module.teal_module returns reactiveVal containing output of the called module.
Value
+ output of currently active module.
-
part of
+
@@ -116,8 +72,7 @@
@@ -128,8 +83,7 @@ UI and server modules of teal
-
Usage
-
+
Usage
ui_teal_with_splash(
id,
data,
@@ -142,46 +96,38 @@ Usage
-
Arguments
-
+
Arguments
-
-- id
-
+- id
(character) Optionally,
a string specifying the shiny module id in cases it is used as a shiny module
rather than a standalone shiny app. This is a legacy feature.
- data
-
+- data
(teal_data, teal_data_module, or reactive returning teal_data)
The data which application will depend on.
- title
-
+- title
(shiny.tag or character(1)) Optionally,
the browser window title. Defaults to a title "teal app" with the icon of NEST.
Can be created using the build_app_title() or
by passing a valid shiny.tag which is a head tag with title and link tag.
(shiny.tag or character(1)) Optionally,
the header of the app.
(shiny.tag or character(1)) Optionally,
the footer of the app.
- modules
-
+- modules
(list or teal_modules or teal_module)
Nested list of teal_modules or teal_module objects or a single
teal_modules or teal_module object. These are the specific output modules which
@@ -189,33 +135,28 @@
Argumentsfilter
-
+- filter
(teal_slices) Optionally,
specifies the initial filter using teal_slices().
-
+
-
Value
-
+
Value
Returns a reactive expression containing a teal_data object when data is loaded or NULL when it is not.
part of
+
@@ -116,8 +72,7 @@
@@ -128,8 +83,7 @@ Module to transform reactive teal_data
-
Usage
-
+
Usage
ui_transform_data(id, transformers = list(), class = "well")
srv_transform_data(
@@ -142,61 +96,50 @@ Usage
-
Arguments
-
+
Arguments
-
-- id
-
+- id
(character(1)) Module id
- transformers
-
+- transformers
(list of teal_data_module) that will be applied to transform the data.
Each transform module UI will appear in the teal's sidebar panel.
Transformers' datanames are added to the datanames. See teal_transform_module().
- data
-
+- data
(reactive teal_data)
- modules
-
+- modules
(teal_modules or teal_module) For datanames validation purpose
- is_transformer_failed
-
+- is_transformer_failed
(reactiveValues) contains logical flags named after each transformer.
Help to determine if any previous transformer failed, so that following transformers can be disabled
and display a generic failure message.
-
+
-
Value
-
+
Value
reactive teal_data
part of
+
@@ -114,8 +70,7 @@
@@ -125,44 +80,36 @@ Retrieve teal_bookmarkable attribute from teal_modules
-
Usage
-
+
Usage
modules_bookmarkable(modules)
-
Arguments
-
+
Arguments
-
-- modules
-
+- modules
(teal_modules or teal_module) object
-
-
Value
-
+
Value
named list of the same structure as modules with TRUE or FALSE values indicating
whether the module is bookmarkable.
part of
+
@@ -127,19 +83,15 @@ Get module depth
-
Usage
-
+
Usage
modules_depth(modules, depth = 0L)
-
Arguments
-
+
Arguments
-
-- modules
-
+- modules
(list or teal_modules or teal_module)
Nested list of teal_modules or teal_module objects or a single
teal_modules or teal_module object. These are the specific output modules which
@@ -147,32 +99,27 @@
Argumentsdepth
-
+- depth
optional integer determining current depth level
-
-
Value
-
+
Value
Depth level for given module.
part of
+
@@ -127,8 +83,7 @@ Template function for TealReportCard creation and customization
-
Usage
-
+
Usage
report_card_template(
title,
label,
@@ -139,58 +94,47 @@ Usage
-
Arguments
-
+
Arguments
-
-- title
-
+- title
(character(1)) title of the card (unless overwritten by label)
- label
-
+- label
(character(1)) label provided by the user when adding the card
- description
-
+- description
(character(1)) optional, additional description
- with_filter
-
+- with_filter
(logical(1)) flag indicating to add filter state
- filter_panel_api
-
+- filter_panel_api
(FilterPanelAPI) object with API that allows the generation
of the filter state in the report
-
+
-
Value
-
+
Value
(TealReportCard) populated with a title, description and filter state.
part of
+
@@ -142,50 +98,41 @@ Create a teal module for previewing a report
-
Usage
-
+
Usage
reporter_previewer_module(label = "Report previewer", server_args = list())
-
Arguments
-
+
Arguments
-
-- label
-
+- label
(character(1)) Label shown in the navigation item for the module or module group.
For modules() defaults to "root". See Details.
- server_args
-
+- server_args
(named list)
Arguments passed to teal.reporter::reporter_previewer_srv().
-
-
Value
-
+
Value
teal_module (extended with teal_module_previewer class) containing the teal.reporter previewer functionality.
part of
+
@@ -124,38 +80,30 @@ Restore value from bookmark.
-
Usage
-
+
Usage
restoreValue(value, default)
-
Arguments
-
+
Arguments
-
-- value
-
+- value
(character(1)) name of value to restore
- default
-
+- default
fallback value
-
-
Value
-
+
Value
In an application restored from a server-side bookmark,
the variable specified by value from the values environment.
Otherwise default.
-
Details
-
+
Details
Bookmarks can store not only inputs but also arbitrary values.
These values are stored by onBookmark callbacks and restored by onBookmarked callbacks,
and they are placed in the values environment in the session$restoreContext field.
@@ -167,19 +115,17 @@
part of
+
@@ -133,50 +89,41 @@ Run JS file from /inst/js/ package directory
-
Arguments
-
+
Arguments
-
-- files
-
+- files
(character) vector of filenames.
-
-
Value
-
+
Value
NULL, invisibly.
-
Details
-
+
Details
system.file should not be used to access files in other packages, it does
not work with devtools. Therefore, we redefine this method in each package
as needed. Thus, we do not export this method.
part of
+
@@ -127,56 +83,46 @@ Show R code modal
-
Arguments
-
+
Arguments
-
-- title
-
+- title
(character(1))
Title of the modal, displayed in the first comment of the R code.
- rcode
-
+- rcode
(character)
vector with R code to show inside the modal.
- session
-
+- session
(ShinySession) optional
shiny session object, defaults to shiny::getDefaultReactiveDomain().
-
part of
+
@@ -127,71 +83,57 @@ Store and restore teal_slices object
-
Usage
-
+
Usage
slices_store(tss, file)
slices_restore(file)
-
Arguments
-
+
Arguments
-
-- tss
-
+- tss
(teal_slices) object to be stored.
- file
-
+- file
(character(1)) file path where teal_slices object will be
saved and restored. The file extension should be ".json".
-
-
Value
-
+
Value
slices_store returns NULL, invisibly.
slices_restore returns a teal_slices object restored from the file.
-
Details
-
-
Date and date time objects are stored in the following formats:
-
-Date class is converted to the "ISO8601" standard (YYYY-MM-DD).
Details
+ Date and date time objects are stored in the following formats:
Date class is converted to the "ISO8601" standard (YYYY-MM-DD).
POSIX*t classes are converted to character by using
format.POSIX*t(usetz = TRUE, tz = "UTC") (YYYY-MM-DD HH:MM:SS UTC, where
UTC is the Coordinated Universal Time timezone short-code).
-This format is assumed during slices_restore. All POSIX*t objects in
+
This format is assumed during slices_restore. All POSIX*t objects in
selected or choices fields of teal_slice objects are always printed in
UTC timezone as well.
part of
+
@@ -139,8 +95,7 @@ Create a tdata object
-
Usage
-
+
Usage
new_tdata(...)
tdata2env(...)
@@ -156,37 +111,30 @@ Usage
-
Arguments
-
+
Arguments
-
-- ...
-
+- ...
ignored
-
+
-
Value
-
+
Value
nothing
part of
+
@@ -116,8 +72,7 @@
-
+
-
+
+
+
-
-
diff --git a/main/reference/teal_data_module.html b/main/reference/teal_data_module.html
index 35b6a63376..1874d21c70 100644
--- a/main/reference/teal_data_module.html
+++ b/main/reference/teal_data_module.html
@@ -1,23 +1,7 @@
-
-
-
-
-
-
-Data module for teal applications — teal_data_module • teal
-
-
-
-
-
-
-
-
-
-
-
+
+Data module for teal applications — teal_data_module • teal
Skip to contents
@@ -25,7 +9,7 @@
teal
- 0.15.2.9079
+ 0.15.2.9080
part of
+
@@ -127,8 +83,7 @@ Data module for teal applications
-
Usage
-
+
Usage
teal_data_module(ui, server, label = "data module", once = TRUE)
# S4 method for class 'teal_data_module,character'
@@ -139,31 +94,25 @@ Usage
-
Arguments
-
+
Arguments
-
-- ui
-
+- ui
(function(id))
shiny module UI function; must only take id argument
- server
-
+- server
(function(id))
shiny module server function; must only take id argument;
must return reactive expression containing teal_data object
- label
-
+- label
(character(1)) Label of the module.
- once
-
+- once
(logical(1))
If TRUE, the data module will be shown only once and will disappear after successful data loading.
App user will no longer be able to interact with this module anymore.
@@ -171,43 +120,35 @@
Argumentsobject
-
+- object
(teal_data_module)
- code
-
+- code
(character or language) code to evaluate. If character, comments are retained.
- data
-
+- data
(teal_data_module) object
- expr
-
+- expr
(expression) to evaluate. Must be inline code. See
- ...
-
+- ...
See Details.
-
+
-
Value
-
+
Value
teal_data_module returns a list of class teal_data_module containing two elements, ui and
server provided via arguments.
eval_code returns a teal_data_module object with a delayed evaluation of code when the module is run.
within returns a teal_data_module object with a delayed evaluation of expr when the module is run.
-
Details
-
+
Details
teal_data_module creates a shiny module to interactively supply or modify data in a teal application.
The module allows for running any code (creation and some modification) after the app starts or reloads.
The body of the server function will be run in the app rather than in the global environment.
@@ -222,14 +163,12 @@
part of
+
@@ -114,8 +70,7 @@
@@ -125,48 +80,39 @@ Create a FilteredData
-
Usage
-
+
Usage
teal_data_to_filtered_data(x, datanames = ls(teal.code::get_env(x)))
-
Arguments
-
+
Arguments
-
-- x
-
+- x
(teal_data) object
- datanames
-
+- datanames
(character) vector of data set names to include; must be subset of datanames(x)
-
-
Value
-
+
Value
A FilteredData object.
part of
+
@@ -124,24 +80,19 @@
-
In teal we need to recreate the teal_data object due to two operations:
-
-
Usage
-
+
Usage
.append_evaluated_code(data, code)
.append_modified_data(data, objects)
@@ -150,58 +101,47 @@ Usage
-
Arguments
-
+
Arguments
-
-- data
-
+- data
(teal_data)
- code
-
+- code
(character) code to append to data@code
- objects
-
+- objects
(list) objects to append to data@env
- datanames
-
+- datanames
(character) names of the datasets
-
+
-
Value
-
+
Value
modified teal_data
-
Details
-
+
Details
Due to above recreation of teal_data object can't be done simply by using public
teal.code and teal.data methods.
part of
+
@@ -127,8 +83,7 @@ Create teal_module and teal_modules objects
-
Usage
-
+
Usage
module(
label = "module",
server = function(id, data, ...) moduleServer(id, function(input, output, session)
@@ -144,38 +99,38 @@
+
set_datanames(modules, datanames)
-
Arguments
-
+
Arguments
-
-- label
-
+- label
(character(1)) Label shown in the navigation item for the module or module group.
For modules() defaults to "root". See Details.
- server
-
--
-
(function) shiny module with following arguments:
-
-- ui
-
--
-
(function) shiny UI module function with following arguments:
-
-- filters
-
+- filters
(character) Deprecated. Use datanames instead.
- datanames
-
--
-
(character) Names of the datasets relevant to the item.
-There are 2 reserved values that have specific behaviors:
-
-The keyword "all" includes all datasets available in the data passed to the teal application.
- datanames
+(character) Names of the datasets relevant to the item.
+There are 2 reserved values that have specific behaviors:
The keyword "all" includes all datasets available in the data passed to the teal application.
NULL hides the sidebar panel completely.
If transformers are specified, their datanames are automatically added to this datanames
argument.
-
-- server_args
-
+- server_args
(named list) with additional arguments passed on to the server function.
- ui_args
-
+- ui_args
(named list) with additional arguments passed on to the UI function.
- transformers
-
+- transformers
(list of teal_data_module) that will be applied to transform the data.
Each transform module UI will appear in the teal's sidebar panel.
Transformers' datanames are added to the datanames. See teal_transform_module().
- ...
-
-
-For modules(): (teal_module or teal_modules) Objects to wrap into a tab.
- ...
+
-- x
-
+- x
(teal_module or teal_modules) Object to format/print.
- indent
-
+- indent
(integer(1)) Indention level; each nested element is indented one level more.
- modules
-
+- is_last
+(logical(1)) Whether this is the last item in its parent's children list.
+Affects the tree branch character used (L- vs |-)
- parent_prefix
+(character(1)) The prefix inherited from parent nodes,
+used to maintain the tree structure in nested levels
- what
+(character) Specifies which metadata to display.
+Possible values: "datasets", "properties", "ui_args", "server_args", "transformers"
- is_root
+(logical(1)) Whether this is the root node of the tree. Only used in
+format.teal_modules(). Determines whether to show "TEAL ROOT" header
- modules
(teal_module or teal_modules)
-
-
Value
-
+
Value
module() returns an object of class teal_module.
-
modules() returns a teal_modules object which contains following fields:
-
-label: taken from the label argument.
modules() returns a teal_modules object which contains following fields:
-
-
Details
-
+
Details
module() creates an instance of a teal_module that can be placed in a teal application.
modules() shapes the structure of a the application by organizing teal_module within the navigation panel.
It wraps teal_module and teal_modules objects in a teal_modules object,
@@ -290,39 +239,29 @@
-
Restricting datasets used by teal_module:
-
+
Restricting datasets used by teal_module:
The datanames argument controls which datasets are used by the module’s server. These datasets,
passed via server's data argument, are the only ones shown in the module's tab.
When datanames is set to "all", all datasets in the data object are treated as relevant.
-However, this may include unnecessary datasets, such as:
-
-Proxy variables for column modifications
To exclude irrelevant datasets, use the set_datanames() function to change datanames from
+
To exclude irrelevant datasets, use the set_datanames() function to change datanames from
"all" to specific names. Trying to modify non-"all" values with set_datanames() will result
in a warning. Datasets with names starting with . are ignored globally unless explicitly listed
in datanames.
-
+
When transformers are specified, their datanames are added to the module’s datanames, which
-changes the behavior as follows:
-
part of
+
@@ -124,8 +80,7 @@ Filter settings for teal applications
-
Usage
-
+
Usage
teal_slices(
...,
exclude_varnames = NULL,
@@ -144,112 +99,85 @@ Usage
-
Arguments
-
+
Arguments
-
-- ...
-
+- ...
any number of teal_slice objects.
- include_varnames, exclude_varnames
-
+- include_varnames, exclude_varnames
(named lists of character) where list names
match names of data sets and vector elements match variable names in respective data sets;
specify which variables are allowed to be filtered; see Details.
- count_type
-
--
-
![[Experimental]](figures/lifecycle-experimental.svg)
+
- count_type
+
This is a new feature. Do kindly share your opinions on
teal.slice's GitHub repository.
(character(1)) string specifying how observations are tallied by these filter states.
-Possible options:
-- allow_add
-
+- allow_add
(logical(1)) logical flag specifying whether the user will be able to add new filters
- module_specific
-
--
-
(logical(1)) optional,
-
-- mapping
-
--
-
+
- mapping
+
This is a new feature. Do kindly share your opinions on
teal's GitHub repository.
(named list) specifies which filters will be active in which modules on app start.
Elements should contain character vector of teal_slice ids (see teal.slice::teal_slice).
-Names of the list should correspond to teal_module label set in module() function.
-- app_id
-
+- app_id
(character(1))
For internal use only, do not set manually.
Added by init so that a teal_slices can be matched to the app in which it was used.
Used for verifying snapshots uploaded from file. See snapshot.
- x
-
+- x
(list) of lists to convert to teal_slices
-
+
-
Value
-
+
Value
A teal_slices object.
-
Details
-
+
Details
Produces a teal_slices object.
The teal_slice components will specify filter states that will be active when the app starts.
Attributes (created with the named arguments) will configure the way the app applies filters.
See argument descriptions for details.
-
Examples
-
+
Examples
filter <- teal_slices(
teal_slice(dataname = "iris", varname = "Species", id = "species"),
teal_slice(dataname = "iris", varname = "Sepal.Length", id = "sepal_length"),
@@ -280,19 +208,17 @@
+
part of
+
@@ -130,8 +86,7 @@ Data module for teal transformers.
-
Usage
-
+
Usage
teal_transform_module(
ui = function(id) NULL,
server = function(id, data) data,
@@ -141,46 +96,36 @@ Usage
-
Arguments
-
+
Arguments
-
-- ui
-
+- ui
(function(id))
shiny module UI function; must only take id argument
- server
-
--
-
(function(id, data))
+
- server
+(function(id, data))
shiny module server function; that takes id and data argument,
where the id is the module id and data is the reactive teal_data input.
The server function must return reactive expression containing teal_data object.
The server function definition should not use eventReactive as it may lead to
unexpected behavior.
-See vignettes("data-transform-as-shiny-module") for more information.
-vignettes("data-transform-as-shiny-module") for more information.
-- label
-
+- label
(character(1)) Label of the module.
- datanames
-
+- datanames
(character)
Names of the datasets that are relevant for this module to evaluate. If set to character(0)
then module would receive modules() datanames.
-
+
-
Details
-
+
Details
teal_transform_module creates a teal_data_module object to transform data in a teal
application. This transformation happens after the data has passed through the filtering activity
in teal. The transformed data is then sent to the server of the teal_module().
@@ -188,8 +133,7 @@
part of
+
@@ -114,8 +70,7 @@
@@ -125,38 +80,31 @@ Function for validating the title parameter of teal::init
-
Usage
-
+
Usage
validate_app_title_tag(shiny_tag)
-
Arguments
-
+
Arguments
-
-- shiny_tag
-
+- shiny_tag
(shiny.tag) Object to validate for a valid title.
-
part of
+
@@ -124,8 +80,7 @@ Validate that dataset has a minimum number of observations
-
Usage
-
+
Usage
validate_has_data(
x,
min_nrow = NULL,
@@ -136,46 +91,36 @@ Usage
-
Arguments
-
+
Arguments
-
-- x
-
+- x
(data.frame)
- min_nrow
-
+- min_nrow
(numeric(1)) Minimum allowed number of rows in x.
- complete
-
+- complete
(logical(1)) Flag specifying whether to check only complete cases. Defaults to FALSE.
- allow_inf
-
+- allow_inf
(logical(1)) Flag specifying whether to allow infinite values. Defaults to TRUE.
- msg
-
+- msg
(character(1)) Additional message to display alongside the default message.
-
+
-
Examples
-
+
Examples
+
part of
+
@@ -124,37 +80,29 @@ Validates that vector has length greater than 0
-
Usage
-
+
Usage
validate_has_elements(x, msg)
-
Arguments
-
+
Arguments
-
-- x
-
+- x
vector
- msg
-
+- msg
message to display
-
-
Examples
-
+
Examples
data <- data.frame(
id = c(1:10, 11:20, 1:10),
strata = rep(c("A", "B"), each = 15)
@@ -189,19 +137,17 @@
+
part of
+
@@ -124,42 +80,33 @@ Validates that dataset contains specific variable
-
Usage
-
+
Usage
validate_has_variable(data, varname, msg)
-
Arguments
-
+
Arguments
-
-- data
-
+- data
(data.frame)
- varname
-
+- varname
(character(1)) name of variable to check for in data
- msg
-
+- msg
(character(1)) message to display if data does not include varname
-
-
Examples
-
+
Examples
data <- data.frame(
one = rep("a", length.out = 20),
two = rep(c("a", "b"), length.out = 20)
@@ -186,19 +133,17 @@
+
part of
+
@@ -124,42 +80,33 @@ Validates that vector includes all expected values
-
Usage
-
+
Usage
validate_in(x, choices, msg)
-
Arguments
-
+
Arguments
-
-- x
-
+- x
Vector of values to test.
- choices
-
+- choices
Vector to test against.
- msg
-
+- msg
(character(1)) Error message to display if some elements of x are not elements of choices.
-
-
Examples
-
+
Examples
+
part of
+
@@ -127,38 +83,30 @@ Send input validation messages to output
-
Usage
-
+
Usage
validate_inputs(..., header = "Some inputs require attention")
-
Arguments
-
+
Arguments
-
-- ...
-
+- ...
either any number of InputValidator objects
or an optionally named, possibly nested list of InputValidator
objects, see Details
(character(1)) generic validation message; set to NULL to omit
-
-
Value
-
+
Value
Returns NULL if the final validation call passes and a shiny.silent.error if it fails.
-
Details
-
+
Details
shiny::validate is used to withhold rendering of an output element until
certain conditions are met and to print a validation message in place
of the output element.
@@ -177,14 +125,12 @@
-
Examples
-
+
Examples
+
part of
+
@@ -124,51 +80,41 @@ Validate that variables has expected number of levels
-
Usage
-
+
Usage
validate_n_levels(x, min_levels = 1, max_levels = 12, var_name)
-
Arguments
-
+
Arguments
-
-- x
-
+- x
variable name. If x is not a factor, the unique values
are treated as levels.
- min_levels
-
+- min_levels
cutoff for minimum number of levels of x
- max_levels
-
+- max_levels
cutoff for maximum number of levels of x
- var_name
-
+- var_name
name of variable being validated for use in
validation message
-
-
Details
-
+
Details
If the number of levels of x is less than min_levels
or greater than max_levels the validation will fail.
This function is a wrapper for shiny::validate.
-
Examples
-
+
Examples
data <- data.frame(
one = rep("a", length.out = 20),
two = rep(c("a", "b"), length.out = 20),
@@ -203,19 +149,17 @@
+
part of
+
@@ -124,42 +80,33 @@ Validates no intersection between two vectors
-
Usage
-
+
Usage
validate_no_intersection(x, y, msg)
-
Arguments
-
+
Arguments
-
-- x
-
+- x
vector
- y
-
+- y
vector
- msg
-
+- msg
(character(1)) message to display if x and y intersect
-
-
Examples
-
+
Examples
data <- data.frame(
id = c(1:10, 11:20, 1:10),
strata = rep(c("A", "B", "C"), each = 10)
@@ -199,19 +146,17 @@
+
part of
+
@@ -124,37 +80,29 @@ Validate that dataset has unique rows for key variables
-
Usage
-
+
Usage
validate_one_row_per_id(x, key = c("USUBJID", "STUDYID"))
-
Arguments
-
+
Arguments
-
-- x
-
+- x
(data.frame)
- key
-
+- key
(character) Vector of ID variables from x that identify unique records.
-
-
Examples
-
+
Examples
+