Package 'MagellanNTK'

Description

This function returns the indice of the last validated step before the current step.

Usage

Add2History(history, step, substep, param.name, value)

Arguments

Value

A 'data.frame()'

Examples

history <- InitializeHistory()
Add2History(history, "Example step", "First sub-step", "my param", "THE value")

Description

The names of the slots in dataIn are a subset of the names of the steps (names(stepsNames)). Each item is the result of a process and when a process has been validated, it creates a new slot with its own name

Usage

BuildData2Send(session, dataIn, stepsNames)

Arguments

Value

A vector of the same length of the vector 'stepsNames' in which each item is an object (the type of object used by the pipeline). This object must have the same behavior of a 'list()'.

Examples

data(lldata)
stepsNames <- c("data1", "data2", "data3")
BuildData2Send(NULL, lldata, stepsNames)

stepsNames <- c("data1", "data2", "data3", "data4", "data5")
BuildData2Send(NULL, lldata, stepsNames)

Description

Wrapper to the function 'do.call'

Usage

call_func(fname, args)

Arguments

Value

The result of the function called

See Also

[do.call()]

Examples

call_func("stats::rnorm", list(n = 10, mean = 3))

Description

This code is heavily based on the following repository: https://github.com/wleepang/shiny-directory-input Display an OS-native folder selection dialog under Mac OS X, Linux GTK+ or Windows.

Given x and y, return y only if both x and y are set

Usage

x %AND% y

file_sep(sysinfo = Sys.info())

choose_dir(default = NA, caption = NA, useNew = TRUE, sysinfo = Sys.info())

choose_dir.darwin(default = NA, caption = NA)

choose_dir.linux(default = NA, caption = NA)

choose_dir.windows(default = NA, caption = NA, useNew = TRUE)

Arguments

Details

Uses an Apple Script, Zenity or Windows Batch script to display an OS-native folder selection dialog.

For Apple Script, with default = NA, the initial folder selection is determined by default behavior of the "choose folder" script. Otherwise, paths are expanded with path.expand.

For Linux, with default = NA, the initial folder selection is determined by defaul behavior of the zenity script.

The new windows batch script allows both initial folder and caption to be set. In the old batch script for Windows the initial folder is always ignored.

Value

A length one character vector, character NA if 'Cancel' was selected.

A length one character vector, character NA if 'Cancel' was selected.

A length one character vector, character NA if 'Cancel' was selected.

A length one character vector, character NA if 'Cancel' was selected.

See Also

choose_dir

Examples

NULL

Description

This class is used to store the configuration of any process used with MagellanNTK It contains the following slots:

Wrapper function to the constructor of the class

Usage

Config(
  fullname = "",
  mode = "",
  steps = NULL,
  mandatory = NULL,
  steps.source.file = NULL
)

## S4 method for signature 'Config'
initialize(.Object, fullname, mode, steps, mandatory, steps.source.file)

Config(
  fullname = "",
  mode = "",
  steps = NULL,
  mandatory = NULL,
  steps.source.file = NULL
)

Arguments

Value

An instance of the class 'Config'

Slots

fullname

The name of the process which is the concatenation of the name of the pipeline and the name of the process itself, separated by '_'.

name

The name of the process nor pipeline.

parent

The name of the pipeline/process which owns this instance

mode

A 'character()' which indicates if the configuration is about a whole process nor a process of a pipeline.

steps

A 'vector' of 'character()' which contains the primary steps of the pipeline. Two steps will be automatically inserted in this vector: 'Description 'in the first position and 'Save' at the end.

mandatory

A 'vector' of 'boolean()' in which each item is the necessary code for the GUI of a step. The size of this vector is the number of steps

ll.UI

A 'vector' of Shiny source code. Each item is the necessary code for the GUI of a step. The size of this vector is the number of steps

steps.source.file

A 'vector' of which each item is the source code of the corresponding step.

steps

A 'vector' of 'character()' which contains the primary steps of the pipeline. Two steps will be automatically inserted in this vector: 'Description 'in the first position and 'Save' at the end.

mandatory

A 'vector' of 'boolean()' in which each item is the necessary code for the GUI of a step. The size of this vector is the number of steps

Examples

# Example of a single process with one step
proc1step <- Config(
  fullname = "PipelineDemo_DataGeneration",
  mode = "process",
  steps = c("DataGeneration"),
  mandatory = c(TRUE)
)


# Example of a single process with two steps
proc2steps <- Config(
  fullname = "PipelineDemo_PreProcessing",
  mode = "process",
  steps = c("Filtering", "Normalization"),
  mandatory = c(TRUE, FALSE)
)

# Example of pipeline with three process
pipe3proc <- Config(
  mode = "pipeline",
  fullname = "PipelineDemo",
  steps = c("DataGeneration", "Preprocessing", "Clustering"),
  mandatory = c(TRUE, FALSE, FALSE)
)


# Example of a particular description module (A process with no step)
description.process <- Config(
  fullname = "PipelineDemo_Description",
  mode = "process",
  steps = "",
  mandatory = ""
)

Description

The following functions are currently available:

- 'keepDatasets(object, range)' keep datasets in object which are in range

- ‘addDatasets(object, dataset, name)' add the ’dataset' to the object (of type list)

This manual page describes manipulation methods using [list] objects. In index or name 'i' can be specified to define the array (by name of index) on which to operate.

The following functions are currently available:

- 'keepDatasets(object, range)' keep datasets in object which are in range

- ‘addDatasets(object, dataset, name)' add the ’dataset' to the object (of type list)

- 'Save(object, file)' stores the object to a .RData file

Usage

addDatasets(object, dataset, name)

keepDatasets(object = NULL, range = seq_along(object))

Arguments

Details

The object must be of type list. Thetwo functions are implemented here for of the package which uses MagellanNTK

The object must be of type list. Thetwo functions are implemented here for of the package which uses MagellanNTK

Value

An instance of class 'MultiAssayExperiment'.

An processed object of the same class as 'object'.

Examples

data(lldata)
obj.se <- lldata[[1]]
new.obj <- addDatasets(lldata, obj.se, "mynewobj")

data(lldata123)
keepDatasets(lldata123, c(1, 3))

NULL

Description

left_panel = left_sidebar + width_sidebar top_sidebar = top_panel width_sidebar = width_process_btns

Usage

default_funcs()

default_base_URL()

default_workflow()

default_layout

default_theme(mode)

Arguments

Value

NA

Examples

NULL

Description

Directory Selection Control

Usage

directoryInput(inputId, label, value = NULL)

Arguments

Details

This widget relies on choose_dir to present an interactive dialog to users for selecting a directory on the local filesystem. Therefore, this widget is intended for shiny apps that are run locally - i.e. on the same system that files/directories are to be accessed - and not from hosted applications (e.g. from shinyapps.io).

Value

A directory input control that can be added to a UI definition.

See Also

updateDirectoryInput, readDirectoryInput, choose_dir

Examples

NULL

Description

Discover Skipped Steps

Usage

Discover_Skipped_Steps(steps.status)

Arguments

Value

A vector of integers of the same length as steps.status and where skipped steps are identified with '-1'

Examples

steps <- c(1, 1, 0, 1)
Discover_Skipped_Steps(steps)

Description

A shiny Module.

Usage

download_dataset_ui(id)

download_dataset_server(
  id,
  dataIn = reactive({
     NULL
 }),
  filename = "myDataset",
  remoteReset = reactive({
     0
 }),
  is.enabled = reactive({
     TRUE
 })
)

download_dataset(dataIn = NULL, filename = "myDataset")

Arguments

Value

NA

Examples

if (interactive()) {
  data(lldata, package = "MagellanNTK")
  download_dataset(lldata)
}

Description

A shiny Module.

Usage

format_DT_ui(id)

format_DT_server(
  id,
  dataIn = reactive({
     NULL
 }),
  hidden = reactive({
     NULL
 }),
  withDLBtns = FALSE,
  showRownames = FALSE,
  dom = "Bt",
  max.rows = 20,
  hc_style = reactive({
     NULL
 }),
  remoteReset = reactive({
     0
 }),
  is.enabled = reactive({
     TRUE
 })
)

format_DT(
  dataIn,
  hidden = NULL,
  withDLBtns = FALSE,
  showRownames = FALSE,
  dom = "Bt",
  hc_style = NULL,
  remoteReset = NULL,
  is.enabled = TRUE
)

Arguments

Value

A shiny App

Examples

if (interactive()) {
  data(lldata)
  obj <- SummarizedExperiment::assay(lldata[[1]])
  obj <- as.data.frame(obj)
  format_DT(obj)

  # Compute style from within third party tab
  obj <- as.data.frame(matrix(seq_len(30), byrow = TRUE, nrow = 6))
  colnames(obj) <- paste0("col", seq_len(5))

  mask <- as.data.frame(matrix(rep(LETTERS[seq_len(5)], 6),
    byrow = TRUE, nrow = 6
  ))

  style <- list(
    cols = colnames(obj),
    vals = colnames(mask),
    unique = unique(mask),
    pal = RColorBrewer::brewer.pal(5, "Dark2")[seq_len(5)]
  )

  format_DT(obj,
    hidden = mask,
    hc_style = style
  )
}

Description

This module allows to change

Usage

open_dataset_ui(id)

open_dataset_server(
  id,
  class = NULL,
  extension = NULL,
  remoteReset = reactive({
     NULL
 }),
  is.enabled = reactive({
     TRUE
 })
)

open_dataset(extension = NULL)

Arguments

Value

A Shiny app

Examples

if (interactive()) {
  open_dataset(extension = "rdata")
}

Description

Get file extension

Usage

GetExtension(name)

Arguments

Value

The extension of the given filename

Examples

GetExtension("foo.xlsx")

Description

Get the first mandatory step not validated

Usage

GetFirstMandatoryNotValidated(range, rv)

Arguments

Value

An integer which is the indice of the identified step in the vector rv$steps.status

Examples

NULL

Description

Get the history of an assay

Usage

GetHistory(dataIn, name)

Arguments

Value

A 'data.frame()'

Examples

data(lldata123)
GetHistory(lldata123, "Clustering")

Description

Get datasets from packages which owns datasets of a given class

Usage

GetListDatasets(class = NULL, demo_package = NULL)

Arguments

Value

A 'vector' in which items are the name of datasets which inherits the class given in parameter

Examples

foo1 <- GetListDatasets()

Description

This function returns the indice of the last validated step among all the steps

Usage

GetMaxValidated_AllSteps(steps.status)

Arguments

Value

A 'integer(1)' which is the indice of the value

Examples

GetMaxValidated_AllSteps(c(1, 1, 0, 1, 0, 0))

Description

This function returns the indice of the last validated step before the current step.

Usage

GetMaxValidated_BeforePos(pos = NULL, rv)

Arguments

Value

A 'integer()'

Examples

pos <- 3
rv <- list(steps.status = c(1, 1, 0, 1, 0, 0), current.pos = 3)
GetMaxValidated_BeforePos(pos, rv)

Description

Get the version of a package installed in the local R distribution

Usage

GetPackageVersion(pkg)

Arguments

Value

A 'character()'

Examples

GetPackageVersion("MagellanNTK")

Description

Global constants and configuration variables used throughout the package.

Usage

tl_v_next_icon

stepStatus

default_pos

listBrewerPalettes

Value

A collection of exported constants, lists and UI configuration objects.

Examples

NULL

Description

Initialisation function for DT

Usage

initComplete()

Value

literal JavaScript code

Examples

initComplete()

Description

This function returns the indice of the last validated step before the current step.

Usage

InitializeHistory()

Value

A ‘data.frame()' with four columns: ’Process', 'Step', 'Parameter' and 'Value'

Examples

InitializeHistory()

Description

Insert source code for config()

Usage

Insert_Call_to_Config(name)

Arguments

Value

A 'character()' containing R source code

Examples

Insert_Call_to_Config("PipelineDemo")

Description

This function generates the necessary code to modify the variable 'config' (slots steps and mandatory). It adds a 'Description' step and a TRUE value at the beginning of the 'steps' and 'mandatory' list, erases all white spaces for the names of the steps.

This function generates the necessary code to modify the variable 'config' (slots steps and mandatory). It adds a 'Description' step and a TRUE value at the beginning of the 'steps' and 'mandatory' list, erases all white spaces for the names of the steps.

This function create the source code needed inside a module to declare the reactive variable called 'widgets.default.values'. # Declaration of the variables that will contain the values of the widgets To avoid confusion, the first string is the name of the step while the second is the name of the widget

This function create the source code needed inside a module to declare the reactive variable called 'rv.custom.default.values'. # Declaration of the variables that will contain the values of the user variables. To avoid confusion, the first string is the name of the step while the second is the name of the widget

Returned value of the process

This function generates dynamically the observeEvent function for each widget

Usage

Get_Code_Update_Config_Variable()

Get_Code_Declare_widgets(widgets.names = NULL)

Get_Code_Declare_rv_custom(rv.custom.names = NULL)

Get_Code_for_ObserveEvent_widgets(widgets.names = NULL)

Get_Code_for_rv_reactiveValues()

Get_Code_for_dataOut()

Get_Code_for_General_observeEvents()

Get_Code_for_remoteReset(
  widgets = TRUE,
  custom = TRUE,
  dataIn = "dataIn()",
  addon = ""
)

Get_Code_for_resetting_widgets()

Get_Code_for_resetting_custom()

Module_Return_Func()

AdditionnalCodeForExternalModules(w.names = NULL, rv.custom.names = NULL)

Get_Workflow_Core_Code(
  mode = NULL,
  name = NULL,
  w.names = NULL,
  rv.custom.names = NULL
)

Get_AdditionalModule_Core_Code(w.names = NULL, rv.custom.names = NULL)

Arguments

Value

A 'string' containing some R code

A 'character()' containing R source code

A 'character()' containing R source code

A 'character()' containing R source code

A 'string' containing some R code

A 'character()' containing R source code

A 'character()' containing R source code

A 'character()' containing R source code

A 'character()' containing R source code

A 'character()' containing R source code

A 'character()' containing R source code

A 'character()' containing R source code

A 'character()' containing R source code

A 'character()' containing R source code

Author(s)

Samuel Wieczorek

Examples

MagellanNTK::Get_AdditionalModule_Core_Code("PipelineDemo", "")

Description

Substring test

Usage

isSubstr(pattern, target)

Arguments

Value

A boolean

Examples

isSubstr("cde", "abcdefghi")

Description

An instance of the class 'MultiAssayExperiment' which contains one assay (instance of class 'SummarizedExperiment'): 'Convert': Contains a data.frame with 6 columns and 100 rows fullfilled with '0'. It also contains a slot 'history' in the metadata(). This dataset is the most bacis one to run the example pipeline and learn how to work with MagellanNTK

Usage

data(lldata)

Format

An object of class 'MultiAssayExperiment'

Description

An instance of the class 'MultiAssayExperiment' which contains two assays (instance of class 'SummarizedExperiment'): 'Convert': Contains a data.frame with 6 columns and 100 rows fullfilled with '0'. 'DataGeneration' which stores the result of the 'DataGeneration' step of the demo pipeline Each assay contains a slot 'history' in the metadata().

Usage

data(lldata1)

Format

An object of class 'MultiAssayExperiment'

Description

An instance of the class 'MultiAssayExperiment' which contains two assays (instance of class 'SummarizedExperiment'): 'Convert': Contains a data.frame with 6 columns and 100 rows fullfilled with '0'. 'DataGeneration' which stores the result of the 'DataGeneration' step of the demo pipeline 'Preprocessing' which stores the result of the 'DataGeneration' and 'Preprocessing' steps of the demo pipeline Each assay contains a slot 'history' in the metadata().

Usage

data(lldata12)

Format

An object of class 'MultiAssayExperiment'

Description

An instance of the class 'MultiAssayExperiment' which contains two assays (instance of class 'SummarizedExperiment'): 'Convert': Contains a data.frame with 6 columns and 100 rows fullfilled with '0'. 'DataGeneration' which stores the result of the 'DataGeneration' step of the demo pipeline 'Preprocessing' which stores the result of the 'DataGeneration' and 'Preprocessing' steps of the demo pipeline 'Clustering' which stores the result of all the three steps of the demo pipeline Each assay contains a slot 'history' in the metadata().

Usage

data(lldata123)

Format

An object of class 'MultiAssayExperiment'

Description

Main Shiny application

Usage

MagellanNTK_ui(id, sidebarSize = "medium")

MagellanNTK_server(
  id,
  workflow.path = reactive({
     NULL
 }),
  workflow.name = reactive({
     NULL
 }),
  verbose = FALSE,
  usermod = "user"
)

MagellanNTK(
  workflow.path = NULL,
  workflow.name = NULL,
  verbose = FALSE,
  usermod = "user",
  sidebarSize = "medium",
  ...
)

Arguments

Value

A shiny app

Examples

if (interactive()) {
  wf.path <- system.file('workflow/PipelineDemo', package = 'MagellanNTK')
  MagellanNTK(wf.path, 'PipelineDemo')
}

Description

This module is not directly used by MagellanNTK core functions. It is rather a useful tool for third part pipelines and processes.

Usage

mod_errorModal_ui(id)

mod_errorModal_server(
  id,
  title = NULL,
  text = NULL,
  footer = modalButton("Close")
)

mod_errorModal(title = NULL, text = NULL)

Arguments

Value

A shiny App

Examples

if (interactive()) {
  mod_errorModal("myTitle", "myContent")
}

Description

A shiny Module.

Usage

mod_homepage_ui(id)

mod_homepage_server(
  id,
  mdfile = file.path(system.file("www/md", package = "MagellanNTK"), "Presentation.Rmd"),
  dataset = reactive({
     NULL
 })
)

mod_homepage()

Arguments

Value

A shiny App

Examples

if (interactive()) {
  mod_homepage()
}

Description

A shiny Module.

Usage

insert_md_ui(id)

insert_md_server(id, url)

insert_md(url)

Arguments

Value

A shiny App

Examples

if (interactive()) {
  base <- system.file("www/md", package = "MagellanNTK")
  url <- file.path(base, "Presentation.Rmd")
  insert_md(url)
}

Description

A shiny Module.

Usage

mainapp_ui(id, session, size = "300px")

mainapp_server(
  id,
  workflow.name = reactive({
     NULL
 }),
  workflow.path = reactive({
     NULL
 }),
  verbose = FALSE,
  usermod = "user"
)

mainapp(usermod = "user")

Arguments

Value

A shiny App

Examples

if (interactive()) {
  mainapp()
}

Description

Displays of formatted modal-dialog with 'Cancel' and 'Ok' buttons. This modal (a shiny module itself) can embed a shiny module and it is able to return the return value of the embeded shiny module.

Usage

mod_modalDialog_ui(id)

mod_modalDialog_server(
  id,
  title = NULL,
  typeWidget = "button",
  width = NULL,
  uiContent = NULL,
  external_mod = NULL,
  external_mod_args = list()
)

mod_modalDialog(
  title,
  typeWidget = "button",
  uiContent = NULL,
  external_mod = NULL,
  external_mod_args = list()
)

Arguments

Value

A Shiny modal-dialog

Examples

if (interactive()) {
  mod_modalDialog(
    title = "test modalDialog",
    uiContent = p("test")
  )
}

Description

A shiny Module.

Usage

open_workflow_ui(id)

open_workflow_server(id)

open_workflow()

Arguments

Value

A shiny App

Examples

if (interactive()) {
  open_workflow()
}

Description

Actually, this module does not work because we do not allow the use of the package 'shinyBS' package (conflicts with BS versions). In the future, one will fix this module with native functions in the package 'bs4Dash' (https://bs4dash.rinterface.com/reference/tooltip).

Usage

mod_popover_for_help_ui(id)

mod_popover_for_help_server(id, title, content)

mod_popover_for_help(title, content)

Arguments

Value

A shiny App

Examples

if (interactive()) {
  mod_popover_for_help("myTitle", "myContent")
}

Description

A shiny Module.

Usage

mod_release_notes_ui(id)

mod_release_notes_server(id, URL_releaseNotes)

mod_release_notes(URL_releaseNotes)

Arguments

Value

A shiny App

Examples

if (interactive()) {
  url <- "http://www.prostar-proteomics.org/md/versionNotes.md"
  mod_release_notes(url)

  local.url <- system.file("/workflow/PipelineDemo/md/links.Rmd",
    package = "MagellanNTK"
  )
  mod_release_notes(local.url)
}

Description

This module is not directly used by MagellanNTK core functions. It is rather a useful tool for third part pipelines and processes.

Usage

mod_SweetAlert_ui(id)

mod_SweetAlert_server(
  id,
  title = NULL,
  text = NULL,
  showClipBtn = TRUE,
  type = "error"
)

mod_SweetAlert(title, text, type = "warning")

Arguments

Value

A shiny App

Examples

if (interactive()) {
  mod_SweetAlert("my title", "my message")
}

Description

This function checks if the ui() and server() parts of a Shiny module are available in the global environment.

Usage

module_exists(base_name)

Arguments

Value

A boolean

Examples

path <- system.file("workflow/PipelineDemo", package = "MagellanNTK")
source_wf_files(path)
module_exists("PipelineDemo_Preprocessing")

Description

The module navigation can be launched via a Shiny app. This is the core module of MagellanNTK

Usage

nav_pipeline_ui(id)

nav_pipeline_server(
  id = NULL,
  dataIn = reactive({
     NULL
 }),
  is.enabled = reactive({
     TRUE
 }),
  remoteReset = reactive({
     0
 }),
  verbose = FALSE,
  usermod = "user"
)

nav_pipeline()

Arguments

Value

A list of four items: * dataOut A dataset of the same class of the parameter dataIn * steps.enabled A vector of 'boolean' of the same length than config@steps * status A vector of 'integer(1)' of the same length than the config@steps vector

Author(s)

Samuel Wieczorek

Examples

if (interactive()) {
  library(shiny)
  nav_pipeline()
}

Description

The module navigation can be launched via a Shiny app. This is the core module of MagellanNTK

Usage

nav_process_ui(id)

nav_process_server(
  id = NULL,
  dataIn = reactive({
     NULL
 }),
  status = reactive({
     NULL
 }),
  is.enabled = reactive({
     TRUE
 }),
  remoteReset = reactive({
     0
 }),
  remoteResetUI = reactive({
     0
 }),
  is.skipped = reactive({
     FALSE
 }),
  verbose = FALSE,
  usermod = "user"
)

nav_process()

Arguments

Value

A shiny App

Author(s)

Samuel Wieczorek

Examples

if (interactive()) {
  nav_process()
}

Description

The module navigation can be launched via a Shiny app. This is the core module of MagellanNTK

Usage

nav_single_process_ui(id)

nav_single_process_server(
  id = NULL,
  dataIn = reactive({
     NULL
 }),
  status = reactive({
     NULL
 }),
  remoteResetUI = reactive({
     0
 }),
  is.enabled = TRUE,
  is.skipped = FALSE,
  verbose = FALSE,
  usermod = "user",
  sendDataIfReset = TRUE
)

nav_single_process()

Arguments

Value

A shiny App

Author(s)

Samuel Wieczorek

Examples

if (interactive()) {
  nav_single_process()
}

Description

Move the position of the cursor

Usage

NavPage(direction, current.pos, len)

Arguments

Value

A 'integer(1)' which is the new current position.

Examples

NavPage(-1, 5, 5)

Description

Checks if a package is available to load it

Checks if a package is available to load it

Usage

pkgsRequire(ll.deps)

pkgsRequire(ll.deps)

Arguments

Value

NA

Author(s)

Samuel Wieczorek

Examples

NULL


pkgsRequire(c("stats"))

Description

Creates a layout to place the sidebar and the main screen for pipelines and processes.

Usage

process_layout(session, ns, sidebar, content)

process_layout_process(session, ns, sidebar, content)

process_layout_pipeline(session, ns, sidebar, content)

Arguments

Value

A 'div()' containing shiny components

Examples

NULL

Description

Read the configuration file of a pipeline and extract formatted (as a list) information

Usage

readConfigFile(path, usermod = "user")

Arguments

Value

A list containing the following items: value <- list( * funcs = tmp, * verbose = get_data(lines, "verbose") == "enabled", * UI_view_debugger: a 'boolean' to show (TRUE) of hide (FALSE) the debugger interface * UI_view_open_pipeline: a 'boolean' to show (TRUE) of hide (FALSE) the UI to open a pipeline * UI_view_convert_dataset a 'boolean' to show (TRUE) of hide (FALSE) the UI for convert/import a dataset * UI_view_change_Look_Feel a 'boolean' to show (TRUE) of hide (FALSE) the UI to change the L&F * UI_view_change_core_funcs a 'boolean' to show (TRUE) of hide (FALSE) the UI to change the generic functions * extension A 'character()' which specifies the extension file allowed to be processed in the pipeline, * class A 'character()' which specifies the class of the dataset to be processed in the pipeline, * package A 'character()' which specifies the package which owns the pipeline * demo_package A 'character()' which specifies a particular package to search * URL_manual The path to the Rmd file containing the user manual of the pipeline. It can be a path to a file on the computer or a link to a file over internet. * URL_ReleaseNotes The path to the Rmd file containing release notes about the pipeline. It can be a path to a file on the computer or a link to a file over internet.

Examples

path <- system.file("workflow/PipelineDemo", package = "MagellanNTK")
readConfigFile(path)

Description

Read the value of a directoryInput

Usage

readDirectoryInput(session, inputId)

Arguments

Details

Reads the value of the text field associated with a directoryInput object that stores the user selected directory path.

Value

NA

Examples

NULL

Description

Runs a demo app with the code

Usage

runDirinputExample()

Details

Runs a demo app with the code. See the code in the example_application folder for how this is accomplished.

Value

NA

Examples

if (interactive()) {
  shiny::runApp(runDirinputExample())
}

Description

Get the position of the last validated item

Usage

SetCurrentPosition(stepsstatus)

Arguments

Value

An integer

Examples

status <- c(1, 1, 1, 0, 0)
SetCurrentPosition(status)

status <- c(1, 1, 0, 1, 0)
SetCurrentPosition(status)

Description

Standardize names

Usage

SetHistory(obj.se, history)

Arguments

Value

An instance of the class 'SummarizedExperiment'

Author(s)

Samuel Wieczorek

Examples

data(lldata)
history <- GetHistory(lldata, "Convert")
history <- Add2History(history, "Step example", "Substep example", "ex_param", "Ex")
lldata[[1]] <- SetHistory(lldata[[1]], history)

Description

Prints the content of a 'Config' class

Usage

## S4 method for signature 'Config'
show(object)

Arguments

Value

NA

Description

These functions content the UI code for the main sidebar in the interface of MagellanNTK

Usage

Insert_User_Sidebar()

Value

Shiny UI component

Examples

Insert_User_Sidebar()

Description

Loads the source code of basic Shiny app files

Usage

source_shinyApp_files()

Value

NA

Examples

if (interactive()) {
  source_shinyApp_files()
}

Description

This function goes into the 'R' directory of the file structure of a pipeline and load into memory the source code of the R scripts (which contains the interfaces of the process)

Usage

source_wf_files(dirpath, verbose = FALSE)

Arguments

Value

NA

Examples

path <- system.file("workflow/PipelineDemo", package = "MagellanNTK")
source_wf_files(path)

Description

Define the appearance of the pipeline timeline.

Define the appearance of the pipeline timeline.

Usage

timeline_process_ui(id)

timeline_process_server(
  id,
  config,
  status = reactive({
     NULL
 }),
  position = reactive({
     1
 }),
  enabled = reactive({
     NULL
 })
)

timeline_process(config, status, position, enabled)

timeline_pipeline_ui(id)

timeline_pipeline_server(id, config, status, position, enabled)

timeline_pipeline(config, status, position, enabled)

Arguments

Value

A shiny app

A shiny App

Examples

if (interactive()) {
  config <- Config(
    mode = "process",
    fullname = "PipelineDemo_Preprocessing",
    steps = c("Filtering", "Normalization"),
    mandatory = c(FALSE, TRUE)
  )
  status <- reactive({
    c(1, 1, 0, 0)
  })
  pos <- reactive({
    2
  })
  enabled <- reactive({
    c(0, 0, 1, 1)
  })
  shiny::runApp(timeline_process(config, status, pos, enabled))
}

if (interactive()) {
  config <- Config(
    mode = "pipeline",
    fullname = "PipelineDemo",
    steps = c("DataGeneration", "Preprocessing", "Clustering"),
    mandatory = c(TRUE, FALSE, FALSE)
  )
  status <- reactive({
    c(1, 1, -1, 1, 0)
  })
  pos <- reactive({
    4
  })
  enabled <- reactive({
    c(0, 0, 0, 0, 1)
  })
  timeline_pipeline(config, status, pos, enabled)
}

Description

Returns the date and time in timestamp UNIX format.

Usage

Timestamp()

Value

A 'integer()'.

Examples

NULL

Description

Enables/disables the buttons 'Next step' and 'Previous step' wrt the current position of the cursor in the timeline.

Usage

ToggleState_NavBtns(current.pos, nSteps)

Arguments

Value

NA

Examples

NULL

Description

Updates the status of steps in a given range

Usage

ToggleState_Screens(cond, range, is.enabled, rv)

Arguments

Value

An updated version of the vector rv$steps.enabled

Examples

NULL

Description

Wrapper for the 'toggleWidget()' function of the package 'shinyjs'

Usage

toggleWidget(widget, condition)

Arguments

Value

NA

Author(s)

Samuel Wieczorek

Examples

NULL

Description

Update the status enabled/disabled of the steps of a pipeline/process

Usage

Update_State_Screens(is.skipped, is.enabled, rv)

Arguments

Value

A 'vector' of boolean which gives the status enabled (TRUE) or disabled (FALSE) of the steps from a pipeline nor a process.

Examples

NULL

Description

Change the value of a directoryInput on the client

Usage

updateDirectoryInput(session, inputId, value = NULL, ...)

Arguments

Details

Sends a message to the client, telling it to change the value of the input object. For directoryInput objects, this changes the value displayed in the text-field and triggers a client-side change event. A directory selection dialog is not displayed.

Value

NA

Examples

NULL

Description

Update the status of steps in a pipeline nor process.

Usage

UpdateStepsStatus(dataIn, config)

Arguments

Value

A vector of boolean in which each item indicates the status (VALIDATED, UNDONE, SKIPPED) of the corresponding step.

Examples

NULL

Description

A shiny Module.

Usage

view_dataset_ui(id)

view_dataset_server(id, dataIn = NULL, ...)

view_dataset(dataIn)

Arguments

Value

A shiny App

Examples

if (interactive()) {
  data(lldata123)
  view_dataset(lldata123)
}