Package 'tkWidgets' reference manual

Title:	R based tk widgets
Description:	Widgets to provide user interfaces. tcltk should have been installed for the widgets to run.
Authors:	J. Zhang <[email protected]>
Maintainer:	J. Zhang <[email protected]>
License:	Artistic-2.0
Version:	1.85.0
Built:	2024-12-13 05:58:36 UTC
Source:	https://github.com/bioc/tkWidgets

List File and Directories for a Given Path

Description

Takes a path and returns a vector of string with the names of files and directories for the path. The directory names will have a system dependent path separator (e. g. / for Unix) appended.

Usage

appendSepDir(path)
appendSepDir(path)

Arguments

path

path character string specifying the path whose contents are to be listed

Value

A character vector containing file and directory names.

Author(s)

Jianhua (John) Zhang

Examples

# File names and directory names are not differentiated
list.files()

# Put a separater at the end of directory names
appendSepDir(getwd())
# File names and directory names are not differentiated
list.files()

# Put a separater at the end of directory names
appendSepDir(getwd())

Converting the formal arguments to a function and converts into an XML format

Description

This function reads the formal arguments to a given function and converts the content into an XML format

Usage

args2XML(fun, xml.name = "", full.names = NULL, priority = NULL)
args2XML(fun, xml.name = "", full.names = NULL, priority = NULL)

Arguments

`fun`	`fun` name of the function of interests
`xml.name`	`xml.name` a character string for the name of the xml file holding the content of the formal arguments to the function
`full.names`	`full.names` a vector of character string with full description of each of the formal arguments to the function. The order of apperance of each description much correspond to the oreder of their appeerance in the formal argument list
`priority`	`priority` a vector of integers or character strings indicating the priority of the arguments.

Details

Priority values are currently used to determine whether the argument will appear on a widget that has entry boxes for modifying the values of the arguments. Users of args2XML may not have any concern of the priority values

Value

No value will be returned.

Author(s)

Jianhua Zhang

Examples

fullNames <- c("Full path names", "Pattern to match",
"Visiable file names", "Include path")
args2XML(list.files, "temp.xml", fullNames, c(1, 2, 2, 2)) 
readLines("temp.xml")
unlink("temp.xml")
fullNames <- c("Full path names", "Pattern to match",
"Visiable file names", "Include path")
args2XML(list.files, "temp.xml", fullNames, c(1, 2, 2, 2)) 
readLines("temp.xml")
unlink("temp.xml")

Functions to construct a widget that takes inputs from users

Description

Given a argument list, the functions construct a widget to allow users to entry or select values for arguments defined by the names of the argument list.

Usage

argsWidget(argsList, defaultNames, inst = "")
getPWidget(argsList, PWEnv, inst = "")
formatArg(toFormat)
getSymbol(args)
funcs2Char(args,funcs)
getTrueNullNa(toFormat)
argsWidget(argsList, defaultNames, inst = "")
getPWidget(argsList, PWEnv, inst = "")
formatArg(toFormat)
getSymbol(args)
funcs2Char(args,funcs)
getTrueNullNa(toFormat)

Arguments

`argsList`	`argsList` a list of arguments with or without default values. The list can be derived from e.g. `formals`
`PWEnv`	`PWEnv` an R environment used object to store data for the argument list
`toFormat`	`toFormat` element to be formated by `formatArg`
`args`	`args` arguments to be formated
`funcs`	`funcs` a list containing the arguments that are functions
`defaultNames`	`defaultNames` a vector of character strings of length 2 for two default buttons to be rendered. The first one is to end the process and the second to abort the process
`inst`	`inst` a character string for a short instuction that will appear on the top of a widget

Details

argsWidget builds a widget with widget elements to allow users to input values for the arguments.

getPWidget instatiates primary widgets that will be used to construct the widget for argements.

formatArg formats the value for a given argument so that the calue can be displayed by a tcltk widget.

getSymbol filters out functions from the argument list.

funcs2Char converts functions to character representations of the functions.

getTrueNullNa converts string "true", "false", "null", and "na" to R primitives for these items.

Value

argsWidget returns a list with user input values for elements of the argument list passed.

getPWidget returns a list of primary widgets.

formatArg returns a list containing the formated values.

getSymbol returns a list containing arguments that are functions.

funcs2Char returns a list containing character representations of functions.

getTrueNullNa returns an R object.

Author(s)

Jianhua Zhang

References

R tcltk

Examples

  if(interactive()){
      argsWidget(list("Entry with default" = "default",
                      "Entry without default" = ""))
  }
if(interactive()){
      argsWidget(list("Entry with default" = "default",
                      "Entry without default" = ""))
  }

Class "colInfo" presents column information for a data frame

Description

This class is for keeping information about a data frame to be processed. The class is mainly for use by importWizard

Objects from the Class

Objects can be created by calls of the form new("colInfo", ...)

Slots

colName:: Object of class "character" - a character string for the name of the column
colType:: Object of class "character" - a character string for the data type of the column. Can only be "character" or "numeric"
dropOrNot:: Object of class "logical" - a boolean indicationg whether the column will be droped

Methods

colName: signature(object = "character"): The get method for slot "colName"
colName<-: signature(object = "character"): The set method for slot "colName"
colType: signature(object = "character"): The get method for slot "colType"
colType<-: signature(object = "character"): The set method for slot "colName"
dropOrNot: signature(object = "logical"): The get method for slot "dropOrNot"
dropOrNot: signature(object = "logical"): The set method for slot "dropOrNot"

Author(s)

Jianhua Zhang

Examples

  newInfo <- new("colInfo", colName = "aaaa", colType = "character",
dropOrNot = FALSE)  
newInfo <- new("colInfo", colName = "aaaa", colType = "character",
dropOrNot = FALSE)

Function to view a data object passed

Description

This function creates a widget to allow users to view the content of a data frame passed and decide whether to save the data or not.

Usage

dataViewer(data, caption = "", save = TRUE)
dataViewer(data, caption = "", save = TRUE)

Arguments

`data`	`data` a data frame (or alike) to be viewed
`caption`	`caption` a character string for the title of the widget
`save`	`save` a boolean to indicate whether to have the option to allow users to save the data

Details

Taking a data frame as one of the arguments, this function builds a widget that allows users to view the content of the data and save the data as a file.

Value

This function does not return any value

Author(s)

Jianhua Zhang

References

R tcltk

Examples

# Create matrix
data <- matrix(1:20, ncol = 4)
if(interactive()){
    # View data using dataViewer
    dataViewer(data, "test", TRUE)
}
# Create matrix
data <- matrix(1:20, ncol = 4)
if(interactive()){
    # View data using dataViewer
    dataViewer(data, "test", TRUE)
}

Function to build a widget for inputing database arguments

Description

This functions creates a interactive widget to allow users to input arguments for database connection for Unix.

Usage

dbArgsWidget()
dbArgsWidget()

Details

Database arguments include database name, user name, password, host name, and table name.

Value

The function returns a list containing the following elements:

`dbname`	a charater string for the name of the database
`host`	a character string for the name or IP address of the host machine
`user`	a character string for the name of the user
`password`	a character string for the password
`tablename`	a character string for the name of the database table

Author(s)

Jianhua Zhang

References

Rdbi

Examples

if(interactive()){
    test <- dbArgsWidget()
}
if(interactive()){
    test <- dbArgsWidget()
}

Functions constuct a widget to explore BioC's data packages

Description

These functions construct a widget that allow users to visually explore a data package of Bioconductor and read selected elements to R

Usage

DPExplorer(pkgName = "", title = "BioC Data Package Explorer", getFocus
= TRUE)
getTopLevel(title)
loadDataPkg(pkgName)
DPExplorer(pkgName = "", title = "BioC Data Package Explorer", getFocus
= TRUE)
getTopLevel(title)
loadDataPkg(pkgName)

Arguments

`pkgName`	`pkgName` a character string for the name of a Bioconductor's data package that has already been loaded
`title`	`title` a character string for the title of the widget
`getFocus`	`getFocus` a boolean indicating whether a widget should grab the focus

Details

If pkgName is not provided when DPExplorer is called, an entry box is available for users to put a pkgName in later. In either cases, the data package specified by pkgName should have been loaded.

getTopLevel creates a top level window for the widget.

loadDataPkg filters out valid environment objects from a data package.

Value

If only one key is selected, DPExplorer returns a vector of one to more elements. If more than one key is selected, loadDataPkg returns a list of vectors.

getTopLevel returns a tkwin object for the top level window.

loadDataPkg returns a vector of character strings for available data environments.

Author(s)

Jianhua Zhang

References

Documents for a Bioconductor data package

Examples

if(interactive() && require("hgu95av2", character.only = TRUE)){
    DPExplorer("hgu95av2")
}
if(interactive() && require("hgu95av2", character.only = TRUE)){
    DPExplorer("hgu95av2")
}

A widget that allows users to explore the example code and help files of a given R package

Description

Given a valid package name as a character string, eExplorer collects all the example code from the "R-ex" directory from the R library for that package and then displays the names of the code examples in a list box. When a name in the list box is clicked, the corresponding code will be displayed and users are allowed to execute the code or view the help file for the function the example code is for.

Usage

eExplorer(pkgName, font = "arial 13", getFocus = TRUE)
getExCode(pkgName)
getHelpFile(pkgName, fileName)
eExplorer(pkgName, font = "arial 13", getFocus = TRUE)
getExCode(pkgName)
getHelpFile(pkgName, fileName)

Arguments

`pkgName`	`pkgName` a character string for the name of an R package of interest. The R package needs to be installed
`font`	`font` a character string for the font to be used by the widget to display the text. The default is "arial 13"
`fileName`	`fileName` a character string for the name of a file in "R-ex" with the ".R" extension removed. The file contains a chunk of example code and may have a corrsponding help file in the "help" directory
`getFocus`	`getFocus` a boolean indicating whether a widget should grab the focus

Details

getExCode and getHelpFile are called by eExplorer to get the code examples or help help files contained by a given package.

Value

eExplorer does not return anything useful.

Author(s)

Jianhua Zhang

References

Writing R Extension for information on "R-ex" and "help" directories

Examples

  if(interactive()){
      require("Biobase") || stop("Does not run without Biobase")
      eExplorer("Biobase")
  }
if(interactive()){
      require("Biobase") || stop("Does not run without Biobase")
      eExplorer("Biobase")
  }

Simple Interface to View and Pick Files

Description

This function provides the widget for users to go up and down a path and view the files. When files are selected and the "End" button is pressed, the function returns a vector of character strings with the full paths of the selected files.

Usage

fileBrowser(path="", testFun = function(x) TRUE, prefix = NULL,
	    suffix = NULL, textToShow = "Select file(s)",
	    nSelect = -1)
fileBrowser(path="", testFun = function(x) TRUE, prefix = NULL,
	    suffix = NULL, textToShow = "Select file(s)",
	    nSelect = -1)

Arguments

`path`	character string for the full path to be view. Defaults to the current working directory if no path is provided.
`testFun`	function that checks to see if a given file name satisfies predefined requirements. The default is no checking.
`prefix`	character string for a prefix used to screen out file names that do not have that prefix as part of their names.
`suffix`	character string for a suffix used to screen out file names that do not have that suffix as part of their names.
`textToShow`	character string to be shown on the widget to given instructions to users.
`nSelect`	integer indicating the number of files that should be selected. No limitation if `nSelect = -1` as per default.

Details

When a path is viewed, files will be displayed as they are and directories will be displayed with a system file separator appended (e.g. "/" for Unix systems). Single click on a file name will make the file selectable when the select button is pressed. Multiple selection is possible by dragging with mouse button 1 pressed. Double click on a directory name will go into that directory and display its files. When a file/directory is selected and the "End" button pressed, the full path for the selected files selected will be returned.

The widget is modal and has to be closed by pressing the "End" button before doing any other operations. Functions, prefix, and suffix can be specified. Examples of validity functions are hasPrefix and hasSuffix.

The following is a list of the buttons and their associated behavior:

Up: Moves the directory whose content is to be displayed in the box for file names one level up along the directory tree. No action if already on top of the tree.
Select \>\>: When a file or files in the box for file names in a directory have been highlighted by clicking or dragging mouse button 1 and this button is pushed, the highlighted file(s) will be displayed in the box for selected file(s) on the right.
\<\< Remove: When a file or files in the box for selected files have been highlighted by clicking or dragging this button is pushed, the highlighted file(s) will be removed from the box.
Clear: Clears everything in the box for selected files when pushed.
end: Returns a vector containing all the names in the box for selected files or NULL if the box is empty. The full path will be appended to the file names.

Value

A vector of character strings containing the full path of each file selected.

Author(s)

Jianhua (John) Zhang

Examples

## The example here is only run interactively since it requires user
## interference which may cause problems if not available:
if(interactive()) {

  # Call the function to view the current directory
  flist <- fileBrowser()
  flist

  # To call the function with a path do
  # fileBrowser(path = "yourPath")
}
## The example here is only run interactively since it requires user
## interference which may cause problems if not available:
if(interactive()) {

  # Call the function to view the current directory
  flist <- fileBrowser()
  flist

  # To call the function with a path do
  # fileBrowser(path = "yourPath")
}

A function that import a text file into R

Description

Given a file name, this function imports the text file into R.

Usage

fileWizard(filename = "", fun = read.table, file = "file",
basic = c("header", "sep"), getFocus = TRUE)
fileWizard(filename = "", fun = read.table, file = "file",
basic = c("header", "sep"), getFocus = TRUE)

Arguments

`filename`	A character string for the name of the text file to be imported
`fun`	An R function that is going to be used to read the file. Default to `read.table`
`file`	A character string for the name of the argument to fun that defines the name of the file to be read
`basic`	A vector of character strings for names of the arguments to fun that will have separate entry boxes on the widget to be produced. Default to "header" and "sep"
`getFocus`	`getFocus` a boolean indicating whether a widget should grab the focus

Details

This function is only partially finished and will be improved soon. It currently allows uesrs to view a given file and change the settings for header and sep arguments of read.table. A file will be read in based on the values of the two arguments and return.

Value

This function returns a data frame for the file read in.

Author(s)

Jianhua Zhang

References

R News Vol. 1/3, September 2001

Examples

if(interactive()) {
  # Only the interface is displyed as no real file is given
  fileWizard()  
}
if(interactive()) {
  # Only the interface is displyed as no real file is given
  fileWizard()  
}

Function to create a light weight widget showing a text string

Description

Given a text string and coordinations, this function creates a light weight tcltk widget with showing the text string passed.

Usage

getLightTW(x, y, text)
getLightTW(x, y, text)

Arguments

`x`	`x` an interger for the horizontal position for the widget to appear
`y`	`y` an integer for the vertical position for the widget to appear
`text`	`text` a character string to be show in the widget

Details

When the function is invoked, a box containing the text will appear at the position specified by x, and y. Click the widget makes it disappear.

Value

This function does not return any value

Author(s)

Jianhua Zhang

Examples

if(interactive()){
    getLightTW(200, 200, "Click Me!")
}
if(interactive()){
    getLightTW(200, 200, "Click Me!")
}

Obtaining values of widgets on a given widget

Description

This function returns a list containing the values for widgets on a widget created by function widgetRender. It takes a list defining the widget and returns a named list containing the values for each of the widgets.

Usage

getWvalues(W)
getWvalues(W)

Arguments

`W`	`W` a list of lists defining the widgets that are used to make a widget

Details

For a widget containing 3 widgets each with some associated functionalities, the list is defined as this:

pW1 <- list(Name="AAA", Value="bbb", toText=function(x) paste(x,collapse= ","), fromText=NULL, canEdit=TRUE, buttonFun = fileBrowser, buttonText = "Browse")

pW2 <- list(Name="BBB", Value="x,y,z", toText=function(x) paste(x, collapse=","), fromText=NULL, canEdit=TRUE, buttonFun = ls, buttonText = "List")

pW3 <- list(Name="CCC", Value="ccc", toText=function(x) paste(x, collapse = ","), fromText=NULL, canEdit=TRUE, buttonFun=NULL, buttonText=NULL)

widget1 <- list(wList = list(a = pW1, b = pW2, c = pW3), preFun = function() "Hi", postFun = function() "Bye")

widget1 will be used to create a widget with 3 entry boxes. When users modify the values through the widget created, new values will be kept in the list and widget1 will be returned up exist. getWvalues is useful to capture the values for each widgets on the widget.

Value

This function returns a list of:

`comp1`	Description of ‘comp1’
`comp2`	Description of ‘comp2’

Author(s)

Jianhua Zhang

Examples

# Define the widgets
  pW1 <- list(Name="AAA", Value="bbb",
            toText=function(x) paste(x,collapse= ","), fromText=NULL,
            canEdit=TRUE,
            buttonFun = fileBrowser, buttonText = "Browse")

  pW2 <- list(Name="BBB", Value="x,y,z",
            toText=function(x) paste(x, collapse=","), fromText=NULL,
            canEdit=TRUE, buttonFun = ls, buttonText = "List")

  pW3 <- list(Name="CCC", Value="ccc",
            toText=function(x) paste(x, collapse = ","), fromText=NULL,
            canEdit=TRUE, buttonFun=NULL,  buttonText=NULL)

  widget1 <- list(wList = list(a = pW1, b = pW2, c = pW3),
                preFun  = function() "Hi",
                postFun = function() "Bye")

  if(interactive()){
      tt <- widgetRender(widget1, "try")
      getWvalues(tt)
  }else{
      getWvalues(widget1)
  }
# Define the widgets
  pW1 <- list(Name="AAA", Value="bbb",
            toText=function(x) paste(x,collapse= ","), fromText=NULL,
            canEdit=TRUE,
            buttonFun = fileBrowser, buttonText = "Browse")

  pW2 <- list(Name="BBB", Value="x,y,z",
            toText=function(x) paste(x, collapse=","), fromText=NULL,
            canEdit=TRUE, buttonFun = ls, buttonText = "List")

  pW3 <- list(Name="CCC", Value="ccc",
            toText=function(x) paste(x, collapse = ","), fromText=NULL,
            canEdit=TRUE, buttonFun=NULL,  buttonText=NULL)

  widget1 <- list(wList = list(a = pW1, b = pW2, c = pW3),
                preFun  = function() "Hi",
                postFun = function() "Bye")

  if(interactive()){
      tt <- widgetRender(widget1, "try")
      getWvalues(tt)
  }else{
      getWvalues(widget1)
  }

Automatically determines whether a data file has a header and what delimiter is used to separate data columns

Description

This function reads a few lines from a data text file and determines whether a header exists, what the delimiter, and what data type each column is for a given file.

Usage

guess.sep(file.name, numLine = 5, seps = "", isFile = TRUE)
guess.header(twoLines, sep)
find.type(file.name, sep, header = FALSE, numLine = 5, isFile = TRUE)
charOrNum(vect)
getRowNames(file.name, sep, header, skip)
guess.sep(file.name, numLine = 5, seps = "", isFile = TRUE)
guess.header(twoLines, sep)
find.type(file.name, sep, header = FALSE, numLine = 5, isFile = TRUE)
charOrNum(vect)
getRowNames(file.name, sep, header, skip)

Arguments

`file.name`	`file.name` a character string for the name of the file of interests
`numLine`	`n` an integer or character indicating the total number of lines to be read from the file for making the determination
`seps`	`seps` a vector of characters of potential delimiters to be used to make the determination. Default delimiters include " ", ",", ";", and "\t". Anything inaddition to the default will have to be included in seps
`twoLines`	`twoLines` a vector of character string including the first two lines of a file that will be used to determine whether the file has a header
`sep`	`sep` a character for the delimiter used to separate columns in a file
`vect`	`vect` a vector of character or numeric string
`header`	`header` a boolean indicating whether a file has headers
`isFile`	`isFile` a boolean that is TRUE when `file.name` is a file or FALSE an object
`skip`	`skip` an integer for the number of lines to be skiped using `read.table`

Details

guess.sep calls guess.sep and find.type to determine the header, delimiter, and column data type of a file.

charOrNum determines which elements of a vector are numeric or character.

Value

This function returns a list containing

`header`	TRUE if there is a header and FALSE otherwise
`separater`	A character string indicating the delimiter used
`type`	A vector of character strings that are either character or numeric

Author(s)

Jianhua Zhang

Examples

# Create a temp file
tempData <- matrix(1:20, ncol = 4)
write.table(tempData, file = "tempData", quote = FALSE, sep =
"\t", row.names = FALSE, col.names = TRUE)

guess.sep("tempData")

unlink("tempData")
# Create a temp file
tempData <- matrix(1:20, ncol = 4)
write.table(tempData, file = "tempData", quote = FALSE, sep =
"\t", row.names = FALSE, col.names = TRUE)

guess.sep("tempData")

unlink("tempData")

String Prefix and Suffix Checking

Description

These functions return a function for determining if a given prefix, suffix, or set of characters passed to this function exists in a character string passed to the returned function.

Usage

hasChar(toCheck, what = "")
hasPrefix(aPrefix)
hasSuffix(aSuffix)
hasChar(toCheck, what = "")
hasPrefix(aPrefix)
hasSuffix(aSuffix)

Arguments

`aPrefix`	character string to be used as the prefix to be checked for
`aSuffix`	character string to be used as the suffix to be checked for
`toCheck`	`toCheck` a character string to be used to check to see if it exists in a character string passed to the returned function
`what`	`what` a character string defining whether toCheck will be used as a prefix (what = "prefix"), suffix (what = "suffix"), or a set of characters (what = "") to check the character string passed to the returned function

Details

The prefix (or suffix) is passed to hasPrefix (or hasSuffix) and then the returned function can be used to check for the existence of that prefix (suffix) in a string passed to that function.

hasChar is a more general function that determines the existence of prefix, sufix, or a set of a characters in a character string passed to the returned function.

Value

A function which itself returns a logical (of length 1) indicating if the prefix/suffix is found (TRUE) or not.

Author(s)

Jianhua (John) Zhang

Examples

# Function for checking for a prefix "xxx" :
chkPfun <- hasChar("xxx", what = "prefix")
# Function for checking for a suffix ".tex" :
chkSfun <- hasChar(".tex", what = "suffix")

chkPfun("xxx.tex")
chkPfun(".xxx")
chkSfun("xxx.tex")
chkSfun("yyyyy")
chkSfun("yxxx.text")
# Function for checking for a prefix "xxx" :
chkPfun <- hasChar("xxx", what = "prefix")
# Function for checking for a suffix ".tex" :
chkSfun <- hasChar(".tex", what = "suffix")

chkPfun("xxx.tex")
chkPfun(".xxx")
chkSfun("xxx.tex")
chkSfun("yyyyy")
chkSfun("yxxx.text")

Functions to input data for an AnnotatedDataFrame object

Description

This functions allow users to read data from an existing file or an R data.frame object and use the data frame to construct an AnnotatedDataFrame object.

Usage

importPhenoData(fileName, sampleNames = NULL, from = NULL)
createPData(pdata, varList)
writePDRowNames(pdata, sampleNames)
writePhenoTable(base, textWidget, pdata)
makePhenoData(pdata)
convert2PData(phenoList)
getOBJWidget(type = NULL)
objExists(name, type = NULL)
getSNCNums(sampleNames)
getCovarDesc(varList)
importPhenoData(fileName, sampleNames = NULL, from = NULL)
createPData(pdata, varList)
writePDRowNames(pdata, sampleNames)
writePhenoTable(base, textWidget, pdata)
makePhenoData(pdata)
convert2PData(phenoList)
getOBJWidget(type = NULL)
objExists(name, type = NULL)
getSNCNums(sampleNames)
getCovarDesc(varList)

Arguments

`fileName`	a character string for the name of a file that is going to be used to build an AnnotatedDataFrame object.
`sampleNames`	a vector of character strings for the names of samples. The length of `sampleNames` should be the same as the number of rows of an existing file or data.frame if an AnnotatedDataFrame object is to be created based on a file or data.frame.
`pdata`	a data.frame for the experimental data.
`base`	an RTcl object for the base window a widget resides.
`textWidget`	an RTcl object for a text box widget.
`phenoList`	a list of lists for tclVar() objects.
`type`	a character string for the class of a object e.g. data.frame, AnnotatedDataFrame.
`name`	a character string for the name of an object.
`varList`	a list of characters with names being covariate names and values being short descriptions of covariate names.
`from`	a character string indicating how an AnnotatedDataFrame object will be created. "file" - create from an existing file, "object" - create from an existing data frame object, "edit" - create by editing an existing AnnotatedDataFrame object, and "new" create a new AnnotatedDataFrame object from scratch. NULL or any other values for `from` will invoke a widget that allows users to select one of the four means from an interface.

Details

When import a data.frame or AnnotatedDataFrame object, the object to be imported should have been stored in .GlobelEnv. All the objects of data.frame or AnnotatedDataFrame will be made available through a browser.

The main widget if importPhenoData that calls other functions/widgets to have the job done.

Package Biobase is required for importPhenoData but the requirement id not forced as it is the only time the package is used. Users have to make sure that Biobase is available.

Value

An AnnotatedDataFrame object.

Note

This function is intended for use by function read.phenoData of Biobase

Author(s)

Jianhua Zhang

References

AnnotatedDataFrame class in Biobase

Examples

if(interactive()){
    importPhenoData()
}
if(interactive()){
    importPhenoData()
}

A widget for importing data to R

Description

Functions constructs a widget that allows users to inport data file to R. The imported data will be returned as an R data frame together with the argument list used to import the data using read.table

Usage

importWizard(filename = "", maxRow = 400)
initImportWizard(env)
getTopCan(base, env)
getAFrame(base, env)
finish(env)
getState1Frame(base, env)
setState1BFrame(frame, env)
setState1TFrame(frame, viewer, delims, env, startList)
showData4State1(widget, env)
setState1MFrame(frame, env, dataViewer)
getState2Frame(base, env, state = "state2", reset = FALSE)
setState2MFrame(frame,env)
setSepRadios(frame, env, state = "state2")
setQuoteList(frame, env)
setQuote(listBox, env, state = "state2")
setState2BFrame(frame, env)
showData4State2(canvas, env, state = "state2")
getState3Frame(base, env)
setState3TFrame(frame, env)
setState3BFrame(frame, env)
getName4Data(filename, objType)
writeCol4Matrix(tempFrame, dataFile, colInfos, env)
popStartLine(startList, env)
readFileByLines(filename)
importWizard(filename = "", maxRow = 400)
initImportWizard(env)
getTopCan(base, env)
getAFrame(base, env)
finish(env)
getState1Frame(base, env)
setState1BFrame(frame, env)
setState1TFrame(frame, viewer, delims, env, startList)
showData4State1(widget, env)
setState1MFrame(frame, env, dataViewer)
getState2Frame(base, env, state = "state2", reset = FALSE)
setState2MFrame(frame,env)
setSepRadios(frame, env, state = "state2")
setQuoteList(frame, env)
setQuote(listBox, env, state = "state2")
setState2BFrame(frame, env)
showData4State2(canvas, env, state = "state2")
getState3Frame(base, env)
setState3TFrame(frame, env)
setState3BFrame(frame, env)
getName4Data(filename, objType)
writeCol4Matrix(tempFrame, dataFile, colInfos, env)
popStartLine(startList, env)
readFileByLines(filename)

Arguments

`filename`	`filename` a character string for the name of the file to be imported. The default is an empty string and users have to click a browse button to get the file name through `fileBrowser`
`maxRow`	`maxRow` an integer for the maximum number of rows of the data file to be imported to be shown on the widget. The default is 200 rows
`env`	`env` an R environment object for storing the required information
`base`	`base` a tcltk window to hold a canvas on the top and frames in the bottom
`frame`	`frame` a tcktl frame
`viewer`	`viewer` a tkwin object for a widget
`delims`	`delims` a character string for a file separater
`widget`	`widget` a tcltk widget
`state`	`state` a character string for the state of importing process
`listBox`	`listBox` a tcltk list box
`canvas`	`canvas` a tcltk canvas
`tempFrame`	`tempFrame` a tcltk frame that will be used to hold widget elements
`dataFile`	`dataFile` a data matrix holding data to be displayed
`colInfos`	`colInfos` an object of class colInfo with a name, type, and drop slot
`reset`	`reset` a boolean that is TRUE when the window needs to be reset
`dataViewer`	`dataViewer` a tkwin object for a list box
`objType`	`objType` a character string indicating the data type of an object to be saved. Defaulted to "object"
`startList`	`startList` a tk text box object

Details

importWizard mimics the interface of MS Excel and collects arguments for the function read.table. Due to performace concern, a maximum number of rows (maxRow) set by users will be displayed. Overly long data set may cause slow response of the system.

initImportWizard initializes the interface for importWizard by creating a widget with an empty top canvas and bottom frame filled with four buttons.

getTopCan Creates a canvas that is going to be filled by a frame created by other functions depending on the state of the importing process.

getAFrame Gets a frame for the canvas created by initImportWizard based on the current state of importing process.

finish Finishes the importing process and returns a data frame read from a file using read.table.

getState1Frame Returns a tcltk frame containing a list box to show a data file read by readLines and widgets for user imports.

setState1BFrame Fills the bottom frame of the frame created by getState1Frame with a list box.

setState1TFrame Fills the top frame of the frame created by getState1Frame with a list box.

showData4State1 Populates a tcltk list or text widget with data read using readLines.

setState1MFrame Fills the mid frame of the frame created by getState1Frame.

getState2Frame Returns a tcltk frame containing a canvas to show a data file read by read.table and widgets for user imports.

setState2MFrame Fills the mid frame of the frame created by getState2Frame.

setSepRadios Renders radio buttons for options of file separators in the frame created by setState2MFrame.

setQuoteList Renders the selection list for the quote used by a data file in the frame created by setState2MFrame.

setQuote Sets the value when a user has selected the quote used by a data file.

setState2BFrame Fills the bottom frame of the frame created by getState2Frame with a canvas.

showData4State2 Populates the canvas created by setState2BFrame using data read by read.table.

getState3Frame Returns a tcltk frame containing a canvas to show a data file read by read.table and widgets for user imports.

setState3TFrame Fills the top frame of the frame created by getState3Frame.

setState3BFrame Fills the bottom frame of the frame created by getState3Frame.

getName4Data Takes user input for a file name using a widget.

writeCol4Matrix Creates a tcltk frame with list boxes as columns displaying data of a data matrix.

Value

getTopCan returns a tcltk canvas.

getAFrame returns a tcltk frame.

finish returns a data.frame.

getState1Frame returns a tcltk frame with several widgets.

setState1BFrame returns the tkwin object of list box.

getState2Frame returns a tcltk frame with several widgets.

getState3Frame returns a tcltk frame with several widgets.

getName4Data returns a character string for the name of a file to be saved.

Author(s)

Jianhua Zhang

Examples

  if(interactive()){
      importWizard()
  }
if(interactive()){
      importWizard()
  }

Utilities Creating a Widget With Selection Boxes

Description

These functions create a widget with selection boxes allowing users to view and make selections of items shown on the interface.

Usage

listSelect(aList, topLbl = "Select Elements From The Following List",
           typeFun = stdType, valueFun = stdView)
writeSelBox(baseW, aList, typeFun = NULL, valueFun = NULL)
   writeBut(baseW, butList, butWidth = 6)
writeLabel(baseW, typeFun, valueFun)
listSelect(aList, topLbl = "Select Elements From The Following List",
           typeFun = stdType, valueFun = stdView)
writeSelBox(baseW, aList, typeFun = NULL, valueFun = NULL)
   writeBut(baseW, butList, butWidth = 6)
writeLabel(baseW, typeFun, valueFun)

Arguments

`aList`	list with names and object pairs (e. g. `a = "AAA"`).
`topLbl`	character string for the text to be shown as a title.
`typeFun`	function that takes an R object as an arguement and returns a description of the object.
`valueFun`	function that takes an R object as an argument and shows the content of the object. The function should get the representation of the object and calls `objViewer` to have the representation rendered in a widget.
`baseW`	a window widget to which the selection boxes will be put.
`butList`	a list with names and function pairs that define the name and behavior of buttons to be put on the widget to be generated
`butWidth`	numerical value specifying the width of buttons to be created.

Details

Both typeFun and valueFun have to take an argument (the R object to be shown). It works well for the valueFun function to call objViewer() with whatever to be shown passed to objViewer as an argument.

Value

listSelect() returns a list with the names of the R objects in the original list associated with TRUE (selected) or FALSE (deselected).

Author(s)

Jianhua Zhang

Examples

aList <- list(a = "AAA", b = c(123, 456, 789),
              c = as.data.frame(matrix(1:10, ncol = 2)),
              d = stdType)
# Since user interference is required, the example code does not run
# automatically
if(interactive())
  listSelect(aList)
aList <- list(a = "AAA", b = c(123, 456, 789),
              c = as.data.frame(matrix(1:10, ncol = 2)),
              d = stdType)
# Since user interference is required, the example code does not run
# automatically
if(interactive())
  listSelect(aList)

View the Objects in the Workspace

Description

This widget allows uers to view and select objects from the workspace. When the End button is pressed, the selected objects will be returned as a list.

Usage

objectBrowser(env = .GlobalEnv,fun = noAuto, textToShow = "Select object(s)", nSelect = -1)  
objectBrowser(env = .GlobalEnv,fun = noAuto, textToShow = "Select object(s)", nSelect = -1)

Arguments

`fun`	function to test whether certain conditions are met by the objects. Only objects that meet the conditions will be displayed.
`textToShow`	character with the message to be shown on the widget as an instruction.
`nSelect`	integer indicating the number of objects to select. No limitation if `nSelect = -1` as per default.
`env`	`env` a default environment object to start object Browser

Details

This function will return a list of lists with a "name" and "obj" pair for each object selected. The "name" will be the name of the object and "obj" will be the value of the object. If the object is a package, a description of the contents of the package will be the value. If the selected object is a function, a text string of the original code will be the value. A function can be passed to impose a filtering mechanisms on the objects to be displayed. See function isCharacter for an example of writing a filtering function for objectBrowser.

The buttons and their expected behavior are

Up: Moves one level up along the search list and displays the content in the box for object names on the left of the widget.
Select \>\>: When objects in the box for object names have been highlighted by clicking or clicking/dragging, this button will display the highlighted object names in the box for selected objects on the right.
Reset: Moves back to .GlobalEnv which is the default starting point of the system.
\<\< Remove: When object names in the box for selected objects have been highlighted by clicking or clicking/dragging and this button is pressed, the highlighted object names will be removed from the display.
Clear: Removes all the object names from the box for selected objects.
Cancel: Exits the widget and returns NULL when pressed.
End: Returns a list of lists with names of the objects in the box for selected objects and their corresponding values or NULL if nothing exists in the box.

Value

A list of lists with a name and value pair for each object.

Author(s)

Jianhua (John) Zhang

Examples

## The example here is only run interactively since it requires user
## interference which may cause problems if not available:
if(interactive()) {

# Call the function with the isCharacter function.
r <- objectBrowser()
str(r) # show what we've got
}
## The example here is only run interactively since it requires user
## interference which may cause problems if not available:
if(interactive()) {

# Call the function with the isCharacter function.
r <- objectBrowser()
str(r) # show what we've got
}

Convert Object Names to List of Lists with (name, object) Pairs

Description

This function supports objectBrowser by converting a vector of selected object names to a list of lists with object names and the corresponding objects.

Usage

objNameToList(objNames, env)
objNameToList(objNames, env)

Arguments

`objNames`	character vector giving the names of objects.
`env`	an R environment where R objects are stored

Details

Each list in the list that is going to be returned contains a name for the object and the real value of the object. If the object name is a package name, the contents of the package will be the value associated with the package name.

Value

A list of lists each with a name and an obj component.

Author(s)

Jianhua (John) Zhang

Examples

# Create two R objects
obj1 <- c("aaa", "bbb", "ccc")
env1 <- new.env(parent = baseenv())

# Get a list containing the two objects
nl <- objNameToList(c("obj1", "env1"), parent.frame())
str(nl)

# Create two R objects
obj1 <- c("aaa", "bbb", "ccc")
env1 <- new.env(parent = baseenv())

# Get a list containing the two objects
nl <- objNameToList(c("obj1", "env1"), parent.frame())
str(nl)

Show the Content of an R Object in a Widget

Description

This function takes an R object and shows the content in a list box on a widget.

Usage

objViewer(toView, width = 40, height = 10)
objViewer(toView, width = 40, height = 10)

Arguments

`toView`	R object whose content is to be viewed
`width`, `height`	positive values specifying the width and height of the widget.

Details

The function makes no check of the R object passed and will show whatever the object will be shown when the name is type at an R prompt. Formatting is required before passing the R object to the function.

Value

This function does not return any value

Author(s)

Jianhua Zhang

Examples

# Since user interference is required, the example code only runs
# interactively
if(interactive())
   objViewer("Just to show that the content gets posted")
# Since user interference is required, the example code only runs
# interactively
if(interactive())
   objViewer("Just to show that the content gets posted")

A widget to explore R packages

Description

This widget allows users to explore R packages in the R library and try the example code.

Usage

pExplorer(pkgName = "", pkgPath = "", exclude = getExclude(), getFocus =
TRUE)
getPkgContents(pkgName, exclude = getExclude())
getFileContents(path, fileName)
getExclude()
getRPkgs(pkgPath)
hasDesc(pkgPath)
procRda(fileName)
procHelp(fileName)
procPDF(fileName)
procHTML(fileName)
pExplorer(pkgName = "", pkgPath = "", exclude = getExclude(), getFocus =
TRUE)
getPkgContents(pkgName, exclude = getExclude())
getFileContents(path, fileName)
getExclude()
getRPkgs(pkgPath)
hasDesc(pkgPath)
procRda(fileName)
procHelp(fileName)
procPDF(fileName)
procHTML(fileName)

Arguments

`pkgPath`	`pkgPath` a character string for the path where R packages are loacted
`path`	`path` a character string for the path of a given file
`pkgName`	`pkgName` a character string for the name (including path) of an R package to be explored
`fileName`	`fileName` a character string for the name (including path) of a file of interest
`exclude`	`exclude` a vector of character strings containing the directory or file names that will not be available for explorering. Package names have to have a system file separator appanded to the end (e. g. "/" under Unix)
`getFocus`	`getFocus` a boolean indicating whether a widget should grab the focus

Details

With or without a package name, the widget will have all the installed R package names in a dropdown list for user to select. As the default, the first element from list.files will be selected and the contents displayed if no package name is given.

getPkgContents gets the contents of a given R package and getFileContents gets the contents of a givan file.

getRPkgs, hasDesc, procRda, procHelp, procPDF, and procHTML are functions called by pExplorer to process different file or directory types.

Value

The widget returns invisiable()

Author(s)

Jianhua Zhang

References

Documentation on R packages

Examples

    require("tkWidgets") || stop("tkWidgets not available")
    getPkgContents(.libPaths(), "tkWidgets")
    getFileContents(file.path(path.package("tkWidgets"), "help"),
        list.files(file.path(path.package("tkWidgets"), "help"))[1])
    if(interactive()){
        pExplorer()
    }
require("tkWidgets") || stop("tkWidgets not available")
    getPkgContents(.libPaths(), "tkWidgets")
    getFileContents(file.path(path.package("tkWidgets"), "help"),
        list.files(file.path(path.package("tkWidgets"), "help"))[1])
    if(interactive()){
        pExplorer()
    }

Pick Elements From Vector of Strings

Description

Takes a vector of strings and then checks to see if the predefined conditions are met for each element. Elements that meet the conditions will be included in the vector returned and the others not.

Usage

pickFiles(fileNames, fun = function(x) TRUE,
          prefix = NULL, suffix = NULL, exclude = .Platform$file.sep)
pickFiles(fileNames, fun = function(x) TRUE,
          prefix = NULL, suffix = NULL, exclude = .Platform$file.sep)

Arguments

`fileNames`	vector of strings that will be checked.
`fun`	function to be used to check the strings. Default is no checking.
`prefix`	character used to check to see if strings in the vector have the prefix.
`suffix`	character used to check to see if strings in the vector have the suffix.
`exclude`	character string with which strings in the vector will be excluded form the checking. The default is to exclude all the directory names and always return them.

Details

The function fun will be used only when both prefix and suffix are NULL. If a prefix is not NULL, that prefix will be checked. A suffix is going to be checked when prefix is NULL.

Value

Character vector of file names satisfying the conditions.

Author(s)

Jianhua Zhang

Examples

# Return every thing from the current directory
pickFiles(list.files())

# Create a temp file
file.create("myFile")

# Returns subdirectory names and file names with a prefix of "my"
pickFiles(list.files(), prefix = "my")

# create another temp file
file.create("temp.tex")

# Return subdirectory names and file names with a suffix of ".tex"
pickFiles(list.files(), suffix = ".tex")

# clearn up
unlink("myFile")
unlink("temp.tex")
# Return every thing from the current directory
pickFiles(list.files())

# Create a temp file
file.create("myFile")

# Returns subdirectory names and file names with a prefix of "my"
pickFiles(list.files(), prefix = "my")

# create another temp file
file.create("temp.tex")

# Return subdirectory names and file names with a suffix of ".tex"
pickFiles(list.files(), suffix = ".tex")

# clearn up
unlink("myFile")
unlink("temp.tex")

Function that builds a widget to allow users to select items from available sources

Description

Given a vector of characters, this function creates a widget containing list box to allow users to visually select elements from the vector.

Usage

pickItems(items, title1 = "Items to pick", title2 = "Picked items")
pickItems(items, title1 = "Items to pick", title2 = "Picked items")

Arguments

`items`	`items` a vector for the available source elements to be selected
`title1`	`title1` a character string for the title of the list box that shows the list of items to be selected from
`title2`	`title2` a character string for the title of the list box that shows the items that have been selected

Details

This function is to provide visual support to other functions and thus may not have much use otherwise.

Value

This function returns a vector of select items.

Author(s)

Jianhua Zhang

References

R tcltk

Examples

options <- paste("Option", 1:10, sep = "")
if(interactive()){
    pickItems(options)
}
options <- paste("Option", 1:10, sep = "")
if(interactive()){
    pickItems(options)
}

Determine What to Be Sent to a Widget

Description

This function takes a vector of object names and determines what will be sent to (e.g. the objectBrowser) widget for display based on the default and user input requirements.

Usage

pickObjs(objNames, fun = noAuto)
noAuto(x)
pickObjs(objNames, fun = noAuto)
noAuto(x)

Arguments

`objNames`	`objNames` character vector with object names to be processed
`fun`	`fun` function checking the object names for satisfaction of certain requirement
`x`	`x` a character string for the name of an object

Details

Packages and environments are always displayed.

Value

Character vector of object names that satisfy the requirements.

Author(s)

Jianhua (John) Zhang

Examples

# Returns names of package and environment objects in the search path.
pickObjs(search())
# Returns names of package and environment objects in the search path.
pickObjs(search())

Functions to support importWizard

Description

The functions are to support importWizard and may not have much practical use otherwise.

Usage

setArgsList(filename, env, isFile = TRUE, init = TRUE)
whatDeli(delimiter)
getMoreArgs()
assignArgs(value, env)
getArgs(env)
assignShowNum(value, env)
getShowNum(env)
assignCState(value, env)
getCState(env)
assignColInfo(value, env)
getColInfo(env)
setColInfos(types, env)
changeState(canvas, backBut, nextBut, env, forward = TRUE, endBut, viewBut)
setNewState(env, backBut, nextBut, forward = TRUE, endBut, viewBut)
addArgs(env)
dropArgs(env)
setSkip(widget, env, state = "state1")
moreArgs(env)
dropColumn(index, env)
setColName(index, entryBox, env)
setColType(index, entryBox, env)
assignLineData(lineData, env)
getLineData(env)
setArgsList(filename, env, isFile = TRUE, init = TRUE)
whatDeli(delimiter)
getMoreArgs()
assignArgs(value, env)
getArgs(env)
assignShowNum(value, env)
getShowNum(env)
assignCState(value, env)
getCState(env)
assignColInfo(value, env)
getColInfo(env)
setColInfos(types, env)
changeState(canvas, backBut, nextBut, env, forward = TRUE, endBut, viewBut)
setNewState(env, backBut, nextBut, forward = TRUE, endBut, viewBut)
addArgs(env)
dropArgs(env)
setSkip(widget, env, state = "state1")
moreArgs(env)
dropColumn(index, env)
setColName(index, entryBox, env)
setColType(index, entryBox, env)
assignLineData(lineData, env)
getLineData(env)

Arguments

`filename`	`filename` a character string for the full name of a file
`env`	`env` an R environment object for storing information
`delimiter`	`delimiter` a character string for the delimiter whose letter representation is sought
`value`	`value` a character or numerical value to be assigned to a variable
`backBut`	`backBut` a tkwin object for the button that shifts back to the previous state
`nextBut`	`nextBut` a tkwin object for the button that shifts to the next state
`forward`	`forward` a boolean indicating the direction of state change
`widget`	`widget` a tcltl widget
`state`	`state` a character string for the state of importing process
`index`	`index` an integer for the index of the list for column information
`entryBox`	`entryBox`

a tcltk entry box.

`canvas`	`canvas` a tcltk canvas
`types`	`types` a vecter of string indicating the types of data columns
`lineData`	`lineData` a vector of character strings read in using `readLines`
`endBut`	`endBut` a tkwin object for the button that ends the process when pressed
`viewBut`	`viewBut` a tkwin object for the button that refresh the window when pressed
`init`	`init` a boolean that is TRUE when the widget is first set up and FALSE otherwise
`isFile`	`isFile` a boolean that is TRUE if `fileName` is a file

Details

setArgsList calls function guess.sep to figure out the the header, sep, and data type of a file and sets the values for argument list and colInfo.

whatDeli gets the word representation of delimiters (e.g. tab for "\t").

getMoreArgs generates a widget using widgetTools to collect some of the arguments for read.table.

assignArgs updates "argsList" stored in a predefined environment.

getArgs Gets "argsList" from a predefined environment.

assignShowNum Updates the value for "showNum" (number of rows to show in the interface.

getShowNum Gets the value for "showNum" (number of rows to show in the interface.

link{assignCState} Updates the value of "currentState" that is stored in a predefined environment.

getCState Gets the vlaue of "currentState" that is stored in a predefined environment.

assignColInfo Updates the values of "colInfos" (column information) that is stroed in a predefined environment.

getColInfo Gets the values of "colInfos" (column information) that is stroed in a predefined environment.

setColInfos Creates colInfo objects and sets the value of 'colInfos' list.

changeState changes the state and thus the interface of a widget.

setNewState sets the state of a importing process.

addArgs adds a new state to the argument list for states.

dropArgs removes a state from the argument list for states.

setSkip Sets the value for the number of lines to skip when readling a data file.

moreArgs Gets some of the arguments for importing data using read.table.

dropColumn Sets the index values for data columns that are going to be droped when read using read.table.

setColName Sets the column names for a data file by getting column names from correct entry boxes.

setColType Sets the column type for a data file by getting column type information from correct entry boxes.

Value

whatDeli returns a character string.

getMoreArgs returns a list of arguments.

getArgs returns a list of the arguments for read.table.

getShowNum returns an integer for the number of rows to show.

getCState returns a character string for the current state.

getColInfo returns a colInfo object contains column information.

Author(s)

Jianhua Zhang

Examples

  # No example is given as functions require the set up of the working
  # environment. 
# No example is given as functions require the set up of the working
  # environment.

Provide Default Behavior for listSelect Helper Functions

Description

The function listSelect takes two functions which define how the type information and content of R objects will be shown on the widget created by listSelect. Functions stdType() and stdView() provide the default behavior.

Usage

stdType(toCheck)
stdView(toView)
stdType(toCheck)
stdView(toView)

Arguments

toCheck, toView

arbitrary R object.

Details

These functions can be viewed as exmaples of defining functions for the typeFun and valueFun arguments of the listSelect function.

Value

stdType() returns a character string describing the type of the R object.

stdView()

Author(s)

Jianhua Zhang

Examples

stdType(123)
stdType("What am I")

str(mydf <- data.frame(x = 2:8, ch = letters[1:7]))
stdType(mydf)# "list"
stdType(stdType)

if(interactive()) {## stdView() needs UI:
  stdView(1:10)
  stdView(mydf)
 }
stdType(123)
stdType("What am I")

str(mydf <- data.frame(x = 2:8, ch = letters[1:7]))
stdType(mydf)# "list"
stdType(stdType)

if(interactive()) {## stdView() needs UI:
  stdView(1:10)
  stdView(mydf)
 }

Simple Interface to enter experimental design information

Description

This function provides a widget for users to enter experimental design MIAME information.

Usage

tkMIAME()
tkMIAME()

Details

This widget provides an interface to enter experimental information following the MIAME (Minimum Information About a Microarray Experiment) standard.

A draft of the latest document (v. 1.1) is http://www.mged.org/Workgroups/MIAME/miame_1.1.html

Brazma et al. divide the MIAME into 6 sections 1. Experimental design, 2. Array design, 3. Samples, 4. Hybridizations, 5. Measurements, and 6. Normalization controls This widget is for the first section. We ask for the user to enter: experimenter name, laboratory, contact information, a single-sentence experiment title, an abstract describing the experiment, URLs. This slot could also include a formal statistical description of the experimental design (e.g. using factors). Some of this info is already stored in AnnotatedDataFrame or elsewhere.

The function returns a list that is intended for the creation of an object of class MIAME. However, we return a list so that the function can work independently of the Biobase package.

Value

A list containing entries:

`ExperimentName`	character string
`LabName`	character string
`ContactInfo`	character string
`ExperimentTitle`	character string
`Description`	character string
`URL`	character string

Author(s)

Majnu John

References

“Minimum information about a microarray experiment (MIAME)-toward standards for microarray data”, A. Brazma, et al., Nature Genetics, vol. 29 (December 2001), pp. 365-371, http://www.mged.org/Workgroups/MIAME/miame_1.1.html

Simple interface to enter AnnotatedDataFrame

Description

This widget provides an interface to create AnnotatedDataFrame-class instances.

Usage

tkphenoData(sampleNames)
tkphenoData(sampleNames)

Arguments

sampleNames

sampleNames for which we will enter phenotypic data.

Details

The function returns a list of character matrices intended to be used as the pData and varLabels slots of an instance of AnnotatedDataFrame-class.

Value

A list of two matrices

`pData`	a character matrix containing phenotypic data.
`varLabels`	a character vector with covariate description.

Author(s)

Majnu John

Simple interface to associate sample names with files

Description

This widget provides an interface to enter names to be associated with files containing array expression information related to a particular sample.

Usage

tkSampleNames(..., filenames = character(0))
tkSampleNames(..., filenames = character(0))

Arguments

`...`	the filenames to be associated with a sample name, supplied individually and/or as a character vector
`filenames`	a character vector of filenames to be associated with a sample name.

Details

AnnotatedDataFrame-class objects will use sample names as row names for its pData. The colnames of the expression matrices in ExpressionSet-class use this as well. Many times, each of these columns are obtained from a file. Rather than use the, sometimes ugly, filename we can use the sample names that this interface associates with each file.

The function returns a character matrix intended to be used to create sample names in AnnotatedDataFrame and ExpressionSet. However, the function can be used independently of the Biobase package.

Value

A character matrix with the first column the filenames the second column the sample names to associate.

Author(s)

Majnu John

Deal with Names and Values of Widget Created by widgetRender()

Description

Functions in this group print or list the names or/and values of the widget elements on a widget created by widgetRender().

Usage

values.Widget(x)
values.Widget(x)

Arguments

`x`	A list (print.pWidget) or list of lists(print.Widget, values.Widget) that representing a widget element (list) on a widget or a widget (list of lists) generated by using the function widgetRender.

Details

print.pWidget takes a list defining a widget element on a widget generated by using the function widgetREnder. An example of a valid list will be:

pW1 <- list(Name="AAA", Value="bbb", toText=function(x) paste(x,collapse = ","), fromText=NULL, canEdit=TRUE, buttonFun = fileBrowser, buttonText = "Browse")

print.Widget and values.Widget take a list of lists defining all the widget elements on a widget generated using the function widgetRender. An example of a valid list will be:

pW1 <- list(Name="AAA", Value="bbb", toText=function(x) paste(x,collapse = ","), fromText=NULL, canEdit=TRUE, buttonFun = fileBrowser, buttonText = "Browse")

pW2 <- list(Name="BBB", Value="x,y,z", toText=function(x) paste(x, sep=","), fromText=NULL, canEdit=TRUE, buttonFun = ls, buttonText = "List")

pW3 <- list(Name="CCC", Value="ccc", toText=function(x) paste(x, collapse = ","), fromText=NULL, canEdit=TRUE, buttonFun=NULL, buttonText=NULL)

widget1 <- list(wList = list(a = pW1, b = pW2, c = pW3), preFun = function() "Hi", postFun = function() "Bye")

Value

returnList

values.Widget returns a list of lists each with the name and value of an entry box on the widget created.

Author(s)

Jianhua (John) Zhang

Examples

# Create the lists and list of lists
  pW1 <- list(Name="AAA", Value="bbb",
              toText=function(x) paste(x,collapse = ","),
              fromText=NULL, canEdit=TRUE, buttonFun = fileBrowser,
              buttonText = "Browse")

  pW2 <- list(Name="BBB", Value="x,y,z", toText=function(x) paste(x, sep=","),
            fromText=NULL, canEdit=TRUE, buttonFun = ls,
           buttonText = "List")

  pW3 <- list(Name="CCC", Value="ccc",
              toText=function(x) paste(x, collapse = ","),
              fromText=NULL, canEdit=TRUE, buttonFun=NULL,
              buttonText=NULL)

  widget1 <- list(wList = list(a = pW1, b = pW2, c = pW3),
                  preFun = function() "Hi",
                  postFun = function() "Bye")

# Define the classes
class(pW1) <- c("pWidget", "textbox")
class(widget1) <- "Widget"

# Call the funcitons
print.pWidget(pW1)
print.Widget(widget1)
values.Widget(widget1)
# Create the lists and list of lists
  pW1 <- list(Name="AAA", Value="bbb",
              toText=function(x) paste(x,collapse = ","),
              fromText=NULL, canEdit=TRUE, buttonFun = fileBrowser,
              buttonText = "Browse")

  pW2 <- list(Name="BBB", Value="x,y,z", toText=function(x) paste(x, sep=","),
            fromText=NULL, canEdit=TRUE, buttonFun = ls,
           buttonText = "List")

  pW3 <- list(Name="CCC", Value="ccc",
              toText=function(x) paste(x, collapse = ","),
              fromText=NULL, canEdit=TRUE, buttonFun=NULL,
              buttonText=NULL)

  widget1 <- list(wList = list(a = pW1, b = pW2, c = pW3),
                  preFun = function() "Hi",
                  postFun = function() "Bye")

# Define the classes
class(pW1) <- c("pWidget", "textbox")
class(widget1) <- "Widget"

# Call the funcitons
print.pWidget(pW1)
print.Widget(widget1)
values.Widget(widget1)

An interface to interact with vignette code chunks

Description

This function provides a widget for viewing, editing, and executing code chunks of vignettes.

Usage

vExplorer(title = "BioC Vignettes Explorer", pkgName = "", font =
ifelse(.Platform$OS.type == "unix", "arial 14", "arial 11"))
viewVignette(title, packName, vigPath, font = "arial 11")
vExplorer(title = "BioC Vignettes Explorer", pkgName = "", font =
ifelse(.Platform$OS.type == "unix", "arial 14", "arial 11"))
viewVignette(title, packName, vigPath, font = "arial 11")

Arguments

`title`	character string for the name to be displayed as the title of the widget to interact with code chunks.
`pkgName`	vector (of length 1 for `pkgName`) of character strings for names of Bioconductor packages the code chunks of whose vignettes will be explored.
`packName`	same as pkgName
`vigPath`	character string for the full qualified name of a vignette to be explored.
`font`	a character string for the name and size of the font to be used for text rendered on the widgets (e. g. "arial 11")

Details

By default, packNames = "", all the installed packages will be examined and those that have vignettes will be listed to allow users to choose from.

Value

This function does not return any useful value.

Note

This function is part of the Bioconductor project at Dana-Faber Cancer Institute to provide Bioinformatics functionalities through R.

Author(s)

Jianhua Zhang

References

http://www.bioconductor.org

Examples

if(interactive()){
    require("DynDoc", character.only = TRUE)
    require("tools", character.only = TRUE)
    require("widgetTools", character.only = TRUE)
    vExplorer()
    path <- path.package("widgetTools")
    vigList <- pkgVignettes("widgetTools")
    viewVignette("BioC VignetteBrowser", "widgetTools", vigList$docs)
}
if(interactive()){
    require("DynDoc", character.only = TRUE)
    require("tools", character.only = TRUE)
    require("widgetTools", character.only = TRUE)
    vExplorer()
    path <- path.package("widgetTools")
    vigList <- pkgVignettes("widgetTools")
    viewVignette("BioC VignetteBrowser", "widgetTools", vigList$docs)
}

Render a Tk Widget from Given Specifications

Description

This function takes a list that specifies the appearance and behavior of a Tk widget and renders the widget accordingly.

Usage

widgetRender(iWidget, tkTitle)
widgetRender(iWidget, tkTitle)

Arguments

`iWidget`	list of lists that specifies the appearance and behavior of the widget to be rendered.
`tkTitle`	character string for the text to appear in the title bar of the widget to be rendered.

Details

The widget to be rendered normally consists of frames with three widgets arranged in a row. The first widget is normally a label for the name of the second widget. The second widget can be any type of widgets. The third widget is a button widget that defines some behavior to be associated with the second widget. For example, a button that will cause something to be displayed in the second widget when pressed. The third widget can be missing if no such association is required.

The widget to be rendered also has two buttons at the bottom part of the widgets. The followings are the name and behavior of the buttons:

Cancel -: The unmodified list passed to the function at the time of invocation will be returned when pressed.
End -: A modified version of the iWidget argument will be returned when pressed. The returned list has the same number of elements as the original one but with the values modified based on the entries in corresponding widgets items.

Value

A list of lists with the original values of the passed modified or unmodified depending on whether the cancel or end button pressed.

Author(s)

Jianhua (John) Zhang

References

Peter Dalgaard (2001) A Primer on the R-Tcl/Tk Package; R News 1 (3), 27–31 http://CRAN.R-project.org/doc/Rnews/

Examples

# Create the list to be passed
pW1 <- list(Name="AAA", Value="bbb",
            toText=function(x) paste(x,collapse= ","), fromText=NULL,
            canEdit=TRUE,
            buttonFun = fileBrowser, buttonText = "Browse")

pW2 <- list(Name="BBB", Value="x,y,z",
            toText=function(x) paste(x, collapse=","), fromText=NULL,
            canEdit=TRUE, buttonFun = ls, buttonText = "List")

pW3 <- list(Name="CCC", Value="ccc",
            toText=function(x) paste(x, collapse = ","), fromText=NULL,
            canEdit=TRUE, buttonFun=NULL,  buttonText=NULL)

widget1 <- list(wList = list(a = pW1, b = pW2, c = pW3),
                preFun  = function() "Hi",
                postFun = function() "Bye")

# Call the function
if(interactive()){
    x <- widgetRender(widget1, "Test Widget")
    str(x)
}
# Create the list to be passed
pW1 <- list(Name="AAA", Value="bbb",
            toText=function(x) paste(x,collapse= ","), fromText=NULL,
            canEdit=TRUE,
            buttonFun = fileBrowser, buttonText = "Browse")

pW2 <- list(Name="BBB", Value="x,y,z",
            toText=function(x) paste(x, collapse=","), fromText=NULL,
            canEdit=TRUE, buttonFun = ls, buttonText = "List")

pW3 <- list(Name="CCC", Value="ccc",
            toText=function(x) paste(x, collapse = ","), fromText=NULL,
            canEdit=TRUE, buttonFun=NULL,  buttonText=NULL)

widget1 <- list(wList = list(a = pW1, b = pW2, c = pW3),
                preFun  = function() "Hi",
                postFun = function() "Bye")

# Call the function
if(interactive()){
    x <- widgetRender(widget1, "Test Widget")
    str(x)
}

Accessors for Primitive Widget Objects

Description

Currently primitive widget objects (pwidgets) are implemented as lists, but this will change. Users should only rely on these accessors functions, not the implementation.

Usage

WName(x)
WValue(x)
WValue(x) <-  value
WtoText(x)
WfromText(x)
WcanEdit(x)
WbuttonText(x)
WbuttonFun(x)
WwList(x)
WwList(x) <- value
WLValue(x, index)
WLValue(x, index) <- value
WRButtons(x)
WpreFun(x)
WpostFun(x)
WEnd(x)
WName(x)
WValue(x)
WValue(x) <-  value
WtoText(x)
WfromText(x)
WcanEdit(x)
WbuttonText(x)
WbuttonFun(x)
WwList(x)
WwList(x) <- value
WLValue(x, index)
WLValue(x, index) <- value
WRButtons(x)
WpreFun(x)
WpostFun(x)
WEnd(x)

Arguments

`x`	list of lists with a Name, Value, toText, fromText, canEdit, buttonText, buttonFun, preFun, postFun element.
`index`	integer or character string as an index or name for the list in the first list of a list of lists for a widget.
`value`	An R data type that is going to be used to update the value.

Details

WName(x) returns the Name element of x. WValue(x) returns the Value element of x. WValue(x) <- value will change the Value element of x to value.

WtoText(x) returns the toText element of x. WfromText(x) returns the fromText element of x. WcanEdit(x) returns the canEdit element of x.

WbuttonText(x) returns the buttonText element of x. WbuttonFun(x) returns the buttonFun element of x. WwList(x) returns the wList element of x. WwList <- value will update the wList element of a Widget list with value.

WLValue(x, index) returns a list indicated by the index in the wList of a widget list. WLValue(x, index) <- value will update indicated by the index in the wList of a widget list with the value.

WpreFun(x) returns the preFun element of x. WpostFun(x) returns the post element of x. WEnd(x) returns the end element of x.

Value

A character string or R function represented by the element of the list whose value is to be retrieved.

Author(s)

Jianhua (John) Zhang

Examples

# Create the list of lists
pW1 <- list(Name="AAA", Value="bbb",
            toText = function(x) paste(x,collapse = ","),
            fromText = NULL, canEdit = TRUE,
            buttonFun = ls, buttonText = "Browse")

widget1 <- list(wList = list(a = pW1),
                preFun = function() "Hi",
                postFun = function() "Bye")

# Call the functions
WName(pW1)
WValue(pW1)
WValue(pW1) <- "lll"
WtoText(pW1)
WfromText(pW1)
WcanEdit(pW1)
WbuttonText(pW1)
WbuttonFun(pW1)
WwList(widget1)
WwList(widget1) <- list(Name = "New list", Value = "New value")
WLValue(widget1, 1)
WLValue(widget1, 1) <- "New value"
WpreFun(widget1)
WpostFun(widget1)
WEnd(widget1)
# Create the list of lists
pW1 <- list(Name="AAA", Value="bbb",
            toText = function(x) paste(x,collapse = ","),
            fromText = NULL, canEdit = TRUE,
            buttonFun = ls, buttonText = "Browse")

widget1 <- list(wList = list(a = pW1),
                preFun = function() "Hi",
                postFun = function() "Bye")

# Call the functions
WName(pW1)
WValue(pW1)
WValue(pW1) <- "lll"
WtoText(pW1)
WfromText(pW1)
WcanEdit(pW1)
WbuttonText(pW1)
WbuttonFun(pW1)
WwList(widget1)
WwList(widget1) <- list(Name = "New list", Value = "New value")
WLValue(widget1, 1)
WLValue(widget1, 1) <- "New value"
WpreFun(widget1)
WpostFun(widget1)
WEnd(widget1)

Package 'tkWidgets'

Help Index

List File and Directories for a Given Path

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Converting the formal arguments to a function and converts into an XML format

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

Functions to construct a widget that takes inputs from users

Description

Usage

Arguments

Details

Value

Author(s)

References

Examples

Class "colInfo" presents column information for a data frame

Description

Objects from the Class

Slots

Methods

Author(s)

See Also

Examples

Function to view a data object passed

Description

Usage

Arguments

Details

Value

Author(s)

References

See Also

Examples

Function to build a widget for inputing database arguments

Description

Usage

Details

Value

Author(s)

References

See Also

Examples

Functions constuct a widget to explore BioC's data packages

Description

Usage

Arguments

Details

Value

Author(s)

References

Examples

A widget that allows users to explore the example code and help files of a given R package

Description

Usage

Arguments

Details

Value

Author(s)

References

See Also

Examples

Simple Interface to View and Pick Files

Description

Usage

Arguments

Details

Value