Nothing
R/rqubic_WIN.R
In RcmdrPlugin.BiclustGUI: 'Rcmdr' Plug-in GUI for Biclustering
# Project: BiclustGUI
#
# Author: lucp8394
###############################################################################
rqubic_WINDOW <- function(){ # Change newmethod to your own method name
new.frames <- .initialize.new.frames()
grid.config <- .initialize.grid.config()
grid.rows <- .initialize.grid.rows()
#####################################################
## GENERAL INFORMATION ABOUT THE NEW METHOD/WINDOW ##
#####################################################
methodname <- "Rqubic"
methodfunction <- "rqubic.GUI"
methodsave <- FALSE
other.arg <- ""
methodhelp <- "rqubic"
data.arg <- "x"
data.transf <- "ExprSet"
# Extra Data Conversion Boxes
data.discr <- FALSE
data.bin <- FALSE
# Possibility to give a seed ?
methodseed <- TRUE
## COMPATIBILITY? ##
# BcDiag
bcdiag.comp <- TRUE
# SuperBiclust
superbiclust.comp <- TRUE
# Biclust only (Not for public use)
extrabiclustplot <- TRUE
########################
#### CLUSTERING TAB ####
########################
input <- "clusterTab"
### 1. ADDING THE FRAMES ###
#### ENTRY FIELDS FRAME ####
type <- "entryfields"
# Change variables accordingly:
frame.name <- "datainputframe"
argument.names <- c("ExpressionSet Name")
argument.types <- c("char")
arguments <- c("eSetData.name")
initial.values <- c("NULL")
title <- ""
border <- FALSE
entry.width <- c("15")
# Do not change this line:
new.frames <- .add.frame(input=input,type=type
,frame.name=frame.name,argument.names=argument.names
,arguments=arguments,initial.values=initial.values
,title=title,border=border,entry.width=entry.width
,argument.types=argument.types ,new.frames=new.frames)
#### CHECK BOXES FRAME ####
type <- "checkboxes"
# Change variables accordingly:
frame.name <- "disccheckframe"
argument.names <- c("Discretize?")
arguments <- c("check.disc")
initial.values <- c(1)
title <- ""
border <- FALSE
# DO NOT CHANGE THIS LINE:
new.frames <- .add.frame(input=input,type=type
,frame.name=frame.name,argument.names=argument.names
,arguments=arguments,initial.values=initial.values
,title=title,border=border,new.frames=new.frames)
#### ENTRY FIELDS FRAME ####
type <- "entryfields"
# Change variables accordingly:
frame.name <- "discentryframe"
argument.names <- c("Estimated Proportion","Levels")
argument.types <- c("num","num")
arguments <- c("q","rank")
initial.values <- c(0.06,1)
title <- ""
border <- FALSE
entry.width <- c("4","4")
# Do not change this line:
new.frames <- .add.frame(input=input,type=type
,frame.name=frame.name,argument.names=argument.names
,arguments=arguments,initial.values=initial.values
,title=title,border=border,entry.width=entry.width
,argument.types=argument.types ,new.frames=new.frames)
#### ENTRY FIELDS FRAME ####
type <- "entryfields"
# Change variables accordingly:
frame.name <- "seedentryframe"
argument.names <- c("Minimum Score")
argument.types <- c("num")
arguments <- c("minColWidth")
initial.values <- c(2)
title <- ""
border <- FALSE
entry.width <- c("3")
# Do not change this line:
new.frames <- .add.frame(input=input,type=type
,frame.name=frame.name,argument.names=argument.names
,arguments=arguments,initial.values=initial.values
,title=title,border=border,entry.width=entry.width
,argument.types=argument.types ,new.frames=new.frames)
#### ENTRY FIELDS FRAME ####
type <- "entryfields"
# Change variables accordingly:
frame.name <- "qubicentryframe"
argument.names <- c("Max Biclusters","Tolerance","Redundant Proportion")
argument.types <- c("num","num","num")
arguments <- c("report.no","tolerance","filter.proportion")
initial.values <- c(100,0.95,1)
title <- ""
border <- FALSE
entry.width <- c("4","4","4")
# Do not change this line:
new.frames <- .add.frame(input=input,type=type
,frame.name=frame.name,argument.names=argument.names
,arguments=arguments,initial.values=initial.values
,title=title,border=border,entry.width=entry.width
,argument.types=argument.types ,new.frames=new.frames)
### 2. CONFIGURING THE GRID ###
grid.config <- .grid.matrix(input=input,c("datainputframe",NA,"disccheckframe","discentryframe","seedentryframe",NA,"qubicentryframe",NA),nrow=4,ncol=2,byrow=TRUE,grid.config=grid.config)
### 3. COMBING THE ROWS ###
grid.rows <- .combine.rows(input=input,rows=c(1),title="Expression Set Input (NULL='Active Dataset') ",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
grid.rows <- .combine.rows(input=input,rows=c(2),title="Quantile Discretization ",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
grid.rows <- .combine.rows(input=input,rows=c(3),title="Generate Seeds ",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
grid.rows <- .combine.rows(input=input,rows=c(4),title="Qualitative Biclustering Options ",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
####################################
#### PLOTTING & DIAGNOSTICS TAB ####
####################################
input <- "plotdiagTab"
### 1. ADDING THE FRAMES ###
### ###
## Parallel Coordinates Plot ##
### ###
#### RADIO BUTTONS FRAME ####
# #
type <- "radiobuttons"
# Change variables accordingly:
frame.name <- "pplottypeframe"
argument.names <- c("Default","Combined (rows & columns)")
arguments <- c("type2")
argument.values <- c("default","combined")
argument.types <- "char"
initial.values <- "default"
title <- "Plot Type:"
border <- FALSE
# DO NOT CHANGE THIS LINE:
new.frames <- .add.frame(input=input,type=type,frame.name=frame.name,argument.names=argument.names,arguments=arguments,argument.values=argument.values,initial.values=initial.values,title=title,border=border,new.frames=new.frames,argument.types=argument.types)
#### CHECK BOXES FRAME ####
# #
type <- "checkboxes"
# Change variables accordingly:
frame.name <- "pplotcheckframe"
argument.names <- c("Plot Only Column","Plot Rows & Columns","Compare")
arguments <- c("plotcol","plotBoth","compare")
initial.values <- c(1,0,1)
title <- "Default Type Options:"
border <- FALSE
# DO NOT CHANGE THIS LINE:
new.frames <- .add.frame(input=input,type=type,frame.name=frame.name,argument.names=argument.names,arguments=arguments,initial.values=initial.values,title=title,border=border,new.frames=new.frames)
###### ENTRY FIELDS FRAME #####
# #
type <- "entryfields"
# Change variables accordingly:
frame.name <- "pplotentryframe"
argument.names <- c("Bicluster Number")
argument.types <- c("num")
arguments <- c("number")
initial.values <- c(1)
title <- ""
border <- FALSE
entry.width <- c("2")
# Do not change this line:
new.frames <- .add.frame(input=input,type=type,frame.name=frame.name,argument.names=argument.names,arguments=arguments,initial.values=initial.values,title=title,border=border,entry.width=entry.width,argument.types=argument.types ,new.frames=new.frames)
#### MANUAL BUTTONS FRAME ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "parallelbuttonframe"
button.name <- "Draw Plot"
button.function <- "parallelCoordinates3"
button.data <- "x"
button.biclust <- "bicResult"
button.otherarg <- ""
save <- FALSE
arg.frames <- c("pplotcheckframe","pplotentryframe","pplottypeframe")
# Do not change this line:
new.frames <- .add.frame(input=input,frame.name=frame.name,save=save,type=type,button.name=button.name,button.otherarg=button.otherarg,button.function=button.function,button.data=button.data,button.biclust=button.biclust,arg.frames=arg.frames,new.frames=new.frames)
###############################################################
### ###
## Heatmap Plot ##
### ###
#### CHECK BOXES FRAME ####
# #
type <- "checkboxes"
# Change variables accordingly:
frame.name <- "heatplotcheckframe"
argument.names <- c("Local")
arguments <- c("local")
initial.values <- c(1)
title <- ""
border <- FALSE
# DO NOT CHANGE THIS LINE:
new.frames <- .add.frame(input=input,type=type,frame.name=frame.name,argument.names=argument.names,arguments=arguments,initial.values=initial.values,title=title,border=border,new.frames=new.frames)
###### ENTRY FIELDS FRAME #####
# #
type <- "entryfields"
# Change variables accordingly:
frame.name <- "heatplotentryframe"
argument.names <- c("Bicluster Number")
argument.types <- c("num")
arguments <- c("number")
initial.values <- c(1)
title <- ""
border <- FALSE
entry.width <- c("2")
# Do not change this line:
new.frames <- .add.frame(input=input,type=type,frame.name=frame.name,argument.names=argument.names,arguments=arguments,initial.values=initial.values,title=title,border=border,entry.width=entry.width,argument.types=argument.types ,new.frames=new.frames)
#### MANUAL BUTTONS FRAME ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "heatbuttonframe"
button.name <- "Draw Plot"
button.function <- "drawHeatmap"
button.data <- "x"
button.biclust <- "bicResult"
save <- FALSE
arg.frames <- c("heatplotcheckframe","heatplotentryframe")
# Do not change this line: (without button.otherarg)
new.frames <- .add.frame(input=input,frame.name=frame.name,type=type,save=save,button.name=button.name,button.function=button.function,button.data=button.data,button.biclust=button.biclust,arg.frames=arg.frames,new.frames=new.frames)
###############################################################
### ###
## Biclust Member Plot ##
### ###
#### CHECK BOXES FRAME ####
# #
type <- "checkboxes"
# Change variables accordingly:
frame.name <- "mplotcheckframe"
argument.names <- c("Mid")
arguments <- c("mid")
initial.values <- c(1)
title <- ""
border <- FALSE
# DO NOT CHANGE THIS LINE:
new.frames <- .add.frame(input=input,type=type,frame.name=frame.name,argument.names=argument.names,arguments=arguments,initial.values=initial.values,title=title,border=border,new.frames=new.frames)
###### ENTRY FIELDS FRAME #####
# #
type <- "entryfields"
# Change variables accordingly:
frame.name <- "mplotentryframe"
argument.names <- c("Bicluster Label")
argument.types <- c("char")
arguments <- c("cl_label")
initial.values <- c("")
title <- ""
border <- FALSE
entry.width <- c("8")
# Do not change this line:
new.frames <- .add.frame(input=input,type=type,frame.name=frame.name,argument.names=argument.names,arguments=arguments,initial.values=initial.values,title=title,border=border,entry.width=entry.width,argument.types=argument.types ,new.frames=new.frames)
#### MANUAL BUTTONS FRAME - EXAMPLE ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "memberbuttonframe"
button.name <- "Draw Plot"
button.function <- "biclustmember"
button.data <- "x"
button.biclust <- "bicResult"
save <- FALSE
arg.frames <- c("mplotcheckframe","mplotentryframe")
# Do not change this line: (without button.otherarg)
new.frames <- .add.frame(input=input,frame.name=frame.name,save=save,type=type,button.name=button.name,button.function=button.function,button.data=button.data,button.biclust=button.biclust,arg.frames=arg.frames,new.frames=new.frames)
###############################################################
### ###
## Summary & Diagnostics Box ##
### ###
#### MANUAL BUTTONS FRAME ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "summarybuttonframe"
button.name <- "Summary"
button.function <- "summary"
button.data <- ""
button.biclust <- "object"
arg.frames <- c()
save <- FALSE
# Do not change this line: (without button.otherarg)
new.frames <- .add.frame(input=input,frame.name=frame.name,save=save,type=type,button.name=button.name,button.function=button.function,button.data=button.data,button.biclust=button.biclust,arg.frames=arg.frames,new.frames=new.frames)
###############################################################
#### MANUAL BUTTONS FRAME ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "fstatbuttonframe"
button.name <- "Obs. F Stat."
button.function <- "computeObservedFstat"
button.data <- "x"
button.biclust <- "bicResult"
arg.frames <- c("fstatentryframe")
button.otherarg <- ""
# Do not change this line: (without button.otherarg)
new.frames <- .add.frame(input=input,frame.name=frame.name,type=type,button.name=button.name,button.otherarg=button.otherarg,button.function=button.function,button.data=button.data,button.biclust=button.biclust,arg.frames=arg.frames,new.frames=new.frames)
###############################################################
###### ENTRY FIELDS FRAME #####
# #
type <- "entryfields"
# Change variables accordingly:
frame.name <- "fstatentryframe"
argument.names <- c("Bicluster Number")
argument.types <- c("num")
arguments <- c("number")
initial.values <- c("1")
title <- ""
border <- FALSE
entry.width <- c("4")
# Do not change this line:
new.frames <- .add.frame(input=input,type=type,frame.name=frame.name,argument.names=argument.names,arguments=arguments,initial.values=initial.values,title=title,border=border,entry.width=entry.width,argument.types=argument.types ,new.frames=new.frames)
###### ENTRY FIELDS FRAME #####
# #
type <- "entryfields"
# Change variables accordingly:
frame.name <- "bootstrapentryframe"
argument.names <- c("Bicluster Number","Number Bootstrap Replicates")
argument.types <- c("num","num")
arguments <- c("number","nResamplings")
initial.values <- c(1,100)
title <- "Bootstrap Options:"
border <- FALSE
entry.width <- c("4","4")
# Do not change this line:
new.frames <- .add.frame(input=input,type=type,frame.name=frame.name,argument.names=argument.names,arguments=arguments,initial.values=initial.values,title=title,border=border,entry.width=entry.width,argument.types=argument.types ,new.frames=new.frames)
#### CHECK BOXES FRAME ####
# #
type <- "checkboxes"
# Change variables accordingly:
frame.name <- "bootstrapreplacementframe"
argument.names <- c("With Replacement?")
arguments <- c("replace")
initial.values <- c(1)
title <- ""
border <- FALSE
# DO NOT CHANGE THIS LINE:
new.frames <- .add.frame(input=input,type=type,frame.name=frame.name,argument.names=argument.names,arguments=arguments,initial.values=initial.values,title=title,border=border,new.frames=new.frames)
#### MANUAL BUTTONS FRAME ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "bootstrapbuttonframe"
button.name <- "Bootstrap"
button.function <- "diagnoseColRow"
button.data <- "x"
button.biclust <- "bicResult"
arg.frames <- c("bootstrapentryframe","bootstrapreplacementframe")
# Do not change this line: (without button.otherarg)
new.frames <- .add.frame(input=input,frame.name=frame.name,type=type,button.name=button.name,button.function=button.function,button.data=button.data,button.biclust=button.biclust,arg.frames=arg.frames,new.frames=new.frames)
#### MANUAL BUTTONS FRAME ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "bootstrapvisualbuttonframe"
button.name <- "Visualize"
button.function <- "diagnosticPlot"
button.data <- ""
button.biclust <- ""
button.otherarg <- "bootstrapOutput=Bootstrap"
save <- FALSE
arg.frames <- c()
# Do not change this line: (without button.otherarg)
new.frames <- .add.frame(input=input,frame.name=frame.name,save=save,type=type,button.name=button.name,button.function=button.function,button.data=button.data,button.biclust=button.biclust,arg.frames=arg.frames,new.frames=new.frames,button.otherarg=button.otherarg)
### 2. CONFIGURING THE GRID ###
grid.config <- .grid.matrix(input=input,c("summarybuttonframe","fstatentryframe","fstatbuttonframe","bootstrapentryframe",NA,NA,"bootstrapreplacementframe","bootstrapbuttonframe","bootstrapvisualbuttonframe" ,"pplottypeframe","pplotentryframe","parallelbuttonframe","pplotcheckframe",NA,NA,"heatplotcheckframe","heatplotentryframe","heatbuttonframe","mplotcheckframe","mplotentryframe","memberbuttonframe"),byrow=TRUE,nrow=7,ncol=3,grid.config=grid.config)
### 3. COMBING THE ROWS ###
grid.rows <- .combine.rows(input=input,rows=c(1,2,3),title="Summary & Diagnostics",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
grid.rows <- .combine.rows(input=input,rows=c(4,5),title="Parallel Coordinate Plot",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
grid.rows <- .combine.rows(input=input,rows=c(6),title="Heatmap Plot",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
grid.rows <- .combine.rows(input=input,rows=c(7),title="Biclustmember Plot",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
#########################################################################
## USE ALL THE ARGUMENTS ABOUT IN THE GENERAL CLUSTERTEMPLATE FUNCTION ##
#########################################################################
cluster_template(methodname=methodname,methodfunction=methodfunction,extrabiclustplot=extrabiclustplot,methodhelp=methodhelp,data.arg=data.arg,other.arg=other.arg,methodseed=methodseed,grid.config=grid.config,grid.rows=grid.rows,new.frames=new.frames,superbiclust.comp=superbiclust.comp,bcdiag.comp=bcdiag.comp,data.transf=data.transf,data.discr=data.discr,data.bin=data.bin,methodshow=methodshow,methodsave=methodsave)
}
#rqubic_WINDOW()
#test <- as.matrix(BicatYeast)
#
#
#
# demo.exprs <- new("ExpressionSet", exprs=test)
### processing the condition information
# demo.cond.split <- strsplit(sub("\\.CEL", "", colnames(BicatYeast)), "_")
# demo.group <- sapply(demo.cond.split, function(x) paste(x[-length(x)], collapse="_"))
# demo.time <- sapply(demo.cond.split, function(x) x[length(x)])
# pData(demo.exprs) <- data.frame(group=demo.group, time=demo.time)
# sampleNames(demo.exprs) <- paste(demo.group, demo.time)
# demo.disc <- quantileDiscretize(demo.exprs)
#
# demo.disc.test <- as.data.frame(exprs(demo.disc))
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# Project: BiclustGUI
#
# Author: lucp8394
###############################################################################
rqubic_WINDOW <- function(){ # Change newmethod to your own method name
new.frames <- .initialize.new.frames()
grid.config <- .initialize.grid.config()
grid.rows <- .initialize.grid.rows()
#####################################################
## GENERAL INFORMATION ABOUT THE NEW METHOD/WINDOW ##
#####################################################
methodname <- "Rqubic"
methodfunction <- "rqubic.GUI"
methodsave <- FALSE
other.arg <- ""
methodhelp <- "rqubic"
data.arg <- "x"
data.transf <- "ExprSet"
# Extra Data Conversion Boxes
data.discr <- FALSE
data.bin <- FALSE
# Possibility to give a seed ?
methodseed <- TRUE
## COMPATIBILITY? ##
# BcDiag
bcdiag.comp <- TRUE
# SuperBiclust
superbiclust.comp <- TRUE
# Biclust only (Not for public use)
extrabiclustplot <- TRUE
########################
#### CLUSTERING TAB ####
########################
input <- "clusterTab"
### 1. ADDING THE FRAMES ###
#### ENTRY FIELDS FRAME ####
type <- "entryfields"
# Change variables accordingly:
frame.name <- "datainputframe"
argument.names <- c("ExpressionSet Name")
argument.types <- c("char")
arguments <- c("eSetData.name")
initial.values <- c("NULL")
title <- ""
border <- FALSE
entry.width <- c("15")
# Do not change this line:
new.frames <- .add.frame(input=input,type=type
,frame.name=frame.name,argument.names=argument.names
,arguments=arguments,initial.values=initial.values
,title=title,border=border,entry.width=entry.width
,argument.types=argument.types ,new.frames=new.frames)
#### CHECK BOXES FRAME ####
type <- "checkboxes"
# Change variables accordingly:
frame.name <- "disccheckframe"
argument.names <- c("Discretize?")
arguments <- c("check.disc")
initial.values <- c(1)
title <- ""
border <- FALSE
# DO NOT CHANGE THIS LINE:
new.frames <- .add.frame(input=input,type=type
,frame.name=frame.name,argument.names=argument.names
,arguments=arguments,initial.values=initial.values
,title=title,border=border,new.frames=new.frames)
#### ENTRY FIELDS FRAME ####
type <- "entryfields"
# Change variables accordingly:
frame.name <- "discentryframe"
argument.names <- c("Estimated Proportion","Levels")
argument.types <- c("num","num")
arguments <- c("q","rank")
initial.values <- c(0.06,1)
title <- ""
border <- FALSE
entry.width <- c("4","4")
# Do not change this line:
new.frames <- .add.frame(input=input,type=type
,frame.name=frame.name,argument.names=argument.names
,arguments=arguments,initial.values=initial.values
,title=title,border=border,entry.width=entry.width
,argument.types=argument.types ,new.frames=new.frames)
#### ENTRY FIELDS FRAME ####
type <- "entryfields"
# Change variables accordingly:
frame.name <- "seedentryframe"
argument.names <- c("Minimum Score")
argument.types <- c("num")
arguments <- c("minColWidth")
initial.values <- c(2)
title <- ""
border <- FALSE
entry.width <- c("3")
# Do not change this line:
new.frames <- .add.frame(input=input,type=type
,frame.name=frame.name,argument.names=argument.names
,arguments=arguments,initial.values=initial.values
,title=title,border=border,entry.width=entry.width
,argument.types=argument.types ,new.frames=new.frames)
#### ENTRY FIELDS FRAME ####
type <- "entryfields"
# Change variables accordingly:
frame.name <- "qubicentryframe"
argument.names <- c("Max Biclusters","Tolerance","Redundant Proportion")
argument.types <- c("num","num","num")
arguments <- c("report.no","tolerance","filter.proportion")
initial.values <- c(100,0.95,1)
title <- ""
border <- FALSE
entry.width <- c("4","4","4")
# Do not change this line:
new.frames <- .add.frame(input=input,type=type
,frame.name=frame.name,argument.names=argument.names
,arguments=arguments,initial.values=initial.values
,title=title,border=border,entry.width=entry.width
,argument.types=argument.types ,new.frames=new.frames)
### 2. CONFIGURING THE GRID ###
grid.config <- .grid.matrix(input=input,c("datainputframe",NA,"disccheckframe","discentryframe","seedentryframe",NA,"qubicentryframe",NA),nrow=4,ncol=2,byrow=TRUE,grid.config=grid.config)
### 3. COMBING THE ROWS ###
grid.rows <- .combine.rows(input=input,rows=c(1),title="Expression Set Input (NULL='Active Dataset') ",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
grid.rows <- .combine.rows(input=input,rows=c(2),title="Quantile Discretization ",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
grid.rows <- .combine.rows(input=input,rows=c(3),title="Generate Seeds ",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
grid.rows <- .combine.rows(input=input,rows=c(4),title="Qualitative Biclustering Options ",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
####################################
#### PLOTTING & DIAGNOSTICS TAB ####
####################################
input <- "plotdiagTab"
### 1. ADDING THE FRAMES ###
### ###
## Parallel Coordinates Plot ##
### ###
#### RADIO BUTTONS FRAME ####
# #
type <- "radiobuttons"
# Change variables accordingly:
frame.name <- "pplottypeframe"
argument.names <- c("Default","Combined (rows & columns)")
arguments <- c("type2")
argument.values <- c("default","combined")
argument.types <- "char"
initial.values <- "default"
title <- "Plot Type:"
border <- FALSE
# DO NOT CHANGE THIS LINE:
new.frames <- .add.frame(input=input,type=type,frame.name=frame.name,argument.names=argument.names,arguments=arguments,argument.values=argument.values,initial.values=initial.values,title=title,border=border,new.frames=new.frames,argument.types=argument.types)
#### CHECK BOXES FRAME ####
# #
type <- "checkboxes"
# Change variables accordingly:
frame.name <- "pplotcheckframe"
argument.names <- c("Plot Only Column","Plot Rows & Columns","Compare")
arguments <- c("plotcol","plotBoth","compare")
initial.values <- c(1,0,1)
title <- "Default Type Options:"
border <- FALSE
# DO NOT CHANGE THIS LINE:
new.frames <- .add.frame(input=input,type=type,frame.name=frame.name,argument.names=argument.names,arguments=arguments,initial.values=initial.values,title=title,border=border,new.frames=new.frames)
###### ENTRY FIELDS FRAME #####
# #
type <- "entryfields"
# Change variables accordingly:
frame.name <- "pplotentryframe"
argument.names <- c("Bicluster Number")
argument.types <- c("num")
arguments <- c("number")
initial.values <- c(1)
title <- ""
border <- FALSE
entry.width <- c("2")
# Do not change this line:
new.frames <- .add.frame(input=input,type=type,frame.name=frame.name,argument.names=argument.names,arguments=arguments,initial.values=initial.values,title=title,border=border,entry.width=entry.width,argument.types=argument.types ,new.frames=new.frames)
#### MANUAL BUTTONS FRAME ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "parallelbuttonframe"
button.name <- "Draw Plot"
button.function <- "parallelCoordinates3"
button.data <- "x"
button.biclust <- "bicResult"
button.otherarg <- ""
save <- FALSE
arg.frames <- c("pplotcheckframe","pplotentryframe","pplottypeframe")
# Do not change this line:
new.frames <- .add.frame(input=input,frame.name=frame.name,save=save,type=type,button.name=button.name,button.otherarg=button.otherarg,button.function=button.function,button.data=button.data,button.biclust=button.biclust,arg.frames=arg.frames,new.frames=new.frames)
###############################################################
### ###
## Heatmap Plot ##
### ###
#### CHECK BOXES FRAME ####
# #
type <- "checkboxes"
# Change variables accordingly:
frame.name <- "heatplotcheckframe"
argument.names <- c("Local")
arguments <- c("local")
initial.values <- c(1)
title <- ""
border <- FALSE
# DO NOT CHANGE THIS LINE:
new.frames <- .add.frame(input=input,type=type,frame.name=frame.name,argument.names=argument.names,arguments=arguments,initial.values=initial.values,title=title,border=border,new.frames=new.frames)
###### ENTRY FIELDS FRAME #####
# #
type <- "entryfields"
# Change variables accordingly:
frame.name <- "heatplotentryframe"
argument.names <- c("Bicluster Number")
argument.types <- c("num")
arguments <- c("number")
initial.values <- c(1)
title <- ""
border <- FALSE
entry.width <- c("2")
# Do not change this line:
new.frames <- .add.frame(input=input,type=type,frame.name=frame.name,argument.names=argument.names,arguments=arguments,initial.values=initial.values,title=title,border=border,entry.width=entry.width,argument.types=argument.types ,new.frames=new.frames)
#### MANUAL BUTTONS FRAME ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "heatbuttonframe"
button.name <- "Draw Plot"
button.function <- "drawHeatmap"
button.data <- "x"
button.biclust <- "bicResult"
save <- FALSE
arg.frames <- c("heatplotcheckframe","heatplotentryframe")
# Do not change this line: (without button.otherarg)
new.frames <- .add.frame(input=input,frame.name=frame.name,type=type,save=save,button.name=button.name,button.function=button.function,button.data=button.data,button.biclust=button.biclust,arg.frames=arg.frames,new.frames=new.frames)
###############################################################
### ###
## Biclust Member Plot ##
### ###
#### CHECK BOXES FRAME ####
# #
type <- "checkboxes"
# Change variables accordingly:
frame.name <- "mplotcheckframe"
argument.names <- c("Mid")
arguments <- c("mid")
initial.values <- c(1)
title <- ""
border <- FALSE
# DO NOT CHANGE THIS LINE:
new.frames <- .add.frame(input=input,type=type,frame.name=frame.name,argument.names=argument.names,arguments=arguments,initial.values=initial.values,title=title,border=border,new.frames=new.frames)
###### ENTRY FIELDS FRAME #####
# #
type <- "entryfields"
# Change variables accordingly:
frame.name <- "mplotentryframe"
argument.names <- c("Bicluster Label")
argument.types <- c("char")
arguments <- c("cl_label")
initial.values <- c("")
title <- ""
border <- FALSE
entry.width <- c("8")
# Do not change this line:
new.frames <- .add.frame(input=input,type=type,frame.name=frame.name,argument.names=argument.names,arguments=arguments,initial.values=initial.values,title=title,border=border,entry.width=entry.width,argument.types=argument.types ,new.frames=new.frames)
#### MANUAL BUTTONS FRAME - EXAMPLE ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "memberbuttonframe"
button.name <- "Draw Plot"
button.function <- "biclustmember"
button.data <- "x"
button.biclust <- "bicResult"
save <- FALSE
arg.frames <- c("mplotcheckframe","mplotentryframe")
# Do not change this line: (without button.otherarg)
new.frames <- .add.frame(input=input,frame.name=frame.name,save=save,type=type,button.name=button.name,button.function=button.function,button.data=button.data,button.biclust=button.biclust,arg.frames=arg.frames,new.frames=new.frames)
###############################################################
### ###
## Summary & Diagnostics Box ##
### ###
#### MANUAL BUTTONS FRAME ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "summarybuttonframe"
button.name <- "Summary"
button.function <- "summary"
button.data <- ""
button.biclust <- "object"
arg.frames <- c()
save <- FALSE
# Do not change this line: (without button.otherarg)
new.frames <- .add.frame(input=input,frame.name=frame.name,save=save,type=type,button.name=button.name,button.function=button.function,button.data=button.data,button.biclust=button.biclust,arg.frames=arg.frames,new.frames=new.frames)
###############################################################
#### MANUAL BUTTONS FRAME ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "fstatbuttonframe"
button.name <- "Obs. F Stat."
button.function <- "computeObservedFstat"
button.data <- "x"
button.biclust <- "bicResult"
arg.frames <- c("fstatentryframe")
button.otherarg <- ""
# Do not change this line: (without button.otherarg)
new.frames <- .add.frame(input=input,frame.name=frame.name,type=type,button.name=button.name,button.otherarg=button.otherarg,button.function=button.function,button.data=button.data,button.biclust=button.biclust,arg.frames=arg.frames,new.frames=new.frames)
###############################################################
###### ENTRY FIELDS FRAME #####
# #
type <- "entryfields"
# Change variables accordingly:
frame.name <- "fstatentryframe"
argument.names <- c("Bicluster Number")
argument.types <- c("num")
arguments <- c("number")
initial.values <- c("1")
title <- ""
border <- FALSE
entry.width <- c("4")
# Do not change this line:
new.frames <- .add.frame(input=input,type=type,frame.name=frame.name,argument.names=argument.names,arguments=arguments,initial.values=initial.values,title=title,border=border,entry.width=entry.width,argument.types=argument.types ,new.frames=new.frames)
###### ENTRY FIELDS FRAME #####
# #
type <- "entryfields"
# Change variables accordingly:
frame.name <- "bootstrapentryframe"
argument.names <- c("Bicluster Number","Number Bootstrap Replicates")
argument.types <- c("num","num")
arguments <- c("number","nResamplings")
initial.values <- c(1,100)
title <- "Bootstrap Options:"
border <- FALSE
entry.width <- c("4","4")
# Do not change this line:
new.frames <- .add.frame(input=input,type=type,frame.name=frame.name,argument.names=argument.names,arguments=arguments,initial.values=initial.values,title=title,border=border,entry.width=entry.width,argument.types=argument.types ,new.frames=new.frames)
#### CHECK BOXES FRAME ####
# #
type <- "checkboxes"
# Change variables accordingly:
frame.name <- "bootstrapreplacementframe"
argument.names <- c("With Replacement?")
arguments <- c("replace")
initial.values <- c(1)
title <- ""
border <- FALSE
# DO NOT CHANGE THIS LINE:
new.frames <- .add.frame(input=input,type=type,frame.name=frame.name,argument.names=argument.names,arguments=arguments,initial.values=initial.values,title=title,border=border,new.frames=new.frames)
#### MANUAL BUTTONS FRAME ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "bootstrapbuttonframe"
button.name <- "Bootstrap"
button.function <- "diagnoseColRow"
button.data <- "x"
button.biclust <- "bicResult"
arg.frames <- c("bootstrapentryframe","bootstrapreplacementframe")
# Do not change this line: (without button.otherarg)
new.frames <- .add.frame(input=input,frame.name=frame.name,type=type,button.name=button.name,button.function=button.function,button.data=button.data,button.biclust=button.biclust,arg.frames=arg.frames,new.frames=new.frames)
#### MANUAL BUTTONS FRAME ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "bootstrapvisualbuttonframe"
button.name <- "Visualize"
button.function <- "diagnosticPlot"
button.data <- ""
button.biclust <- ""
button.otherarg <- "bootstrapOutput=Bootstrap"
save <- FALSE
arg.frames <- c()
# Do not change this line: (without button.otherarg)
new.frames <- .add.frame(input=input,frame.name=frame.name,save=save,type=type,button.name=button.name,button.function=button.function,button.data=button.data,button.biclust=button.biclust,arg.frames=arg.frames,new.frames=new.frames,button.otherarg=button.otherarg)
### 2. CONFIGURING THE GRID ###
grid.config <- .grid.matrix(input=input,c("summarybuttonframe","fstatentryframe","fstatbuttonframe","bootstrapentryframe",NA,NA,"bootstrapreplacementframe","bootstrapbuttonframe","bootstrapvisualbuttonframe" ,"pplottypeframe","pplotentryframe","parallelbuttonframe","pplotcheckframe",NA,NA,"heatplotcheckframe","heatplotentryframe","heatbuttonframe","mplotcheckframe","mplotentryframe","memberbuttonframe"),byrow=TRUE,nrow=7,ncol=3,grid.config=grid.config)
### 3. COMBING THE ROWS ###
grid.rows <- .combine.rows(input=input,rows=c(1,2,3),title="Summary & Diagnostics",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
grid.rows <- .combine.rows(input=input,rows=c(4,5),title="Parallel Coordinate Plot",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
grid.rows <- .combine.rows(input=input,rows=c(6),title="Heatmap Plot",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
grid.rows <- .combine.rows(input=input,rows=c(7),title="Biclustmember Plot",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
#########################################################################
## USE ALL THE ARGUMENTS ABOUT IN THE GENERAL CLUSTERTEMPLATE FUNCTION ##
#########################################################################
cluster_template(methodname=methodname,methodfunction=methodfunction,extrabiclustplot=extrabiclustplot,methodhelp=methodhelp,data.arg=data.arg,other.arg=other.arg,methodseed=methodseed,grid.config=grid.config,grid.rows=grid.rows,new.frames=new.frames,superbiclust.comp=superbiclust.comp,bcdiag.comp=bcdiag.comp,data.transf=data.transf,data.discr=data.discr,data.bin=data.bin,methodshow=methodshow,methodsave=methodsave)
}
#rqubic_WINDOW()
#test <- as.matrix(BicatYeast)
#
#
#
# demo.exprs <- new("ExpressionSet", exprs=test)
### processing the condition information
# demo.cond.split <- strsplit(sub("\\.CEL", "", colnames(BicatYeast)), "_")
# demo.group <- sapply(demo.cond.split, function(x) paste(x[-length(x)], collapse="_"))
# demo.time <- sapply(demo.cond.split, function(x) x[length(x)])
# pData(demo.exprs) <- data.frame(group=demo.group, time=demo.time)
# sampleNames(demo.exprs) <- paste(demo.group, demo.time)
# demo.disc <- quantileDiscretize(demo.exprs)
#
# demo.disc.test <- as.data.frame(exprs(demo.disc))
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