Nothing
# Project: Master Thesis
#
# Author: Gebruiker
###############################################################################
# Project: Master Thesis
#
# Author: Ewoud
###############################################################################
isadefault_WIN <- function(){ # Change newmethod to your own method name
new.frames <- .initialize.new.frames()
grid.config <- .initialize.grid.config()
grid.rows <- .initialize.grid.rows()
# List of frame objects. add.frame will return new.frames with an additional frame
# Possible improvement: Instead of overwriting new.frames each time.
# Maybe save the variable to something global or in a separate environment.
###############################################################################################################################################################################
## GENERAL INFORMATION ABOUT THE NEW METHOD/WINDOW ##
#####################################################
# Note that the idea is that each new dialog coincides with 1 clustering function on which
# multiple plot or diagnostic functions can be used (or even general ones).
# compatibility (with superclust & bcdiag)
# clusterfunction, plotfunctions, diagnosticfunctions
# name
# Define the name of the method as it will appear in the top of the window:
methodname <- "ISA"
method_result <- gsub(" ","",methodname,fixed=TRUE)
method_result <- gsub("-","",method_result,fixed=TRUE)
# Define the function (as it is named in your package)
# Note: If you have got a support function which is used for iterations, use it in this 'mainfunction'
methodfunction <- "isa.GUI"
# Define the name of the data argument for your function
data.arg <- "data"
methodshow <- FALSE
methodsave <- FALSE
# Define any other arguments in the function, which should not be changed by the user.
other.arg <- ""
# Help Object
methodhelp <- "isa"
# Possibility to give a seed ?
methodseed <- TRUE
# Add a discretize box?
data.discr <- FALSE
# Add a binarize box?
data.bin <- FALSE
## COMPATIBILITY? ##
# BcDiag
bcdiag.comp <- TRUE
# SuperBiclust
superbiclust.comp <- TRUE
# Biclust only
extrabiclustplot <- FALSE
# ISA only
extrabiclustforisa <- TRUE
###############################################################################################################################################################################
###############################################################################################################################################################################
###############################################################################################################################################################################
## ADDING OF ARGUMENT FRAMES ##
###############################
########################
#### CLUSTERING TAB ####
########################
input <- "clusterTab"
###### ENTRY FIELDS FRAME #####
# #
type <- "entryfields"
# Change variables accordingly:
frame.name <- "rowentry"
argument.names <- c("From","To","By")
argument.types <- c("num","num","num")
arguments <- c("thr.row.from","thr.row.to","thr.row.by")
initial.values <- c(1,3,0.5)
title <- "Row Thresholds"
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)
###### ENTRY FIELDS FRAME #####
# #
type <- "entryfields"
# Change variables accordingly:
frame.name <- "colentry"
argument.names <- c("From","To","By")
argument.types <- c("num","num","num")
arguments <- c("thr.col.from","thr.col.to","thr.col.by")
initial.values <- c(1,3,0.5)
title <- "Columns Thresholds"
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)
###### ENTRY FIELDS FRAME #####
# #
type <- "entryfields"
# Change variables accordingly:
frame.name <- "seedentry"
argument.names <- c("Number of Seeds")
argument.types <- c("num")
arguments <- c("no.seeds")
initial.values <- c(100)
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)
#### RADIO BUTTONS FRAME ####
# #
type <- "radiobuttons"
# Change variables accordingly:
frame.name <- "rowradio"
argument.names <- c("Lower than Average","Higher than Average","Both")
arguments <- c("dir.row")
argument.types <- "char"
argument.values <- c("down","up","updown")
initial.values <- "updown"
title <- "Row Direction:"
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)
#### RADIO BUTTONS FRAME ####
# #
type <- "radiobuttons"
# Change variables accordingly:
frame.name <- "colradio"
argument.names <- c("Lower than Average","Higher than Average","Both")
arguments <- c("dir.col")
argument.types <- "char"
argument.values <- c("down","up","updown")
initial.values <- "updown"
title <- "Column Direction:"
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)
###############################################################################################################################################################################
## CONFIGURATION OF GRID OF FRAMES - CLUSTERTAB ##
##################################################
#########################
#### THE GRID MATRIX ####
#########################
grid.config <- .grid.matrix(input=input,c("rowentry","colentry","seedentry","rowradio","colradio",NA),byrow=TRUE,nrow=2,ncol=3,grid.config=grid.config)
####################################
#### COMBINING ROWS -CLUSTERTAB ####
####################################
grid.rows <- .combine.rows(input=input,rows=c(1,2),title="ISA Specifications",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
###############################################################################################################################################################################
###############################################################################################################################################################################
####################################
#### PLOTTING & DIAGNOSTICS TAB ####
####################################
input <- "plotdiagTab"
#### ####
## SUMMARY BUTTON ##
#### ####
#### MANUAL BUTTONS FRAME ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "summaryframe"
button.name <- "Summary"
button.function <- "isa.summary"
button.data <- ""
button.biclust <- "ISA"
save <- FALSE
arg.frames <- c()
# 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)
###############################################################
#### ####
## EXTRACT BUTTON ##
#### ####
#### MANUAL BUTTONS FRAME ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "extractframe"
button.name <- "Extract"
button.function <- "isa.extract"
button.data <- ""
button.biclust <- "modules"
save <- TRUE
arg.frames <- c()
# 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)
###############################################################
#### ####
## SCOREPLOTS ##
#### ####
#### RADIO BUTTONS FRAME ####
# #
type <- "radiobuttons"
# Change variables accordingly:
frame.name <- "scoreplotsradio"
argument.names <- c("Rows","Columns")
arguments <- c("type")
argument.values <- c("row","col")
argument.types <- "char"
initial.values <- "row"
title <- "Scores Plot:"
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)
###### ENTRY FIELDS FRAME #####
# #
type <- "entryfields"
# Change variables accordingly:
frame.name <- "scoreplotsentry"
argument.names <- c("Vector of Biclusters")
argument.types <- c("num")
arguments <- c("biclust")
initial.values <- c("c(1)")
title <- ""
border <- FALSE
entry.width <- c("10")
# 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 <- "scoreplotsbutton"
button.name <- "Score Plot"
button.function <- "isa.scoreplots"
button.data <- ""
button.biclust <- "ISA"
save <- FALSE
arg.frames <- c("scoreplotsradio","scoreplotsentry")
# 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)
###############################################################
#### ####
## PLOTMODULE ##
#### ####
#### CHECK BOXES FRAME ####
# #
type <- "checkboxes"
# Change variables accordingly:
frame.name <- "plotmodulecheck"
argument.names <- c("Binary?")
arguments <- c("binary")
initial.values <- c(1)
title <- "Plot Modules:"
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 <- "plotmoduleentry"
argument.names <- c("Vector of Biclusters")
argument.types <- c("num")
arguments <- c("to.plot")
initial.values <- c("c(1)")
title <- ""
border <- FALSE
entry.width <- c("10")
# 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 <- "plotmodulebutton"
button.name <- "Moduleplot"
button.function <- "plotModules"
button.data <- "data"
button.biclust <- "modules"
save <- FALSE
arg.frames <- c("plotmodulecheck","plotmoduleentry")
# 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 DIAGNOSTICS ##
#### ####
#### MANUAL BUTTONS FRAME ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "fstatbuttonframe"
button.name <- "Obs. F Stat."
button.function <- "computeObservedFstat"
button.data <- "x"
button.biclust <- ""
arg.frames <- c("fstatentryframe")
button.otherarg <- paste(",bicResult=.isa2biclust(",method_result,")",sep="")
# Do not change this line:
new.frames <- .add.frame(button.otherarg=button.otherarg,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)
###############################################################
###### 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 <- ""
arg.frames <- c("bootstrapentryframe","bootstrapreplacementframe")
button.otherarg <- paste(",bicResult=.isa2biclust(",method_result,")",sep="")
# Do not change this line:
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,button.otherarg=button.otherarg)
#### 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)
### ###
## 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 <- ""
button.otherarg <- paste(",bicResult=.isa2biclust(",method_result,")",sep="")
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)
###############################################################
###############################################################################################################################################################################
## CONFIGURATION OF GRID OF FRAMES - PLOTDIAGTAB ##
###################################################
#########################
#### THE GRID MATRIX ####
#########################
grid.config <- .grid.matrix(input=input,c("summaryframe","extractframe",NA,"scoreplotsradio","scoreplotsentry","scoreplotsbutton","plotmodulecheck","plotmoduleentry","plotmodulebutton","fstatentryframe","fstatbuttonframe",NA,"bootstrapentryframe",NA,NA,"bootstrapreplacementframe","bootstrapbuttonframe","bootstrapvisualbuttonframe","pplottypeframe","pplotentryframe","parallelbuttonframe","pplotcheckframe",NA,NA),byrow=TRUE,nrow=8,ncol=3,grid.config=grid.config)
########################
#### COMBINING ROWS ####
########################
grid.rows <- .combine.rows(input=input,rows=c(1,2,3),title="Summary & ISA Plots",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
grid.rows <- .combine.rows(input=input,rows=c(4,5,6),title="Biclust Diagnostics",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
grid.rows <- .combine.rows(input=input,rows=c(7,8),title="Biclust - Parallel Coordinate 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,methodsave=methodsave,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.discr=data.discr,data.bin=data.bin,extrabiclustplot=extrabiclustplot,methodshow=methodshow,extrabiclustforisa=extrabiclustforisa)
}
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