R/fabia_biclustWIN.R
In ewouddt/RcmdrPlugin.BiclustGUI: 'Rcmdr' Plug-in GUI for Biclustering
Defines functions
fabiabiclust_WINDOW
Documented in
fabiabiclust_WINDOW
# Project: BiclustGUI
#
# Author: Ewoud
###############################################################################
fabiabiclust_WINDOW <- function(methodname,thresZ,thresL){
# fabia.names <- c("Fabia Laplace Prior","Fabia Post-Projection","Fabia Sparseness Projection","Fabia SPARSE")
method_result <- gsub(" ","",methodname,fixed=TRUE)
method_result <- gsub("-","",method_result,fixed=TRUE)
if(is.null(thresL)){thresL <- "NULL"}
new.frames <- .initialize.new.frames()
grid.config <- .initialize.grid.config()
grid.rows <- .initialize.grid.rows()
###############################################################################################################################################################################
## GENERAL INFORMATION ABOUT THE NEW TOOL ##
#####################################################
toolname <- "Biclust Plots"
toolhelp <- "biclust"
#######################
## MAKING THE WINDOW ##
#######################
####################################
#### PLOTTING & DIAGNOSTICS TAB ####
####################################
input <- "plotdiagTab"
### ###
## 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=.fabia2biclust(",method_result,",",thresZ,",",thresL,")",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)
###############################################################
### ###
## 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 <- ""
button.otherarg <- paste(",bicResult=.fabia2biclust(",method_result,",",thresZ,",",thresL,")",sep="")
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.otherarg=button.otherarg,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 <- ""
button.otherarg <- paste(",bicResult=.fabia2biclust(",method_result,",",thresZ,",",thresL,")",sep="")
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.otherarg=button.otherarg,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 <- "fstatbuttonframe"
button.name <- "Obs. F Stat."
button.function <- "computeObservedFstat"
button.data <- "x"
button.biclust <- ""
button.otherarg <- paste(",bicResult=.fabia2biclust(",method_result,",",thresZ,",",thresL,")",sep="")
arg.frames <- c("fstatentryframe")
# Do not change this line: (without button.otherarg)
new.frames <- .add.frame(input=input,frame.name=frame.name,type=type,button.otherarg=button.otherarg,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 <- ""
button.otherarg <- paste(",bicResult=.fabia2biclust(",method_result,",",thresZ,",",thresL,")",sep="")
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.otherarg=button.otherarg,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)
#### ####
## MAKE BARCHART PLOT ##
#### ####
#### MANUAL BUTTONS FRAME ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "barchartbuttonframe"
button.name <- "Barchart"
button.function <- "biclustbarchart"
button.data <- "x"
button.biclust <- ""
button.otherarg <- paste(",Bicres=.fabia2biclust(",method_result,",",thresZ,",",thresL,")",sep="")
save <- FALSE
arg.frames <- c()
# Do not change this line:
new.frames <- .add.frame(input=input,save=save,frame.name=frame.name,type=type,button.otherarg=button.otherarg,button.name=button.name,button.function=button.function,button.data=button.data,button.biclust=button.biclust,arg.frames=arg.frames,new.frames=new.frames)
#### ####
## MAKE BUBBLE PLOT ##
#### ####
#### RADIO BUTTONS FRAME - EXAMPLE ####
# #
type <- "radiobuttons"
# Change variables accordingly:
frame.name <- "bubbleplotprojframe"
argument.names <- c("Mean","Iso Mds","Cmd Scale")
arguments <- c("projection")
argument.values <- c("mean","isomds","cmdscale")
argument.types <- "char"
initial.values <- "mean"
title <- "Projection:"
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 <- "bubbleplotlabelframe"
argument.names <- c("Show Labels?")
arguments <- c("showLabels")
initial.values <- c(0)
title <- "Bubble 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,initial.values=initial.values,title=title,border=border,new.frames=new.frames)
#### MANUAL BUTTONS FRAME ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "bubbleplotbuttonframe"
button.name <- "Bubble Plot"
button.function <- "bubbleplot"
button.data <- "x"
button.biclust <- ""
button.otherarg <- paste(",bicResult1=.fabia2biclust(",method_result,",",thresZ,",",thresL,")",sep="")
arg.frames <- c("bubbleplotprojframe","bubbleplotlabelframe")
# Do not change this line: (without button.otherarg)
new.frames <- .add.frame(input=input,frame.name=frame.name,type=type,button.otherarg=button.otherarg,button.name=button.name,button.function=button.function,button.data=button.data,button.biclust=button.biclust,arg.frames=arg.frames,new.frames=new.frames)
#### ####
## Barplot of bicluster ##
#### ####
###### ENTRY FIELDS FRAME #####
# #
type <- "entryfields"
# Change variables accordingly:
frame.name <- "plotclustentryframe"
argument.names <- c("Total Number of Biclusters")
argument.types <- c("num")
arguments <- c("noC")
initial.values <- c("6")
title <- "Barplot"
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)
#### CHECK BOXES FRAME ####
# #
type <- "checkboxes"
# Change variables accordingly:
frame.name <- "plotclustcheckframe"
argument.names <- c("Legend?")
arguments <- c("legende")
initial.values <- c(0)
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 <- "plotclustbuttonframe"
button.name <- "BarPlot"
button.function <- "plotclust"
button.data <- "x"
button.biclust <- ""
button.otherarg <- paste(",res=.fabia2biclust(",method_result,",",thresZ,",",thresL,")",sep="")
save <- FALSE
arg.frames <- c("plotclustcheckframe","plotclustentryframe")
# Do not change this line:
new.frames <- .add.frame(input=input,save=save,frame.name=frame.name,button.otherarg=button.otherarg,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)
#### CHECK BOXES FRAME ####
# #
type <- "checkboxes"
# Change variables accordingly:
frame.name <- "testentry"
argument.names <- c("")
arguments <- c("")
initial.values <- c(0)
title <- "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)
###############################################################################################################################################################################
## CONFIGURATION OF GRID OF FRAMES - PLOTDIAGTAB ##
###################################################
#########################
#### THE GRID MATRIX ####
#########################
grid.config <- .grid.matrix(input=input,c("barchartbuttonframe","fstatentryframe","fstatbuttonframe","bootstrapentryframe",NA,NA,"bootstrapreplacementframe","bootstrapbuttonframe","bootstrapvisualbuttonframe" ,"pplottypeframe","pplotentryframe","parallelbuttonframe","pplotcheckframe",NA,NA,"heatplotcheckframe","heatplotentryframe","heatbuttonframe","mplotcheckframe","mplotentryframe","memberbuttonframe","plotclustentryframe","plotclustcheckframe","plotclustbuttonframe","bubbleplotlabelframe","bubbleplotprojframe","bubbleplotbuttonframe"),byrow=TRUE,nrow=9,ncol=3,grid.config=grid.config)
########################
#### COMBINING ROWS ####
########################
grid.rows <- .combine.rows(input=input,rows=c(1,2,3),title="Barchart & 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)
grid.rows <- .combine.rows(input=input,rows=c(8,9),title="Biclust Bubble Plot & Barplot",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
#grid.rows <- .combine.rows(input=input,rows=c(10),title="Barplot of Bicluster",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
##################################################################
## USE ALL THE ARGUMENTS ABOUT IN THE GENERAL NEW TOOL FUNCTION ##
##################################################################
newtool_template(toolname=toolname,methodname=methodname,toolhelp=toolhelp,grid.config=grid.config,grid.rows=grid.rows,new.frames=new.frames)
}
ewouddt/RcmdrPlugin.BiclustGUI documentation built on July 19, 2020, 9:42 a.m.
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Defines functions fabiabiclust_WINDOW
Documented in fabiabiclust_WINDOW
# Project: BiclustGUI
#
# Author: Ewoud
###############################################################################
fabiabiclust_WINDOW <- function(methodname,thresZ,thresL){
# fabia.names <- c("Fabia Laplace Prior","Fabia Post-Projection","Fabia Sparseness Projection","Fabia SPARSE")
method_result <- gsub(" ","",methodname,fixed=TRUE)
method_result <- gsub("-","",method_result,fixed=TRUE)
if(is.null(thresL)){thresL <- "NULL"}
new.frames <- .initialize.new.frames()
grid.config <- .initialize.grid.config()
grid.rows <- .initialize.grid.rows()
###############################################################################################################################################################################
## GENERAL INFORMATION ABOUT THE NEW TOOL ##
#####################################################
toolname <- "Biclust Plots"
toolhelp <- "biclust"
#######################
## MAKING THE WINDOW ##
#######################
####################################
#### PLOTTING & DIAGNOSTICS TAB ####
####################################
input <- "plotdiagTab"
### ###
## 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=.fabia2biclust(",method_result,",",thresZ,",",thresL,")",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)
###############################################################
### ###
## 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 <- ""
button.otherarg <- paste(",bicResult=.fabia2biclust(",method_result,",",thresZ,",",thresL,")",sep="")
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.otherarg=button.otherarg,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 <- ""
button.otherarg <- paste(",bicResult=.fabia2biclust(",method_result,",",thresZ,",",thresL,")",sep="")
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.otherarg=button.otherarg,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 <- "fstatbuttonframe"
button.name <- "Obs. F Stat."
button.function <- "computeObservedFstat"
button.data <- "x"
button.biclust <- ""
button.otherarg <- paste(",bicResult=.fabia2biclust(",method_result,",",thresZ,",",thresL,")",sep="")
arg.frames <- c("fstatentryframe")
# Do not change this line: (without button.otherarg)
new.frames <- .add.frame(input=input,frame.name=frame.name,type=type,button.otherarg=button.otherarg,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 <- ""
button.otherarg <- paste(",bicResult=.fabia2biclust(",method_result,",",thresZ,",",thresL,")",sep="")
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.otherarg=button.otherarg,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)
#### ####
## MAKE BARCHART PLOT ##
#### ####
#### MANUAL BUTTONS FRAME ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "barchartbuttonframe"
button.name <- "Barchart"
button.function <- "biclustbarchart"
button.data <- "x"
button.biclust <- ""
button.otherarg <- paste(",Bicres=.fabia2biclust(",method_result,",",thresZ,",",thresL,")",sep="")
save <- FALSE
arg.frames <- c()
# Do not change this line:
new.frames <- .add.frame(input=input,save=save,frame.name=frame.name,type=type,button.otherarg=button.otherarg,button.name=button.name,button.function=button.function,button.data=button.data,button.biclust=button.biclust,arg.frames=arg.frames,new.frames=new.frames)
#### ####
## MAKE BUBBLE PLOT ##
#### ####
#### RADIO BUTTONS FRAME - EXAMPLE ####
# #
type <- "radiobuttons"
# Change variables accordingly:
frame.name <- "bubbleplotprojframe"
argument.names <- c("Mean","Iso Mds","Cmd Scale")
arguments <- c("projection")
argument.values <- c("mean","isomds","cmdscale")
argument.types <- "char"
initial.values <- "mean"
title <- "Projection:"
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 <- "bubbleplotlabelframe"
argument.names <- c("Show Labels?")
arguments <- c("showLabels")
initial.values <- c(0)
title <- "Bubble 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,initial.values=initial.values,title=title,border=border,new.frames=new.frames)
#### MANUAL BUTTONS FRAME ####
# #
type <- "buttons"
# Change variables accordingly:
frame.name <- "bubbleplotbuttonframe"
button.name <- "Bubble Plot"
button.function <- "bubbleplot"
button.data <- "x"
button.biclust <- ""
button.otherarg <- paste(",bicResult1=.fabia2biclust(",method_result,",",thresZ,",",thresL,")",sep="")
arg.frames <- c("bubbleplotprojframe","bubbleplotlabelframe")
# Do not change this line: (without button.otherarg)
new.frames <- .add.frame(input=input,frame.name=frame.name,type=type,button.otherarg=button.otherarg,button.name=button.name,button.function=button.function,button.data=button.data,button.biclust=button.biclust,arg.frames=arg.frames,new.frames=new.frames)
#### ####
## Barplot of bicluster ##
#### ####
###### ENTRY FIELDS FRAME #####
# #
type <- "entryfields"
# Change variables accordingly:
frame.name <- "plotclustentryframe"
argument.names <- c("Total Number of Biclusters")
argument.types <- c("num")
arguments <- c("noC")
initial.values <- c("6")
title <- "Barplot"
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)
#### CHECK BOXES FRAME ####
# #
type <- "checkboxes"
# Change variables accordingly:
frame.name <- "plotclustcheckframe"
argument.names <- c("Legend?")
arguments <- c("legende")
initial.values <- c(0)
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 <- "plotclustbuttonframe"
button.name <- "BarPlot"
button.function <- "plotclust"
button.data <- "x"
button.biclust <- ""
button.otherarg <- paste(",res=.fabia2biclust(",method_result,",",thresZ,",",thresL,")",sep="")
save <- FALSE
arg.frames <- c("plotclustcheckframe","plotclustentryframe")
# Do not change this line:
new.frames <- .add.frame(input=input,save=save,frame.name=frame.name,button.otherarg=button.otherarg,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)
#### CHECK BOXES FRAME ####
# #
type <- "checkboxes"
# Change variables accordingly:
frame.name <- "testentry"
argument.names <- c("")
arguments <- c("")
initial.values <- c(0)
title <- "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)
###############################################################################################################################################################################
## CONFIGURATION OF GRID OF FRAMES - PLOTDIAGTAB ##
###################################################
#########################
#### THE GRID MATRIX ####
#########################
grid.config <- .grid.matrix(input=input,c("barchartbuttonframe","fstatentryframe","fstatbuttonframe","bootstrapentryframe",NA,NA,"bootstrapreplacementframe","bootstrapbuttonframe","bootstrapvisualbuttonframe" ,"pplottypeframe","pplotentryframe","parallelbuttonframe","pplotcheckframe",NA,NA,"heatplotcheckframe","heatplotentryframe","heatbuttonframe","mplotcheckframe","mplotentryframe","memberbuttonframe","plotclustentryframe","plotclustcheckframe","plotclustbuttonframe","bubbleplotlabelframe","bubbleplotprojframe","bubbleplotbuttonframe"),byrow=TRUE,nrow=9,ncol=3,grid.config=grid.config)
########################
#### COMBINING ROWS ####
########################
grid.rows <- .combine.rows(input=input,rows=c(1,2,3),title="Barchart & 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)
grid.rows <- .combine.rows(input=input,rows=c(8,9),title="Biclust Bubble Plot & Barplot",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
#grid.rows <- .combine.rows(input=input,rows=c(10),title="Barplot of Bicluster",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
##################################################################
## USE ALL THE ARGUMENTS ABOUT IN THE GENERAL NEW TOOL FUNCTION ##
##################################################################
newtool_template(toolname=toolname,methodname=methodname,toolhelp=toolhelp,grid.config=grid.config,grid.rows=grid.rows,new.frames=new.frames)
}
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