Nothing
# Project: BiclustGUI
#
# Author: Gebruiker
###############################################################################
# as.char!!: eSetData.name, blocGene , blocSample, r
bicare_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 <- "BICARE"
methodfunction <- "bicare.GUI"
data.arg <- "Data"
methodshow <- TRUE
methodsave <- FALSE
other.arg <- ""
methodhelp <- "BicARE"
# Transform the data from data.arg
data.transf <- "" # Values: "matrix" (default), "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
########################
#### CLUSTERING TAB ####
########################
input <- "clusterTab"
### 1. ADDING THE FRAMES ###
#### ENTRY FIELDS FRAME ####
type <- "entryfields"
# Change variables accordingly:
frame.name <- "eSetentry"
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)
#### ENTRY FIELDS FRAME ####
type <- "entryfields"
# Change variables accordingly:
frame.name <- "optionsentry"
argument.names <- c("Number of biclusters searched","Genes init. membership prob.","Samples init/ membership prob.","Residue Threshold ( NULL=(Data Residue)/10 )","Min. number genes per bicluster","Min. number cond. per bicluster","Number of iterations")
argument.types <- c("num","num","char","char","num","num","num")
arguments <- c("k","pGene","pSample","r","N","M","t")
initial.values <- c("20","0.5","pGene","NULL","8","6","500")
title <- ""
border <- FALSE
entry.width <- c("6","6","6","6","6","6","6")
# 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 <- "initentry"
argument.names <- c("Direct Init. matrix for genes","Direct Init. matrix for cond.")
argument.types <- c("char","char")
arguments <- c("blocGene","blocSample")
initial.values <- c("NULL","NULL")
title <- "Direct Initialisations? (NULL=Random)"
border <- FALSE
entry.width <- c("15","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)
### 2. CONFIGURING THE GRID ###
grid.config <- .grid.matrix(input=input,c("eSetentry","optionsentry","initentry"),nrow=3,ncol=1,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(2,3),title="BicARE Options ",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
####################################
#### PLOTTING & DIAGNOSTICS TAB ####
####################################
input <- "plotdiagTab"
### 1. ADDING THE FRAMES ###
#### MANUAL BUTTONS FRAME ####
type <- "buttons"
# Change variables accordingly:
frame.name <- "summarybutton"
button.name <- "Summary"
button.function <- "summaryBICARE"
button.data <- ""
button.biclust <- "x"
button.width <- "12"
button.data.transf <- ""
arg.frames <- c()
save <- FALSE
show <- TRUE
button.otherarg <- ""
# 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,button.otherarg=button.otherarg,
button.width=button.width,button.data.transf=button.data.transf,
arg.frames=arg.frames,save=save,show=show,new.frames=new.frames)
#### MANUAL BUTTONS FRAME ####
type <- "buttons"
# Change variables accordingly:
frame.name <- "residuplotbutton"
button.name <- "Residue Plot"
button.function <- "bicare.residuplot"
button.data <- ""
button.biclust <- "result"
button.width <- "12"
button.data.transf <- ""
arg.frames <- c()
save <- FALSE
show <- TRUE
button.otherarg <- ""
# 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,button.otherarg=button.otherarg,
button.width=button.width,button.data.transf=button.data.transf,
arg.frames=arg.frames,save=save,show=show,new.frames=new.frames)
#### ENTRY FIELDS FRAME ####
type <- "entryfields"
# Change variables accordingly:
frame.name <- "biclusterentry"
argument.names <- c("Bicluster Number")
argument.types <- c("num")
arguments <- c("k")
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)
#### CHECK BOXES FRAME ####
type <- "checkboxes"
# Change variables accordingly:
frame.name <- "biclustercheck"
argument.names <- c("Plot?")
arguments <- c("graph")
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 <- "biclusterbutton"
button.name <- "Extract Bicluster"
button.function <- "bicluster"
button.data <- ""
button.biclust <- "biclustering"
button.width <- "16"
button.data.transf <- ""
arg.frames <- c("biclusterentry","biclustercheck")
save <- TRUE
show <- TRUE
button.otherarg <- ""
# 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,button.otherarg=button.otherarg,
button.width=button.width,button.data.transf=button.data.transf,
arg.frames=arg.frames,save=save,show=show,new.frames=new.frames)
#### ENTRY FIELDS FRAME ####
type <- "entryfields"
# Change variables accordingly:
frame.name <- "genesetentry"
argument.names <- c("Geneset Type")
argument.types <- c("char")
arguments <- c("setType")
initial.values <- c("GOCollection()")
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)
#### MANUAL BUTTONS FRAME ####
type <- "buttons"
# Change variables accordingly:
frame.name <- "genesethelp"
button.name <- "Genesets Help"
button.function <- "help"
button.data <- ""
button.biclust <- ""
button.width <- "16"
button.data.transf <- ""
arg.frames <- c()
save <- FALSE
show <- TRUE
button.otherarg <- "'CollectionType-class'"
# 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,button.otherarg=button.otherarg,
button.width=button.width,button.data.transf=button.data.transf,
arg.frames=arg.frames,save=save,show=show,new.frames=new.frames)
#### ENTRY FIELDS FRAME ####
type <- "entryfields"
# Change variables accordingly:
frame.name <- "genesetentry2"
argument.names <- c("From","To")
argument.types <- c("num","num")
arguments <- c("gene.from","gene.to")
initial.values <- c("1","50")
title <- "Which genes?"
border <- FALSE
entry.width <- c("3","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)
#### MANUAL BUTTONS FRAME ####
type <- "buttons"
# Change variables accordingly:
frame.name <- "genesetbutton"
button.name <- "Genes Enrichment"
button.function <- "bicare.genesetenrichment"
button.data <- ""
button.biclust <- "result"
button.width <- "16"
button.data.transf <- ""
arg.frames <- c("genesetentry","genesetentry2")
save <- FALSE
show <- FALSE
button.otherarg <- ""
# 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,button.otherarg=button.otherarg,
button.width=button.width,button.data.transf=button.data.transf,
arg.frames=arg.frames,save=save,show=show,new.frames=new.frames)
#### MANUAL BUTTONS FRAME ####
type <- "buttons"
# Change variables accordingly:
frame.name <- "pdatabutton"
button.name <- "pData"
button.function <- "bicare.pdata"
button.data <- ""
button.biclust <- "result"
button.width <- "18"
button.data.transf <- ""
arg.frames <- c()
save <- FALSE
show <- TRUE
button.otherarg <- ""
# 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,button.otherarg=button.otherarg,
button.width=button.width,button.data.transf=button.data.transf,
arg.frames=arg.frames,save=save,show=show,new.frames=new.frames)
#### ENTRY FIELDS FRAME ####
type <- "entryfields"
# Change variables accordingly:
frame.name <- "pdatacovariates"
argument.names <- c("Columns in pData")
argument.types <- c("char")
arguments <- c("covariates")
initial.values <- c("c(1)")
title <- "Covariates to use? (e.g. c(1,2) )"
border <- FALSE
entry.width <- c("20")
# 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 <- "samplesbutton"
button.name <- "Samples Enrichment"
button.function <- "bicare.samplesenrichment"
button.data <- ""
button.biclust <- "result"
button.width <- "18"
button.data.transf <- ""
arg.frames <- c("pdatacovariates")
save <- FALSE
show <- FALSE
button.otherarg <- ""
# 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,button.otherarg=button.otherarg,
button.width=button.width,button.data.transf=button.data.transf,
arg.frames=arg.frames,save=save,show=show,new.frames=new.frames)
#### ENTRY FIELDS FRAME ####
type <- "entryfields"
# Change variables accordingly:
frame.name <- "reportentry"
argument.names <- c("Report Name")
argument.types <- c("char")
arguments <- c("dirName")
initial.values <- c("name")
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)
#### MANUAL BUTTONS FRAME ####
type <- "buttons"
# Change variables accordingly:
frame.name <- "reportbutton"
button.name <- "Make Report"
button.function <- "bicare.makereport"
button.data <- ""
button.biclust <- ""
button.width <- "12"
button.data.transf <- ""
arg.frames <- c("reportentry")
save <- FALSE
show <- FALSE
button.otherarg <- ""
# 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,button.otherarg=button.otherarg,
button.width=button.width,button.data.transf=button.data.transf,
arg.frames=arg.frames,save=save,show=show,new.frames=new.frames)
#### MANUAL BUTTONS FRAME ####
type <- "buttons"
# Change variables accordingly:
frame.name <- "biclustplotbutton"
button.name <- "Biclust Plots"
button.function <- "bicarebiclust_WINDOW"
button.data <- ""
button.biclust <- ""
button.width <- "12"
button.data.transf <- ""
arg.frames <- c()
save <- FALSE
show <- FALSE
button.otherarg <- paste("methodname='",methodname,"'",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,button.otherarg=button.otherarg,
button.width=button.width,button.data.transf=button.data.transf,
arg.frames=arg.frames,save=save,show=show,new.frames=new.frames)
### 2. CONFIGURING THE GRID ###
grid.config <- .grid.matrix(input=input,c("summarybutton",NA,NA,"residuplotbutton",NA,NA,"biclusterentry","biclustercheck","biclusterbutton","genesetentry","genesethelp",NA,"genesetentry2","genesetbutton",NA,"pdatabutton","pdatacovariates",NA,"samplesbutton",NA,NA,"reportentry","reportbutton",NA,"biclustplotbutton",NA,NA),nrow=9,ncol=3,byrow=TRUE,grid.config=grid.config)
### 3. COMBING THE ROWS ###
grid.rows <- .combine.rows(input=input,rows=c(1,2,3),title="General Diagnostics & Plots",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
grid.rows <- .combine.rows(input=input,rows=c(4,5),title="Genesets Enrichment (Need complete eSet)",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
grid.rows <- .combine.rows(input=input,rows=c(6,7),title="Samples Enrichment (Need complete eSet)",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
grid.rows <- .combine.rows(input=input,rows=c(8),title="Make Report",border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
grid.rows <- .combine.rows(input=input,rows=c(9),title="Extra Plots",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,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)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.