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## ----newmethod_script1,echo=TRUE,eval=FALSE-----------------------------------
# newmethod_WINDOW <- function(){
#
# new.frames <- .initialize.new.frames()
# grid.config <- .initialize.grid.config()
# grid.rows <- .initialize.grid.rows()
#
# #####################################################
# ## GENERAL INFORMATION ABOUT THE NEW METHOD/WINDOW ##
# #####################################################
#
# methodname <- "A new method"
#
# methodfunction <- "methodfunction"
# data.arg <- "d"
# methodshow <- TRUE
# methodsave <- TRUE
# other.arg <- ""
# methodhelp <- ""
#
# # Transform the data from data.arg
# data.transf <- "matrix" # 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 <- FALSE
#
# # SuperBiclust
# superbiclust.comp <- FALSE
#
#
# } # Note: The curly bracket is placed here for syntax reasons.
# # It should be placed after the call of cluster_template.
## ----newmethod_script2,eval=FALSE,echo=TRUE-----------------------------------
# ########################
# #### CLUSTERING TAB ####
# ########################
#
# input <- "clusterTab"
#
# ### 1. ADDING THE FRAMES ###
#
# # Add frames here
#
# ### 2. CONFIGURING THE GRID ###
#
# grid.config <- .grid.matrix(input=input,c("frame1","frame2","frame3",NA,"frame4",NA),
# nrow=3,ncol=2,byrow=TRUE,grid.config=grid.config)
#
#
# ### 3. COMBING THE ROWS ###
#
# grid.rows <- .combine.rows(input=input,rows=c(1),title="A nice box: ",
# border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
# grid.rows <- .combine.rows(input=input,rows=c(2,3),title="A nice box: ",
# border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
#
## ----newmethod_script3,eval=FALSE,echo=TRUE-----------------------------------
# ####################################
# #### PLOTTING & DIAGNOSTICS TAB ####
# ####################################
# { # ignore this bracket
#
# input <- "plotdiagTab"
#
# ### 1. ADDING THE FRAMES ###
#
# # Add frames here
#
# ### 2. CONFIGURING THE GRID ###
#
# grid.config <- .grid.matrix(input=input,c("frame5","frame6"),nrow=1,ncol=2,
# byrow=TRUE,grid.config=grid.config)
#
# ### 3. COMBING THE ROWS ###
#
# grid.rows <- .combine.rows(input=input,rows=c(1),title="Plot 1",border=TRUE,
# grid.rows=grid.rows,grid.config=grid.config)
#
# ###################################################################
# ## USE ALL THE ARGUMENTS 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)
# }
## ----plaid_script1,eval=FALSE,echo=TRUE---------------------------------------
# #####################################################
# ## GENERAL INFORMATION ABOUT THE NEW METHOD/WINDOW ##
# #####################################################
#
# methodname <- "Plaid"
# methodfunction <- "biclust"
# data.arg <- "x"
# other.arg <- ",method=BCPlaid()"
# methodhelp <- "BCPlaid"
# methodseed <- TRUE
# data.discr <- FALSE
# data.bin <- FALSE
# bcdiag.comp <- TRUE
# superbiclust.comp <- TRUE
#
# # Biclust only (Not for public use)
# extrabiclustplot <- TRUE
## ----plaid_script2,eval=FALSE,echo=TRUE---------------------------------------
# ### 2. CONFIGURING THE GRID ###
# grid.config <- .grid.matrix(input=input,c("toclusterframe","modelframe",
# "backgroundcheckframe",NA,"backgroundentryframe1","backgroundentryframe2"),
# byrow=TRUE,nrow=3,ncol=2,grid.config=grid.config)
#
# ### 3. COMBING THE ROWS ###
# grid.rows <- .combine.rows(input=input,rows=c(1),title="Plaid Specifications",
# border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
# grid.rows <- .combine.rows(input=input,rows=c(2,3),title="Layer Specifications",
# border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
## ----newtool_script,eval=FALSE,echo=TRUE--------------------------------------
# newtool_WINDOW <- function(methodname){
#
# new.frames <- .initialize.new.frames()
# grid.config <- .initialize.grid.config()
# grid.rows <- .initialize.grid.rows()
#
# #####################################################
# ## GENERAL INFORMATION ABOUT THE NEW TOOL ##
# #####################################################
#
# toolname <- "A new tool"
# toolhelp <- "helppage"
#
# # Do not change this line:
# input <- "plotdiagTab"
#
# ### ADDING FRAMES ####
#
# # Analogous to plotdiag tab.
#
# ### CONFIGURING GRID ###
# grid.config <- .grid.matrix(input=input,c(),nrow=1,ncol=2,
# byrow=TRUE,grid.config=grid.config)
#
#
# ### COMBINING ROWS ###
# grid.rows <- .combine.rows(input=input,rows=c(),title="Plot 1",
# border=TRUE,grid.rows=grid.rows,grid.config=grid.config)
#
# ############################################################
# ## USE ALL THE ARGUMENTS 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)
# }
## ----bcdiag_script,eval=FALSE,echo=TRUE---------------------------------------
# bcdiag_WINDOW <- function(methodname){
#
# new.frames <- .initialize.new.frames()
# grid.config <- .initialize.grid.config()
# grid.rows <- .initialize.grid.rows()
#
# # Some extra code to determine the input type: "biclust", "fabia", "isa2"
# biclust.names <- c("Bimax","CC","Plaid","Questmotif","Spectral",
# "XMotifs","IBBIG")
# fabia.names <- c("Fabia Laplace Prior","Fabia Post-Projection",
# "Fabia Sparseness Projection","Fabia SPARSE")
# isa.names <- c("ISA")
#
# if(methodname %in% biclust.names){
# extra.arg <- ",mname='biclust'"
# }
# if(methodname %in% fabia.names){
# extra.arg <- ",mname='fabia'"
# }
# if(methodname %in% isa.names){
# extra.arg <- ",mname='isa2'"
# }
#
# #####################################################
# ## GENERAL INFORMATION ABOUT THE NEW TOOL ##
# #####################################################
#
# toolname <- "BCDIAG"
# toolhelp <- "BcDiag-package"
#
# }#ignore
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