R/tree.R

In stela2502/IMGThelper: An R package to access IMGT reult files

#' @name tree
#' @aliases tree,IMGThelper-method
#' @rdname tree-methods
#' @docType methods
#' @description create the data table used for the treemap plots (based on 6_Junctions.txt)
#' @param x the IMGThelper object
#' @param splitAt separate the plot at splitAt (ask Stijn of how to phrase that) default= 5
#' @param color a global CDR3 vs color table ( default NULL -> rainbow colors)
#' @title description of function tree
#' @export 
setGeneric('tree', ## Name
	function ( x, splitAt = 5, color=NULL ) { ## Argumente der generischen Funktion
		standardGeneric('tree') ## der Aufruf von standardGeneric sorgt für das Dispatching
	}
)

setMethod('tree', signature = c ('IMGThelper'),
	definition = function ( x, splitAt = 5, color=NULL ) {
    if ( ! is.null(x$usedObj$treeDat )) {
      return (x$usedObj$treeDat )
    }

    more = recurringProductives( x, cutoff= splitAt)
    #browser()
    tabmore<-table(more$CDR3AA)
  
    #tabmore<-as.data.frame(table(more$CDR3AA))
    #colnames(tabmore)<-c("CDR3", "Freq")

    x$usedObj$CDR3elements = unique (names(tabmore), x$usedObj$CDR3elements)
    tabmore<-table(more$CDR3AA)
    if ( is.null(color) ){
     color = data.frame( 
      'CDR3'  = x$usedObj$CDR3elements, 
      'color' = sample( rainbow(length(x$usedObj$CDR3elements)), length(x$usedObj$CDR3elements)), 
      'Freq'  = tabmore[ match( x$usedObj$CDR3elements, names(tabmore))]
     )
    }

    x$usedObj$color = color
    #x$usedObj$treeDat = tabout
    #tabout
    x$usedObj$color
} )