R/treemap.R

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

#' @name treemap
#' @aliases treemap,IMGThelper-method
#' @rdname treemap-methods
#' @docType methods
#' @description draw a treemap of clone sizes
#' @param x the IMGThelper object
#' @param ofile the pdf file name
#' @param name the experiment this VDJ analysis came from
#' @param ... options for the tree function
#' @title description of function treemap
#' @export 
setGeneric('treemap', ## Name
	function ( x, name, ofile, ... ) { ## Argumente der generischen Funktion
		standardGeneric('treemap') ## der Aufruf von standardGeneric sorgt für das Dispatching
	}
)

setMethod('treemap', signature = c ('IMGThelper'),
	definition = function ( x, name, ofile, ... ) {

    print ("creating tree" )
	  treeDat <- tree( x, ... )
    #browser()
    clones<-nrow(treeDat)

    out.title<-paste(name,"; ", clones, " CDR3 clones in this treemap", sep="")
 
    figure.fname<-paste(name, "list with", clones, "clones in treemap", paste= " ")
  
    ofile = paste( ofile, 'pdf', sep="." )
    pdf( ofile, width=7, height=7)
    print ( "Plotting" )
   # browser()
    treemap::treemap(treeDat, index=c("CDR3"), vSize="Freq.Freq", vColor="color", type="color",
  	algorithm="squarified",fontsize.labels=10,sortID="size",title=out.title, 
  	border.lwds=0.5, drop.unused.levels = FALSE)
    dev.off()
  
} )