R/rulerPlot.R

In idiogramFISH: Shiny App. Idiograms with Marks and Karyotype Indices

#' rulerPlot
#' This is an internal function that plots rulers
#'
#' It returns rulers (axis)
#'
#' @keywords internal
#'
#' @param ycoord y coords
#' @param listOfdfChromSize list of all d.f chr size
#' @param listOfdfChromSizeCenType only d.f. of this cen. type
#' @param fromZerotoMax intervals
#' @param rulerNumberSize font
#' @param rulerPos pos. of ruler
#' @param ruler.tck tick size and orient.
#'
#' @return axis
#' @importFrom graphics axis rug
#'

rulerPlot <- function(ycoord,listOfdfChromSize,listOfdfChromSizeCenType,fromZerotoMax,rulerNumberSize,rulerPos,ruler.tck,lwd.chr,
                    moveKarHor2,mkhValue,useMinorTicks,miniTickFactor,verticalPlot,moveAllKarValueHor){

  amount<-if(verticalPlot){length(ycoord)} else {1}

  rulerNumberSize <- if(rulerNumberSize<=0){0.1} else {rulerNumberSize}

  for (i in 1:amount ) {

    corr_index<-which(names(listOfdfChromSize) %in% names(listOfdfChromSizeCenType)[[i]] )

    divisor2 <- as.numeric(attr(listOfdfChromSize[[corr_index]],"divisor"))

    if(names(listOfdfChromSize)[corr_index] %in% moveKarHor2 ) {
      rulerPos2 <- rulerPos+mkhValue+moveAllKarValueHor
    } else {
      rulerPos2 <- rulerPos+moveAllKarValueHor
    }

    if ( attr(listOfdfChromSizeCenType[[i]], "ytitle" )=="cM" ) {
      labels<-unlist(fromZerotoMax[[i]] )*divisor2
    } else if( attr(listOfdfChromSizeCenType[[i]], "ytitle" )=="Mb" ) {
      labels<-unlist(fromZerotoMax[[i]] )*divisor2/1e6
    } else  { # ytitle notmb
      labels<-unlist(fromZerotoMax[[i]] )*divisor2
    }

    #
    #     long tick and labels
    #

    locations<-unlist(ycoord[[i]])
    miniInterval  <-(locations[2]-locations[1] ) / miniTickFactor
    locationsMinor<-seq(locations[1], locations[length(locations)] , miniInterval)

    graphics::axis(side=2,
                   at = locations,
                   labels = labels
                   ,cex.axis = rulerNumberSize
                   ,las=1
                   ,pos= rulerPos2
                   ,tck=ruler.tck
                   ,lwd=lwd.chr
                   ,lwd.ticks = lwd.chr
    )
    if(useMinorTicks){
    rug(x = locationsMinor, ticksize = ruler.tck/2, side = 2, pos=rulerPos2)
    }

    # ) # l
  } # FOR
}