R/textLabelDots.R

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

#' textLabelDots
#' This is an internal function that plot labels of cM marks
#'
#' It returns a plot
#'
#' @keywords internal
#'
#' @param xMark x coords
#' @param yMark y coords
#' @param listOfdfChromSize radius
#' @param listOfdfMarkPosCr color
#' @param specialChrSpacing vertices number
#' @param chrSpacing aspect
#' @param markLabelSize size of mark label font
#' @param pattern pattern to remove from mark name
#' @param xBoundariesQuar x size
#'
#' @return plotted text
#' @importFrom graphics polygon text
#'

textLabelDots<-function(xMarkCr,yMarkCr,listOfdfChromSize,listOfdfMarkPosCr,specialChrSpacing,
                    chrSpacing,markLabelSize,pattern, bannedMarkName, xBoundariesQuar) {
    for (s in 1:length(xMarkCr) ) {
      corr_index<-which(names(listOfdfChromSize) %in% names(listOfdfMarkPosCr)[[s]] )
      if(attr(listOfdfChromSize[[corr_index]],"ytitle")=="cM"){
        chrSpacing2<-specialChrSpacing
      } else {
        chrSpacing2<-chrSpacing
      }
      # lapply(1:length(xMarkCr[[s]]), function (m)
        for ( m in 1:length(xMarkCr[[s]] ) ) {

          if( !listOfdfMarkPosCr[[s]]$markName[m] %in% bannedMarkName ){
        mapply(function(x,y,z) graphics::text(x=x,
                                              y=y,
                                              label=z,
                                              cex=markLabelSize,
                                              # pos=4,
                                              adj=0
        ),
        x=xMarkCr[[s]][[m]][[2]]+xBoundariesQuar+chrSpacing2*.1,
        y=(yMarkCr[[s]][[m]][1]),
        z=sub(pattern,"",listOfdfMarkPosCr[[s]]$markName[m])
        # t
        ) #m

          } # if
        }
    }
}