R/arrowPlotMark.R

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

#' arrowPlotMark
#' This is an internal function that plot marks
#'
#' It returns a plot
#'
#' @keywords internal
#'
#' @param squareness squareness of vertices <
#' @param xMark x component of polygon
#' @param yMark yMark component of polygon
#' @param dfMarkColorInt colors for marks
#' @param listOfdfMarkPosArrow list of df. of mark pos.
#' @param chrWidth numeric, width of chr.
#' @param n numeric, to define vertices of rounded portions
#' @param lwd.chr thick of border line
#' @param circularPlot boolean TRUE for circ.
#' @param y list, y coords.
#' @param markLabelSize numeric, font size
#' @param separFactor numeric, sep. kars.
#' @param labelSpacing numeric, spacing
#' @param circleCenter numeric
#' @param circleCenterY numeric
#' @param radius numeric
#' @param ylistTransChr list, transf. coords.
#' @param rotation rotate*
#'
#' @return plot
#' @importFrom graphics polygon text
#' @importFrom scales alpha
#'
arrowPlotMark <- function(squareness, xMark, yMark, # nolint: object_usage_linter
                          dfMarkColorInt, listOfdfMarkPosArrow,
                          chrWidth,
                          n,
                          lwd.chr,
                          circularPlot,
                          y,
                          x,
                          markLabelSize,
                          separFactor,
                          labelSpacing,
                          circleCenter, circleCenterY, radius,
                          ylistTransChr, rotation, arrowheadWidthShrink, alpha_val) {
  if (circularPlot == FALSE) {
    for (w in seq_along(xMark)) {
      for (n in seq_along(xMark[[w]])) {

        x <- xMark[[w]][[n]]
        y <- yMark[[w]][[n]]
        z <- listOfdfMarkPosArrow[[w]]$markName[[n]]

        graphics::polygon(
          x = x,
          y = y,
          col = alpha(dfMarkColorInt$markColor[match(z, dfMarkColorInt$markName)], alpha_val), #nolint: object_usage_linter
          lwd = lwd.chr,
          border =
            dfMarkColorInt$markBorderColor[match(z, dfMarkColorInt$markName)]
        )
      }
    }
  } else { # circ true

    yMarkPer <- markMapPer(yMark, y)
    xlistNew <- xMarkMap(xMark, x, arrowheadWidthShrink)
    ylistTransMark <- transyListMark(yMarkPer, ylistTransChr)
    circleMapsMarks <- applyMapCircle(radius, circleCenter, circleCenterY, separFactor,
      ylistTransMark, xlistNew, n, 0, chrWidth,
      rotation = rotation
    )

    drawPlotMark(circleMapsMarks, dfMarkColorInt, listOfdfMarkPosArrow, lwd.chr, alpha_val)
  }
}