# chromosome data, if only 1 species, column OTU is optional
require(plyr)
dfOfChrSize$OTU   <- "Species mono"
dfChrSizeHolo$OTU <- "Species holo"

monoholoCS <- plyr::rbind.fill(dfOfChrSize, dfChrSizeHolo)

dfOfMarks2$OTU     <- "Species mono"
dfOfMarks2[which(dfOfMarks2$markName == "5S"), ]$markSize <- .7
dfMarkPosHolo$OTU <- "Species holo"

monoholoMarks <- plyr::rbind.fill(dfOfMarks2, dfMarkPosHolo)

library(idiogramFISH)

# svg("testing.svg",width=14,height=10 )
png("monoholoCS.png", width = 700, height = 600)
par(mar = rep(0, 4))
plotIdiograms(dfChrSize   = monoholoCS,   # data.frame of chr. size
  dfMarkColor = dfMarkColor,   # df of mark style
  dfMarkPos   = monoholoMarks, # df of mark positions, includes cen. marks

  chrSize     = TRUE,         # show chr. size under chr.

  squareness  = 4,            # vertices squareness
  addOTUName  = TRUE,         # add OTU names
  OTUTextSize = .7,           # font size of OTU
  distTextChr = .5,           # separ. among chr. and text and among chr. name and indices

  karHeiSpace = 4,            # karyotype height inc. spacing
  karIndexPos = .2,           # move karyotype index

  legendHeight = 1,            # height of legend labels
  legendWidth = 1,             # width of legend labels
  fixCenBorder = TRUE,         # use chrColor as border color of cen. or cen. marks

  rulerPos    = 0,             # position of ruler
  ruler.tck   = -0.02,         # size and orientation of ruler ticks
  rulerNumberPos = .9,         # position of numbers of rulers
  xPosRulerTitle = 3.5,        # ruler title (units) position

  xlimLeftMod = 1,             # modify xlim left argument of plot
  xlimRightMod = 3,            # modify xlim right argument of plot
  ylimBotMod  = .2             # modify ylim bottom argument of plot

  , chromatids = FALSE         # do not show separ. chromatids

  # ,useOneDot=TRUE

  # ,circularPlot = TRUE       # circularPlot
  # ,shrinkFactor = .9         # percentage 1 = 100% of circle with chr.
  # ,circleCenter = 3          # X coordinate of circleCenter (affects legend pos.)
  # ,chrLabelSpacing = .9      # chr. names spacing

  # ,OTUsrt = 0                # angle for OTU name (or number)
  # ,OTUplacing = "number"     # Use number and legend instead of name
  # ,OTULabelSpacerx = -0.6    # modify position of OTU label, when OTUplacing="number" or "simple"
  # ,OTUlegendHeight = 1.5     # space among OTU names when in legend - OTUplacing
  # ,separFactor = 0.75        # alter separ. of kar.
)
dev.off() # close png

chrAndMarksMap <- mapGGChrMark(dfChrSizeHolo, dfMarkPosHolo, chrSpacing = .5)

require(ggplot2)

myColors <- c("chartreuse3", "red", "darkgoldenrod1", "dodgerblue")
names(myColors) <- c("45S", "5S", "CMA", "DAPI")

ggplot() +
  geom_polygon(aes(x = x,
    y = y,
    group = Chr
  ),
  data = chrAndMarksMap$dataChr,
  color = "gray",
  fill = "gray"
  ) +
  geom_polygon(aes(x = x, y = y,
    group = id,
    color = markName,
    fill = markName
  ),
  data = chrAndMarksMap$dataMark
  ) +
  theme_classic() +
  scale_color_manual(
    values = myColors
  ) +
  scale_fill_manual(
    values = myColors
  ) +
  scale_x_continuous(breaks = seq(1, nrow(dfChrSizeHolo), 1)
  ) +
  scale_y_continuous(breaks = seq(0, 5, 0.5)
  ) +
  geom_segment(aes(y = 0, yend = 5, x = -Inf, xend = -Inf)
  ) +
  theme(axis.line   = element_blank(),
    axis.ticks.x = element_blank(),
    axis.title  = element_blank(),
    title      = element_blank()
  )

require(svglite)
ggsave(file = "ggplot.svg", width = 6, height = 4)

# mark general characteristics' data.frame:

mydfMarkColorHolo2 <- read.table(text =
  "  markName    markColor      style
     5S        red            dots
     45S       chartreuse3    square
     gene2     salmon         downArrow
     gene3     \"#056522\"    cMLeft
     gene4     darkmagenta    cM
     DAPI      dodgerblue     square
     protein   cornflowerblue exProtein
     B         black          square
     gene1     chocolate      upArrow
     CMA       darkgoldenrod1 square
     c45S      chartreuse3    cenStyle    # <- simulate Cen.
     myCen2    red            cenStyle
     myCen     chartreuse2    cenStyle
     constr    NA             cenStyle",  header = TRUE, stringsAsFactors = FALSE, fill = TRUE)


# add new cenStyle marks to data.frame of marks' position, created above

mydfMarkPosHolo2 <- plyr::rbind.fill(mydfMarkPosHolo,
  data.frame(OTU = "Species one",
    chrName = c(1:3, "X"),
    markName = c("c45S", "myCen2", "constr", "myCen"), # <- use new mark
    markPos = c(rep(2.5, 3), 1),
    markSize = NA
  )
)

# png("mydChrSizeHolo.png", width=600, height=300)
par(mar = c(0, 0, 0, 1)) # bottom left top right

plotIdiograms(dfChrSize  = mydfChrSizeHolo,     # data.frame of chr. sizes
  dfMarkColor = mydfMarkColorHolo2,  # df of mark style
  dfMarkPos  = mydfMarkPosHolo2,    # df of mark positions
  addOTUName = FALSE,             # add OTU names

  xlimLeftMod = 2,              # modify xlim left argument
  ylimTopMod = -1,              # modify ylim top argument
  ylimBotMod = -2               # modify ylim bottom argument
  , rulerPos = 0,
  ruler.tck = -0.01,
  xPosRulerTitle = 2.6,
  legendWidth = 1               # width of legend
  , legendHeight = .5           # height of legend item
  , lwd.mimicCen = 2.5          # line width of const. mark
  , pattern = "^c"              # regex pattern to remove from mark names
  , remSimiMarkLeg = TRUE       # remove pseudoduplicated mark names (got equal after pattern removal)
  , bannedMarkName = c("myCen", "myCen2", "B") # hide label
  # ,legend="inline"           # legends inline
) # ; dev.off() closes png

require(idiogramFISH)
# transform data.frames for simplicity
bigdfChrSizeHoloMb <- bigdfChrSizeHolo # included in idiogramFISH
bigdfChrSizeHoloMb$chrSize <- bigdfChrSizeHoloMb$chrSize * 98000000
bigdfMarkPosHoloMb <- bigdfMarkPosHolo
bigdfMarkPosHoloMb$markPos <- bigdfMarkPosHoloMb$markPos * 98000000
bigdfMarkPosHoloMb$markSize <- bigdfMarkPosHoloMb$markSize * 98000000

# fig.width=7, fig.height=7
bigdfOfChrSize3_100Mb <- bigdfOfChrSize3Mb
bigdfOfChrSize3_100Mb$chrSize <- bigdfOfChrSize3Mb$chrSize * 33

bigdfOfMarks3_100Mb <- bigdfOfMarks3Mb
bigdfOfMarks3_100Mb$markPos <- bigdfOfMarks3_100Mb$markPos * 33
bigdfOfMarks3_100Mb$markSize <- bigdfOfMarks3_100Mb$markSize * 33

par(mar = rep(0, 4))
plotIdiograms(dfChrSize   = bigdfOfChrSize3_100Mb,  # chr. size data.frame
  dfMarkPos   = bigdfOfMarks3_100Mb,    # mark position df

  chrWidth = .6,                # width of chr.
  chrSpacing = .6,            # space among chr.
  karHeight = 3,              # kar. height without interspace
  karHeiSpace = 5,            # vertical size of karyotype including spacer
  amoSepar = 2,               # separ. among kar.

  indexIdTextSize = .6,       # font size of chr. name and indices
  markLabelSize = .7,         # font size of mark legends
  distTextChr = .65,          # separation among chr. names and indices

  fixCenBorder = TRUE         # use chrColor as border color of cen. or cen. marks
  , legendWidth = 1.5         # legend items width

  , xPosRulerTitle = 3.5       # position of Mb (title) in ruler
  , rulerPos = 0,              # ruler position
  ruler.tck = -0.005,          # ticks of ruler size and orientation
  rulerNumberPos = .7,         # position of numbers in ruler
  rulerNumberSize = .7,        # font size of ruler numbers
  rulerInterval = 1.5,        # ruler interval for micrometeres
  rulerIntervalMb = 50,       # ruler interval for Mb

  ylimBotMod = 0.4,           # modify ylim bottom argument
  ylimTopMod = 0              # modify ylim top argument
  , chromatids = FALSE        # do not show chromatids

  ####  NEW    #####
  , threshold = 90            # this will allow to not to shrink data greater than 350 Mb
)

# fig.width=10, fig.height=10
# modify data in millions to hundreds of millions of Mb
bigdfOfChrSize3_100Mb <- bigdfOfChrSize3Mb[1:8, ]
bigdfOfChrSize3_100Mb$chrSize <- bigdfOfChrSize3_100Mb$chrSize * 100

bigdfOfMarks3_100Mb <- bigdfOfMarks3Mb
bigdfOfMarks3_100Mb$markPos <- bigdfOfMarks3_100Mb$markPos * 100
bigdfOfMarks3_100Mb$markSize <- bigdfOfMarks3_100Mb$markSize * 100

# merge data.frames in micrometers and number of bases
mixedThreeSpChrSize <- plyr::rbind.fill(bigdfOfChrSize[1:8, ], bigdfOfChrSize3_100Mb)
# sort by OTU name
mixedThreeSpChrSize <- mixedThreeSpChrSize[order(mixedThreeSpChrSize$OTU), ]

# add cenStyle marks to simulate centromeres in karyo. in Mb (holocen.)
# compare rulers
bigdfSimCenMarks <- bigdfOfChrSize3_100Mb
bigdfSimCenMarks$markPos <- bigdfSimCenMarks$chrSize / 2

bigdfSimCenMarks$markName <- "sim. cen."
bigdfSimCenMarks$chrSize <- NULL

# merge marks in micrometers and bases
mixedThreeSpMarks <- plyr::rbind.fill(bigdfOfMarks, bigdfOfMarks3_100Mb, bigdfSimCenMarks)

# remove cenStyle mark info.
mixedThreeSpMarks <- mixedThreeSpMarks[which(!(mixedThreeSpMarks$OTU %in% "Species 2 genome" &
  mixedThreeSpMarks$chrName %in% c(1, 4) &
  mixedThreeSpMarks$markName %in% "sim. cen.")), ]

# constric. marks
mixedThreeSpMarks[which(mixedThreeSpMarks$OTU %in% "Species 2 genome" &
  mixedThreeSpMarks$chrName %in% c(1, 4)), ]$markName <- c("cDAPI", "cCMA")

# add arrow mark
mixedThreeSpMarks <- dplyr::bind_rows(mixedThreeSpMarks, mixedThreeSpMarks[nrow(mixedThreeSpMarks), ])
mixedThreeSpMarks[nrow(mixedThreeSpMarks), ]$markName <- "S58A"
mixedThreeSpMarks[nrow(mixedThreeSpMarks), ]$markPos <- .7e+08
mixedThreeSpMarks[nrow(mixedThreeSpMarks), ]$markSize <- .7e+08

dfMarkColorAndStyle <- makedfMarkColorMycolors(unique(mixedThreeSpMarks$markName),
  c("red", "chartreuse3", "dodgerblue", "darkgoldenrod1", "dodgerblue", "darkgoldenrod1", "black")
)

# d.f. of marks'styles

dfMarkColorAndStyle$style[5:7] <- "cenStyle"
dfMarkColorAndStyle$markColor[7] <- NA
dfMarkColorAndStyle$style[8] <- "upArrow"

dfMarkColorAndStyle
#    markName      markColor    style
# 1        5S            red     dots
# 2       45S    chartreuse3   square
# 3      DAPI     dodgerblue   square
# 4       CMA darkgoldenrod1   square
# 5     cDAPI     dodgerblue cenStyle
# 6      cCMA darkgoldenrod1 cenStyle
# 7 sim. cen.           <NA> cenStyle
# 8      S58A            red  upArrow

par(mar = rep(0, 4))
plotIdiograms(dfChrSize   = mixedThreeSpChrSize,  # chr. size data.frame
  dfMarkPos   = mixedThreeSpMarks,    # mark position df
  dfMarkColor = dfMarkColorAndStyle,

  chrWidth = .6,              # width of chr.
  chrSpacing = .6,            # space among chr.
  karHeight = 3,              # kar. height without interspace
  karHeiSpace = 5,            # vertical size of karyotype including spacer
  amoSepar = 2,               # separ. among kar.

  indexIdTextSize = .6,       # font size of chr. name and indices
  markLabelSize = .7,         # font size of mark legends
  distTextChr = .65,          # separation among chr. names and indices
  lwd.mimicCen = 1.5,         # constric. line width

  legendWidth = 1.5,          # legend items width
  fixCenBorder = TRUE,        # use chrColor as border color of cen. or cen. marks

  xPosRulerTitle = 3.7,       # position of Mb (title) in ruler
  rulerPos = 0,               # ruler position
  ruler.tck = -0.005,         # ticks of ruler size and orientation
  rulerNumberPos = .7,        # position of numbers in ruler
  rulerNumberSize = .7,       # font size of ruler numbers
  rulerInterval = 1.5,        # ruler interval for micrometeres
  rulerIntervalMb = 150,      # ruler interval for Mb
  ceilingFactor = 1,          # affects rounding for ruler max. value

  ylimBotMod = 0.4,           # modify ylim bottom argument
  ylimTopMod = 0              # modify ylim top argument
  , holocenNotAsChromatids = TRUE # do not use chromatids in holocen.
  , pattern = "^c"             # regex pattern to remove from mark names
  , remSimiMarkLeg = TRUE      # remove pseudoduplicate names arising from pattern removal
)

# fig.width=10, fig.height=10
# merge data.frames in micrometers and cM
bigdfOfChrSize3cM <- bigdfOfChrSize3Mb[1:8, ]
bigdfOfChrSize3cM$chrSize <- bigdfOfChrSize3cM$chrSize / 100000
mixedThreeSpChrSize2 <- plyr::rbind.fill(bigdfOfChrSize[1:8, ], bigdfOfChrSize3cM)

# sort by OTU name
mixedThreeSpChrSize2 <- mixedThreeSpChrSize2[order(mixedThreeSpChrSize2$OTU), ]

# create data with cM. markSize col. is not necessary because style is cM
bigdfOfMarks3cM <- bigdfOfMarks3Mb
bigdfOfMarks3cM$markPos <- bigdfOfMarks3Mb$markPos / 100000
bigdfOfMarks3cM$markSize <- NA
# As we want only the cM idiograms to be plotted as cM (lines), change mark names
bigdfOfMarks3cM$markName <- paste0("cM", bigdfOfMarks3cM$markName)

# d.f of all marks
mixedThreeSpMarks2 <- plyr::rbind.fill(bigdfOfMarks, bigdfOfMarks3cM)

# create a data.frame with mark characteristics
mixedDfMarkStyle  <- makedfMarkColorMycolors(unique(mixedThreeSpMarks2$markName),
  c("red", "chartreuse3", "dodgerblue", "darkgoldenrod1")
)

# mark names of cM marks with "cM" style (lines): not dots, not squares
mixedDfMarkStyle[which(mixedDfMarkStyle$markName %in%
  grep("cM", mixedDfMarkStyle$markName, value = TRUE)), ]$style <- "cM"

par(mar = rep(0, 4))
plotIdiograms(dfChrSize   = mixedThreeSpChrSize2,  # chr. size data.frame
  dfMarkPos   = mixedThreeSpMarks2,    # mark position data.frame
  dfMarkColor = mixedDfMarkStyle,     # mark style data.frame

  chrWidth = .6,                # width of chr.
  chrSpacing = .7,            # space among chr.

  specialOTUNames = bigdfOfMarks3cM$OTU, # OTUs in this object will have different ruler units
  specialyTitle = "cM",       # ruler title for specialOTUNames
  specialChrWidth = .2,       # modify chr width of OTUs in specialOTUNames
  specialChrSpacing = 1.1,    # modify chr spacing of OTUs in specialOTUNames

  karHeight = 3,              # kar. height without interspace
  karHeiSpace = 6,            # vertical size of karyotype including spacer
  amoSepar = 3,               # separ. among kar.

  chrSize = TRUE,             # show chr. size under chr.
  indexIdTextSize = .6,       # font size of chr. name and indices
  distTextChr = .85,          # separation among chr. names and indices

  protruding = 1,             # extension of cM mark type
  pattern = "cM",             # regex pattern to remove from mark names
  markLabelSize = .7          # font size of mark legends
  , legendWidth = 2           # legend items width
  , fixCenBorder = TRUE       # use chrColor as border color of cen. or cen. marks
  , lwd.cM = 2                # thickness of cM marks
  , holocenNotAsChromatids = TRUE # do not use chromatids in holocen. kar.

  , xPosRulerTitle = 3.2       # position of Mb or cM (title) in ruler
  , rulerPos = 0,              # ruler position
  ruler.tck = -0.005,          # ticks of ruler size and orientation
  rulerNumberPos = .7,         # position of numbers in ruler
  rulerNumberSize = 0.7,       # font size of ruler numbers
  rulerIntervalcM = 12,       # ruler interval for OTU in specialOTUnames and MbThreshold not met
  ceilingFactor = 1,          # affects max. value in ruler. See also rulerInterval

  ylimBotMod = 0.4,           # modify ylim bottom argument
  ylimTopMod = 0              # modify ylim top argument
)

{
  #
  # c. schweinfurthii chr sizes d.f.
  #

  cschweinformula <- "14D + 4F"
  require(idiogramFISH)

  citrusschwein <- citrusSize(D = 14,
    F = 4,
    OTU = "C. schweinfurthii",
    longArm = 1.2)

  #
  # c. schweinfurthii CMA and GISH marks
  #

  citrusschweinMarkPosDF <- citrusMarkPos(citrusschwein)

  #
  #   data.frame of genomic marks
  #
  citrusschweinMarkPosDF2 <- data.frame(chrName = c(paste0("D_", 1:7), paste0("F_", 1:2)),
    chrRegion = "w",
    markName = "schweingenome",
    OTU = unique(citrusschwein$OTU)
  )

  #
  #   merge marks pos.
  #

  citrusschweinMarkPosDF <- dplyr::bind_rows(citrusschweinMarkPosDF2, citrusschweinMarkPosDF)

  #
  #   Inversion of some chr. (D marks up)
  #

  csSwap <- swapChrRegionDfSizeAndMarks(citrusschwein, citrusschweinMarkPosDF, c(paste0("D_", 1:14)))
  citrusschwein         <- csSwap$dfChrSize
  citrusschweinMarkPosDF <- csSwap$dfMarkPos

  #
  #   mark style
  #

  unique(citrusschweinMarkPosDF$markName)
  {
    markStyleschweinDF   <- makedfMarkColorMycolors(
      unique(citrusschweinMarkPosDF$markName), c("chartreuse3", "darkgoldenrod1"))
  }

  #
  #   d.f. of notes
  #

  leftNotesschwein  <- data.frame(OTU = unique(citrusschwein$OTU), note = paste0("Female gamete: 7D + 2E"))
  leftNotesschweinUp <- data.frame(OTU = unique(citrusschwein$OTU), note = paste0(unique(citrusschwein$OTU), " (", cschweinformula, ")"))
  notesschwein <- data.frame(OTU = unique(citrusschwein$OTU), note = "Yasuda et al. (2010)")
}

{

  cnanpuformula <- "1A + 4C + 5D + 8F" # Guerra nom.

  #
  # 'Nanpu' tangor chr. sizes
  #

  citrusnanpu <- citrusSize(A = 1, C = 4, D = 5, F = 8 #
    , OTU = "nanpu tangor",
    longArm = 1.2)
  #
  # c. nanpu CMA marks
  #

  citrusnanpuMarkPosDF <- citrusMarkPos(citrusnanpu)

  #
  #   d.f. of genomic marks
  #

  citrusnanpuMarkPosDF2 <- data.frame(chrName = c("A", "C_1", paste0("D_", 1:4), paste0("F_", 1:3)),
    chrRegion = "w",
    markName = "nanpugenome",
    OTU = unique(citrusnanpu$OTU)
  )

  #
  #   merge marks pos.
  #

  citrusnanpuMarkPosDF <- dplyr::bind_rows(citrusnanpuMarkPosDF2, citrusnanpuMarkPosDF)

  #
  #   mark style d.f.
  #

  unique(citrusnanpuMarkPosDF$markName)
  {
    markStylenanpuDF   <- makedfMarkColorMycolors(
      unique(citrusnanpuMarkPosDF$markName), c("chocolate", "darkgoldenrod1"))
  }

  #
  #   invert some chr.
  #

  csSwap <- swapChrRegionDfSizeAndMarks(citrusnanpu, citrusnanpuMarkPosDF, c(paste0("D_", 1:5)))
  citrusnanpu          <- csSwap$dfChrSize
  citrusnanpuMarkPosDF <- csSwap$dfMarkPos

  #
  #   notes data.frames
  #

  leftNotesnanpu  <- data.frame(OTU = unique(citrusnanpu$OTU), note = paste0("Male gamete: 1A + 1C + 4D + 3E"))
  leftNotesnanpuUp <- data.frame(OTU = unique(citrusnanpu$OTU), note = paste0("'Nanpu' tangor (", cnanpuformula, ")"))

  notesnanpu <- data.frame(OTU = unique(citrusnanpu$OTU), note = "Yasuda et al. (2010)")

}

{
  cschnanpuformula <- "1A + 1C + 11D + 5F"

  require(idiogramFISH)

  #
  #   hybrid chr. size
  #

  citrusschnanpu <- citrusSize(A = 1, C = 1, D = 11, F = 5 #
    , OTU = "schweinfurthii + nanpu",
    longArm = 1.2)
  #
  # hybrid CMA marks
  #

  citrusschnanpuMarkPosDF <- citrusMarkPos(citrusschnanpu)

  #
  #    invert some chr.
  #

  csSwap <- swapChrRegionDfSizeAndMarks(citrusschnanpu, citrusschnanpuMarkPosDF, c(paste0("D_", 1:11)))
  citrusschnanpu         <- csSwap$dfChrSize
  citrusschnanpuMarkPosDF <- csSwap$dfMarkPos

  #
  #   d.f. of gish marks
  #

  citrusschnanpuMarkPosDF2 <- data.frame(chrName = c(paste0("D_", 5:11), paste0("F_", 1:2)),
    chrRegion = "w",
    markName = "schweingenome",
    OTU = unique(citrusschnanpu$OTU)
  )

  citrusschnanpuMarkPosDF3 <- data.frame(chrName = c("A", "C", paste0("D_", 1:4), paste0("F_", 3:5)),
    chrRegion = "w",
    markName = "nanpugenome",
    OTU = unique(citrusschnanpu$OTU)
  )

  #
  #   merge marks
  #

  citrusschnanpuMarkPosDF <- dplyr::bind_rows(citrusschnanpuMarkPosDF2, citrusschnanpuMarkPosDF3, citrusschnanpuMarkPosDF)

  #
  #   style of marks d.f.
  #

  unique(citrusschnanpuMarkPosDF$markName)
  {
    markStyleschnanpuDF   <- makedfMarkColorMycolors(
      unique(citrusschnanpuMarkPosDF$markName), c("chartreuse3", "chocolate", "darkgoldenrod1"))
  }

  #
  #   notes for hybrid
  #
  # italics!       #  rest: \"                 to                           \"
  name <-  paste0("italic('C. schweinfurthii'),      \" × 'Nanpu' tangor (CN3) (", cschnanpuformula, ")\"")
  # to parse italics, use parseStr2lang = TRUE

  leftNotesschnanpuUp <- data.frame(OTU = unique(citrusschnanpu$OTU), note = name)
  notesschnanpu       <- data.frame(OTU = unique(citrusschnanpu$OTU), note = "'Yasuda et al. (2010)'")
}

#
#   plot of parentals only
#

{
  par(mar = rep(0, 4), oma = rep(0, 4))
  plotIdiograms(callPlot = TRUE,
    dfChrSize = bothParentalsChr,   # chr. size data.frame
    dfMarkPos = bothParentalsMarks, # mark position data.frame
    dfMarkColor = bothPmarkStyle,   # mark style d.f.

    orderChr = "original"      # order of chr. as in d.f.

    , chrWidth = .5            # chr. width
    , chrSpacing = .5          # separ. among chr.
    , karHeight = 4            # kar. height
    , karHeiSpace = 5          # anchor height

    , chromatids = FALSE       # don't use chromatids
    , chrColor = "white"     # chr. color

    , ruler = FALSE            # don't use ruler
    , chrId = ""               # don't use chr. name
    , chrIndex = ""            # don't use chr. indices
    , morpho = ""              # don't use morphology
    , karIndex = FALSE         # don't use kar. indices
    , colorBorderMark = "black" # color of border of marks
    , addOTUName = FALSE       # do not add OTU names

    , lwd.chr = 1.6            # border width
    , lwd.marks = 1            # border width marks
    , gishCenBorder = TRUE     # cen. border of gish as mark color
    , hideCenLines = 1.75      # hide cen. border

    , legend = ""              # no legend for marks

    , leftNotes  =  bothPleftNotes    # data.frame with left notes
    , leftNotesUp =  bothPleftNotesUp # data.frame with Up left notes
    , leftNoteFontUp = 3      # italics

    , leftNotesTextSize = 1.3     # font size of notes
    , leftNotesUpTextSize = 1.3   # font size of notes

    , leftNotesPosX = 0      # horizontal pos. of left notes
    , leftNotesPosY = 0      # vertical pos. of left down notes

    , leftNotesUpPosX = 0    # horizontal pos. of left up notes
    , leftNotesUpPosY = 2    # vertical pos. of left up notes

    , verticalPlot = FALSE     # horizontal plot
    , karSpaceHor = 3          # horizontal spacing among kar.

    , karAnchorLeft = "C. schweinfurthii" # anchor to the left of
    , anchor = TRUE            # add anchor

    , ylimBotMod = 1         # modify ylim bottom argument
    , ylimTopMod = 0         # modify ylim top argument
    , xlimLeftMod = 0        # modify left xlim
    , xlimRightMod = 2       # modify right xlim

  )
}

#  add plot of hybrid over parents plot

{
  plotIdiograms(callPlot = FALSE,                     # plot over previous plot
    dfChrSize = citrusschnanpu,          # chr. size data.frame
    dfMarkPos = citrusschnanpuMarkPosDF, # mark position data.frame
    dfMarkColor = markStyleschnanpuDF,    # mark style d.f.

    orderChr = "original",  # order of chr. as in d.f.

    chrWidth = .5,          # chr. width
    chrSpacing = .5,        # separ. among chr.
    karHeight = 4           # kar. height
    , chromatids = FALSE    # don't use chromatids
    , chrColor = "white"    # chr. color

    , ruler = FALSE            # don't use ruler
    , chrId = ""               # don't use chr. name
    , chrIndex = ""            # don't use chr. indices
    , morpho = ""              # don't use morphology
    , karIndex = FALSE         # don't use kar. indices
    , colorBorderMark = "black" # color of border of marks
    , addOTUName = FALSE       # don't add OTU name

    , lwd.chr = 1.6            # border width
    , lwd.marks = 1            # border width marks

    , leftNotesUp = leftNotesschnanpuUp # up notes: name of hybrid
    , parseStr2lang = TRUE   # for italics, see notes data.frame
    , notesTextSize = 1.3    # font size of notes
    , leftNotesUpTextSize = 1.3   # font size of notes

    , leftNotesPosX = 0      # horizontal pos. of notes
    , leftNotesUpPosY = 2    # vertical pos. left up notes
    , notes = notesschnanpu  # right notes - authors
    , notesPosX = 3          # notes hor. pos

    , ylimBotMod = 1         # modify ylim bottom argument
    , ylimTopMod = -5        # modify ylim top argument
    , xlimLeftMod = 0        # modify left xlim
    , xlimRightMod = 2       # modify right xlim

    , gishCenBorder = TRUE     # cen. border as mark color
    , legend = ""              # no legend for marks
    , hideCenLines = 1.75      # hide cen. lines
    , moveAllKarValueHor = 9.5 # move kar. to right
    , moveAllKarValueY = -10   # move kar. down
  )
} # hybrid

data("dfChrSizeHolo")
data("dfMarkPosHolo")
dfMarkPosHoloHetero <- dfMarkPosHolo
dfMarkPosHoloHetero$chrName <- c(3, 3, "1A", 2, "1B", "1B")
dfMarkPosHoloHetero$OTU <- "heteromorphic"

dfChrSizeHoloHetero <- dfChrSizeHolo
dfChrSizeHoloHetero$chrName <- c("1A", "1B", 2, 3)
dfChrSizeHoloHetero$OTU <- "heteromorphic"

# Adding the group column
dfChrSizeHoloHetero$group <- c(1, 1, NA, NA)