Chapter 11 Citrus


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11.1 C. maxima as da-Costa-Silva et al. (2019)

data.frame of chr. size and marks

Main three data.frames:

  • One for chr. sizes (parameter dfChrSize)
  • One for marks’ positions (parameter dfMarkPos)
  • One (optional) for mark style (parameter dfMarkColor)

In this example two of them (1 and 2) will be obtained from a larger data.frame citrusMaximaChrMark.

Column chrNameUp will be used in this case for unifying the chr. names (chrName) in both data.frames.

# C. maxima 'pink'
# 4A 2C 4D 6F 2FL

{
citrusMaximaChrMark<-read.table(text="
chrName chrNameUp shortArmSize  longArmSize markName    chrRegion   markDistCen markSize
FL 1    67  97  24c13   p   52  10
D  2    62  75  21L13   q   35  8
D  2    62  75  CMA     q   43  32
A  3    70  103 45S     p   6   16
A  3    70  103 14A12   p   32  8
A  3    70  103 CMA     p   40  30
A  3    70  103 28A07   q   54  10
A  3    70  103 CMA     q   64  39
D  4    59  84  02C12   p   31  10
D  4    59  84  20C13   q   32  9
D  4    59  84  cma     q   48  36
F  5    52  74  5s      p   18  10
C  6    62  86  28A05   p   22  9
C  6    62  86  cma     p   40  22
C  6    62  86  cma     q   61  25
A  7    57  96  45S     p    6  18
A  7    57  96  cma     p   38  19
A  7    57  96  cma     q   62  34
F  8    41  72  01b09   q   47  8
F  9    40  72  55b01/59C23   q 24  13", header =TRUE)
}

data.frame of chr. sizes

Main columns: chrName, shortArmSize, longArmSize, OTU (optional when only one OTU), group (optional)

Column chrNameUp will be used in this case for unifying the chr. names (chrName) between data.frames.

{
require(idiogramFISH)
  
# column and row subset
citrusMaxima<- citrusMaximaChrMark[,1:4][!duplicated(citrusMaximaChrMark[,1:4]),]

# chr. name change (unique)
citrusMaxima$chrName<-make.uniqueIF(citrusMaxima$chrName)

# chr. size in pixels
chrSizes <- citrusMaxima$shortArmSize+citrusMaxima$longArmSize

# max. size in μm.
maxSize <-3.6
maxPixel<-max(chrSizes)

# pixel to microm. 
citrusMaxima$shortArmSize<-citrusMaxima$shortArmSize/(maxPixel/maxSize)
citrusMaxima$longArmSize <-citrusMaxima$longArmSize /(maxPixel/maxSize)

citrusMaxima$OTU<- "C. maxima 'Pink'"

# add groups (pairs)
citrusMaxima$group<-1:9
}

data.frame of marks’ positions

Main columns: chrName, markName, chrRegion (arm), markDistCen (mark distance to centr.), markSize

Column chrNameUp will be used in this case for unifying the chr. names (chrName) between data.frames.

Column OTU is mandatory because is present in first data.frame (citrusMaxima)

{
# Select columns
citrusMaximaMarkPos<- citrusMaximaChrMark[,c(1:2,5:8)][!duplicated(citrusMaximaChrMark[,c(1:2,5:8)] ),]

# transcribe chr.names - changed above. needs common column (i.e. chrNameUp)
citrusMaximaMarkPos$chrName<-citrusMaxima$chrName[match(citrusMaximaMarkPos$chrNameUp,citrusMaxima$chrNameUp )]

#pixel to μm. 
citrusMaximaMarkPos$markDistCen<-citrusMaximaMarkPos$markDistCen/(maxPixel/maxSize)
citrusMaximaMarkPos$markSize<-citrusMaximaMarkPos$markSize/(maxPixel/maxSize)

# OTU column
citrusMaximaMarkPos$OTU<-unique(citrusMaxima$OTU)

# fix case
citrusMaximaMarkPos$markName<-toupper(citrusMaximaMarkPos$markName)
}

data.frame of marks’ style

Optional data.frame. Add color and style for marks present in citrusMaximaMarkPos

{
unique(citrusMaximaMarkPos$markName)
# "24C13" "21L13" "CMA" "45S" "14A12"   "28A07" "02C12"   "20C13" "5S"  "28A05" "01B09" "55B01/59C23"

# make d.f. of styles of marks
markStyleDF   <- makedfMarkColorMycolors(
  unique(citrusMaximaMarkPos$markName), 
  c("chocolate","chocolate","darkgoldenrod1","chartreuse3", rep("chocolate",4),"red", rep("chocolate",3) )
)

}

Notes and plot

Two optional data.frames for adding notes to plot with columns OTU and note.

Parameters: leftNotes and notes

# notes
{
# formula
maxima<-"4A + 2C + 4D + 6F + 2FL [4A/45S,2F/5S]"
leftNotesdf<- data.frame(OTU=unique(citrusMaxima$OTU), note= maxima  )

# authors
notesdf<- data.frame(OTU=unique(citrusMaxima$OTU), note="da-Costa-Silva et al. 2019" )
}

# add group column to show that each one is a pair
{
par(mar=rep(0,4),oma=rep(0,4))
plotIdiograms(dfChrSize= citrusMaxima,        # chr. size data.frame
              dfMarkPos= citrusMaximaMarkPos, # mark position data.frame 
              dfMarkColor=markStyleDF,        # mark style d.f.
              
              orderChr = "original",  # order of chr. as in d.f.
              chrIdPatternRem="_.*",  # regex pattern to remove from chr. names
              classChrName = "Type",  # chr. names title
              chrWidth = 0.3,         # chr. width
              chrSpacing=0.40,        # separ. among chr.
              groupSepar = 1          # factor to multiply chr. spacing among groups
              ,chromatids = FALSE     # don't use chromatids
              ,chrColor= "white"      # chr. color
              ,classGroupName = "Pair"# groups title
              ,chrBorderColor ="black"# border color
              ,lwd.chr = 0.5          # border width
              
              ,legend="inline"        # label location
              ,bannedMarkName = c("CMA","45S","5S") # don't show this (inline)
              ,bMarkNameAside =TRUE   # show banned marks "aside" 
              ,legendHeight=1.7       # height of labels (aside)
              ,colorBorderMark="black"# color of border of marks
              
              ,markNewLine = "/"      # split mark name to new line
              
              ,ruler=FALSE            # don't use ruler
              ,threshold=40           # fix scale, when too much shrinking
              
              ,distTextChr = .7       # distance text to chr.
              ,chrIndex = ""          # don't use chr. indices
              ,morpho=""              # don't use morphology
              ,karIndex = FALSE       # don't use kar. indices
              
              ,OTUfont=3              # OTU name in italics
              
              ,notesTextSize = 1.3    # font size of notes
              ,leftNotes=leftNotesdf  # data.frame with left notes
              ,leftNotesPosX = 0       # horizontal pos. of formula
              ,leftNotesPosY = 0.5
              ,notes = notesdf        # right notes - authors
              
              ,ylimBotMod = 1         # modify ylim bottom argument
              ,ylimTopMod = 0         # modify ylim top argument
              ,xlimLeftMod = 2        # modify left xlim
              ,xlimRightMod = 3       # modify right xlim
)
}

11.2 C. reticulata as da-Costa-Silva et al. (2015)

Chr. size data.frame


#
#   chr. size - arms in pixels
#

{
  citrusReticulata<-read.table(text="
chrName shortArmSize longArmSize totalMicro  Mbp   group
f       67            91          2.65       50.96 1
d       61            77          2.32       44.60 2
c       59            78          2.18       41.81 3
d       61            83          2.49       47.75 4
d       34            63          1.87       35.90 5
d       34            63          1.87       35.90 5
d       50            66          1.93       37    6
d       50            83          2.28       43.72 7
f       42            77          2.02       38.78 8
f       28            67          1.70       32.57 9", header =T)
  
  citrusReticulata$pixeltotal <- citrusReticulata$shortArmSize+citrusReticulata$longArmSize
  
  # pixel to micrometers
  citrusReticulata$shortArmSize<- citrusReticulata$shortArmSize/(citrusReticulata$pixeltotal/citrusReticulata$totalMicro)
  citrusReticulata$longArmSize <- citrusReticulata$longArmSize /(citrusReticulata$pixeltotal/citrusReticulata$totalMicro)
  
  # change chr. names avoiding duplicates
  citrusReticulata$chrName<-toupper(citrusReticulata$chrName)
  citrusReticulata$chrName<-make.uniqueIF(citrusReticulata$chrName)
  
  # add OTU
  citrusReticulata$OTU<-"C. reticulata 'Cravo'"
  
  # replicate name for plotting it over chrs.
  citrusReticulata$chrNameUp<-citrusReticulata$chrName
}

Marks

citrusReticulataMarkPosDF<-  read.table(text="
chrName chrRegion markName markDistCen markSize    
     F_1      p    24C13   0.87  0.12
       C      p      CMA   0.64  0.30 
       C      q      CMA   0.84  0.40
       C      p     14A12  0.48  0.11
       C      q    28A07   0.77  0.14
       C      p      45S   0.00  0.10
     D_1      q      CMA   0.54  0.75
     D_1      p    21L13   0.67  0.14
     D_2      q      CMA   0.88  0.55
     D_2      p    02C12   0.5   0.14
     D_2      q    20C13   0.42  0.14
     D_3      p      CMA   0.35  0.30 
     D_3      p     c45S   0.35  0.35
     D_3      p      CMA   0.8   0.15
     D_3      p     c45S   0.8   0.15
     D_4      p      CMA   0.35  0.30 
     D_4      p      45S   0.35  0.30 
     D_5      p    28A05   0.66  0.14 
     D_5      q      CMA   0.50  0.60 
     D_6      q      CMA   0.72  0.70 
     F_2      q    01B09   0.8   0.14
     F_3      q    55B01   0.3   0.18
     F_3      q    59C23   0.3   0.18", header =T, stringsAsFactors=F) 

# marks' style data.frame
unique(citrusReticulataMarkPosDF$markName)
#  [1] "24C13" "CMA"   "14A12" "28A07" "45S"   "21L13"
#  [7] "02C12" "20C13" "c45S"  "28A05" "01B09" "55B01"
# [13] "59C23"

markStyleDF   <- makedfMarkColorMycolors(
  unique(citrusReticulataMarkPosDF$markName), 
  c("chocolate","darkgoldenrod1","chocolate","chocolate","chartreuse3",rep("chocolate",3),"chartreuse3",rep("chocolate",4) ) 
)

# square mark with label to the left (squareLeft style)
markStyleDF[which(markStyleDF$markName=="59C23"),]$style<-"squareLeft"

# add OTU!
citrusReticulataMarkPosDF$OTU<-unique(citrusReticulata$OTU)

Plotting


# notes to the left
reticulata <- "2C + 10D + 6F [2C/45S, 2D/45S]"

leftNotesdf<- data.frame(OTU=unique(citrusReticulata$OTU), note= reticulata )

# authors in notes (right side)
notesdf<- data.frame(OTU=unique(citrusReticulata$OTU), note="da-Costa-Silva et al. (2015)" )

par(mar=rep(0,4),oma=rep(0,4))

{
require(idiogramFISH)
plotIdiograms(dfChrSize= citrusReticulata,         # chr. size data.frame
             dfMarkPos = citrusReticulataMarkPosDF,# mark position data.frame (inc. cen.)
             dfMarkColor=markStyleDF,# mark style d.f.
             
             orderChr = "original",  # order of chr. as in d.f.
             chrIdPatternRem="_.*",  # pattern to remove from chr. names
           
             chrColor= "white"       # color of chr.
             ,chrBorderColor="black" # borders
             
             ,chrIndex = "AR"        # add index r
             ,morpho=""              # don't add morphology cat.
             ,karIndex = FALSE       # don't add kar. indeex
             ,chrNameUp = TRUE       # add. info. of col. chrNameUp over kar.
             
             ,centromereSize = 0     # size of cen.
             ,colorBorderMark="black"# color of border of marks
             ,lwd.chr = 1            # border width
             
             ,OTUfont=3              # OTU name in italics
             
             ,leftNotes=leftNotesdf  # data.frame with notes
             ,notesTextSize = 1      # font size of notes
             ,leftNotesPosX = 0      # horizontal pos. of formula- left notes
             ,leftNotesPosY = 1.9    # y pos. of left notes
             
             ,notes = notesdf        # authors in notes (right)
             ,notesPosX = 1          # move right notes to right
           
             ,rulerInterval = .5     # ruler label int.
             ,ruler.tck = -.01       # ruler ticks
             ,rulerPos = -0.5        # ruler pos.
             ,xPosRulerTitle = 7     # move title (units) of ruler, beginning in 1st chr.
           
             ,ylimBotMod = 2         # modify ylim bottom argument
             ,ylimTopMod = 1         # modify ylim top argument
             ,xlimLeftMod = 1        # modify left xlim
             ,xlimRightMod = 2       # modify right xlim
             
             ,chromatids=FALSE       # do not plot chromatids
             ,squareness = 2         # corners rounded
             ,useMinorTicks = TRUE   # ruler minor ticks
             ,miniTickFactor = 5     # number of small ticks per big ticks
             ,distTextChr=.7         # distance indices to chr.
           
             ,chrId=""               # don't add chr. names (below)
             ,chrSize = TRUE         # add chr. size
             ,chrSizeMbp = TRUE      # add info of col. Mbp
             ,nsmall=2               # significative digits for indices
             
             ,markPer = "CMA"        # calculate % of chr. for this mark
             ,showMarkPos = TRUE     # show mark. position as fraction, under kar.
             ,bToRemove = c("CMA","45S","c45S")   # do not use these in showMarkPos
             
             ,legend = "inline"         # labels inline
             ,legendHeight = 1.5        # legend height (right)
             ,bannedMarkName = "CMA"    # do not add label of this mark
             ,bMarkNameAside=TRUE       # add banned mark aside
             ,forbiddenMark = "c45S"    # do not add this mark label
             
             ,groupSepar = 1.8       # separation among groups, see col. group (x chrSpacing)
             ,chrSpacing=.20         # separ. among chr.
             ,chrWidth = .20         # chr. width
             ,nameChrIndexPos = 4    # move name of indices to the left
)
}  

Download Citrus scripts from: https://ferroao.gitlab.io/idiogramfishhelppages/citrushelp.R

11.3 Exploring Citrus functions

Published by Carvalho et al. (2005)

C. jambhiri/ C. volkameriana

1B + 11D + 4F + 2FL0

Create data.frame of chr. size

{
library(idiogramFISH)

citrusSizeDF <- citrusSize(B=1,D=11,F=4,FL0=2,
                           OTU="C. jambhiri")

# add simple secondary names
citrusSizeDF$chrNameUp <- 1:nrow(citrusSizeDF)

head(citrusSizeDF,3)
tail(citrusSizeDF,3)

# Editing data.frame:
# citrusSizeDF <- edit(citrusSizeDF)

# Initial plot, only sizes:
par(mar = rep(0,4),oma=rep(0,4) )
plotIdiograms(dfChrSize= citrusSizeDF,      # chr. size data.frame
              orderChr = "original",        # order of chr.
              ruler=FALSE,
              ylimBotMod = 2,               # modify bottom margin
              ylimTopMod = 1,
              
              chrNameUp = TRUE,             # use col. chrNameUp
              classChrName = "Type",        # change default title of inferior name
              classChrNameUp = "Chr."       # change default title of upper name
)
}

Use the group column to define pairs

citrusSizeDF$chrName
 [1] "B"     "D_1"   "D_2"   "D_3"   "D_4"   "D_5"  
 [7] "D_6"   "D_7"   "D_8"   "D_9"   "D_10"  "D_11" 
[13] "F_1"   "F_2"   "F_3"   "F_4"   "FL0_1" "FL0_2"

#" "B" "D_1" "D_2" "D_3" "D_4" "D_5" "D_6" "D_7" "D_8"   "D_9"  "D_10"  "D_11"  "F_1"   "F_2"   "F_3"   "F_4"   "FL0_1" "FL0_2"
#   -------   ---------   ---------   ---------   -----------    ------------    -----------    ------------     ------------- 
#"     1          2           3           4            5              6              7               8                9

citrusSizeDF$group<-unlist(lapply(1:9, function(x) rep(x,2)) )
citrusSizeDF$group
 [1] 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8 9 9

# make secondary names
citrusSizeDF$chrNameUp <- unlist(lapply(1:9, function(x) rep(x,2)) )
citrusSizeDF$chrNameUp <- make.uniqueIF(citrusSizeDF$chrNameUp, sep="", letter=TRUE)

data.frame of marks’ position


# CMA bands
citrusMarkPosDF <- citrusMarkPos(citrusSizeDF)
head(citrusMarkPosDF,3)
#   chrName chrRegion markName markDistCen markSize
# 1       B         p      CMA        0.00     0.35
# 2       B         q      CMA        1.35     0.35
# 3     D_1         q      CMA        1.35     0.35
#           OTU
# 1 C. jambhiri
# 2 C. jambhiri
# 3 C. jambhiri
tail(citrusMarkPosDF,3)
#    chrName chrRegion markName markDistCen markSize
# 11     D_7         q      CMA        1.35     0.35
# 12     D_8         q      CMA        1.35     0.35
# 13     D_9         q      CMA        1.35     0.35
#            OTU
# 11 C. jambhiri
# 12 C. jambhiri
# 13 C. jambhiri

# marks with overlap with CMA

# add mark of 45S rDNA in B, short arm (p)
citrusMarkPosDF45S <- markOverCMA(citrusMarkPosDF, # d.f. of CMA bands 
                                chrType="B",       # chr. of new mark
                                chrRegion="p",     # arm of new mark
                                markName="45S")    # name of mark

# add 45S in D (D_1) long arm
citrusMarkPosDF45S <- markOverCMA(citrusMarkPosDF45S, # d.f. including CMA bands
                                chrName="D_1", 
                                chrRegion="q", 
                                markName="45S")

# creating additional data.frames of marks (non-CMA overlap)

citrusMarkPosDF45S_D11 <- data.frame(chrName="D_11", # cr.
                                     chrRegion="q",  # arm
                                     markName="45S", 
                                     markDistCen=1,  # dist. to centrom.
                                     markSize=0.2,   # mark size
                                     OTU="C. jambhiri")

citrusMarkPosDF45S_F4  <- data.frame(chrName="F_4", 
                                     chrRegion="q",
                                     markName="45S",
                                     markDistCen=1, 
                                     markSize=0.2,
                                     OTU="C. jambhiri")

# fuse data.frames
citrusMarkPosDF45S <- dplyr::bind_rows(citrusMarkPosDF45S,     # CMA marks and overlapped
                                       citrusMarkPosDF45S_D11, # 45S in D (no overlap)
                                       citrusMarkPosDF45S_F4 ) # 45S in F (no overlap)

data.frame of mark style

# current marks
unique(citrusMarkPosDF45S$markName)
[1] "CMA" "45S"

markStyleDF   <- makedfMarkColorMycolors(
  unique(citrusMarkPosDF45S$markName), c("darkgoldenrod1","chartreuse3") )

# modify styles
markStyleDF$style<-c("square","dots")

Add karyotype formulas

notesdf<- data.frame(OTU=unique(citrusSizeDF$OTU), note="1B + 11D + 4F + 2FL0") # spacing matters

Plot

par(mar = rep(0,4),oma=rep(0,4) )
library(idiogramFISH)
plotIdiograms(dfChrSize= citrusSizeDF,      # chr. size data.frame
              dfMarkPos= citrusMarkPosDF45S,# mark position data.frame (inc. cen.)
              dfMarkColor=markStyleDF,      # mark style d.f.

              orderChr = "original",        # preserve order of chr. of d.f.
              
              # chrId = "",                 # remove name of chr.
              chrIdPatternRem="_.*",        # regex pattern for removal of names of chr.
              chrSpacing=0.2,               # separ. among chr.
              chrColor= "dodgerblue",
              
              chrNameUp = TRUE,             # use col. chrNameUp
              classChrName = "Type",        # change default title of inferior name
              classChrNameUp = "Chr."       # change default title of upper name
                            
              ,legendWidth = .8             # legend item width
              ,legendHeight = 3             # legend item height
              ,markLabelSpacer = 2          # legend spacer
              ,ruler=F                      # no ruler
              ,chrIndex = ""                # no chr. index
              ,morpho=""                    # no morpho.
              ,karIndex = FALSE             # no kar. ind.
              
              ,leftNotes=notesdf            # data.frame with notes
              ,notesTextSize = 1.3          # font size of notes
              ,leftNotesPosX = 10.2          # pos. formula x axis
              ,leftNotesPosY = 0            # pos. formula y axis

              ,ylimBotMod = 1               # modify ylim bottom argument
              ,xlimRightMod = 4             # modify right xlim
)

11.4 Representing only one chromosome per pair

As in the article (Carvalho et al., 2005)

C. jambhiri/ C. volkameriana

1B + 11D + 4F + 2FL0

{
# data.frame of  chr. sizes
citrusSizeDF_2 <- citrusSize(B=1,D=8,F=3,FL0=1, # MODIFIED, SEE ABOVE
                           OTU="C. jambhiri_2")
head(citrusSizeDF_2)

# data.frame of CMA band pos.
citrusMarkPosDF_2 <- citrusMarkPos(citrusSizeDF_2)
head(citrusMarkPosDF_2)

# marks with overlap with CMA

# 45S in B, short arm
citrusMarkPosDF45S_2<-markOverCMA(citrusMarkPosDF_2, 
                                  chrType="B", 
                                  chrRegion="p", 
                                  markName="45S")

# 45S in D (D_1), long arm
citrusMarkPosDF45S_2<-markOverCMA(citrusMarkPosDF45S_2, 
                                  chrName="D_1", 
                                  chrRegion="q", 
                                  markName="45S")

# add mark from scratch (no overlap with CMA)

citrusMarkPosDF45S_D8  <- data.frame(chrName="D_8", # name of chr. 
                                     chrRegion="q", # arm
                                     markName="45S",# 
                                     markDistCen=1, # dist. to centrom.
                                     markSize=0.2,  # mark size
                                     OTU="C. jambhiri_2")

citrusMarkPosDF45S_F3  <- data.frame(chrName="F_3", 
                                     chrRegion="q",
                                     markName="45S",
                                     markDistCen=1, 
                                     markSize=0.2,
                                     OTU="C. jambhiri_2")
# fuse data.frames
citrusMarkPosDF45S_2 <- dplyr::bind_rows(citrusMarkPosDF45S_2,
                                         citrusMarkPosDF45S_D8,
                                         citrusMarkPosDF45S_F3 
                                         )

# current marks
unique(citrusMarkPosDF45S$markName)

# data.frame of mark style
markStyleDF   <- makedfMarkColorMycolors(
  unique(citrusMarkPosDF45S_2$markName), c("darkgoldenrod1","chartreuse3") )

# modify styles
markStyleDF$style<-c("square","dots")

# organize pairs, group

citrusSizeDF_2$chrName 
# "B"   "D_1"  "D_2" "D_3" "D_4" "D_5" "D_6" "D_7" "D_8" "F_1" "F_2" "F_3" "FL0"
#  ________    ____   ___   ________   ____   _________   ____   ________   ___
#     1          2     3       4         5        6         7        8       9

citrusSizeDF_2$group <- c(1,1,2,3,4,4,5,6,6,7,8,8,9) 

# add names over chr.
citrusSizeDF_2$chrNameUp <- citrusSizeDF_2$group
citrusSizeDF_2$chrNameUp <- make.uniqueIF(citrusSizeDF_2$chrNameUp, sep="", letter=TRUE)

# formula
notesdf <- data.frame(OTU=unique(citrusSizeDF_2$OTU), note="1B + 11D + 4F + 2FL0") # keep spacing
}

par(mar = c(0, 0, 0, 0), oma=rep(0,4) )
library(idiogramFISH)
plotIdiograms(dfChrSize= citrusSizeDF_2,      # d.f. of chr. size
              dfMarkPos= citrusMarkPosDF45S_2,# d.f. of mark pos
              dfMarkColor=markStyleDF,        # d.f. of mark style
              orderChr = "original",          # chr. order as in d.f.
              chrIdPatternRem = "_.*",        # modif name of chr. removing this pattern
              chrSpacing=.20,                 # separ. among chr.
              chrColor= "dodgerblue"

              ,legendWidth = .8            # legend item width
              ,legendHeight = 2.5          # legend item height
              ,markLabelSpacer = 2         # legend spacer
              ,ruler=F
              ,chrIndex = ""
              ,morpho=""
              ,karIndex = FALSE
              
              ,chrNameUp = TRUE           # use col. chrNameUp
              ,classChrName = "Type"      # change default title of inferior name
              ,classChrNameUp = "Chr."    # change default title of upper name
              ,classGroupName = "Pair"    # name for groups
              
              ,leftNotes=notesdf          # data.frame with notes
              ,notesTextSize = 1.3        # font size of notes
              ,leftNotesPosX = 10.2        # formula horiz. pos.
              ,leftNotesPosY = 0

              ,ylimBotMod = 1             # modify ylim bottom argument
              ,ylimTopMod = 0             # modify ylim top argument
              ,xlimLeftMod = 2            # modify left xlim
              ,xlimRightMod = 3           # modify right xlim
)

11.5 Several karyotypes per plot

Column OTU is mandatory for several OTU.

# data.frames of size - merge
bothSize    <-dplyr::bind_rows(citrusSizeDF, citrusSizeDF_2)

# data.frames of band pos. merge
bothMarkPos <-dplyr::bind_rows(citrusMarkPosDF45S, citrusMarkPosDF45S_2)

# formulas

notesdf<- data.frame(OTU=unique(bothSize$OTU), note="1B + 11D + 4F + 2FL0")

par(mar=rep(0,4),oma=rep(0,4))

plotIdiograms(dfChrSize= bothSize,    # chr. size data.frame
              dfMarkPos= bothMarkPos, # mark position data.frame (inc. cen.)
              dfMarkColor=markStyleDF,# mark style d.f.

              orderChr = "original",  # order of chr. as in d.f.
              chrIdPatternRem="_.*",  # pattern to remove from chr. names
              karHeight = 2,          # karyotype height
              karHeiSpace = 5,        # height + separ. among karyot.

              chrSpacing=.20,         # separ. among chr.
              chrColor= "dodgerblue" 
              ,distTextChr = .9       # distance text to chr.

              ,legendWidth = .8       # legend item width
              ,legendHeight = 3       # legend item height
              ,markLabelSpacer = 2    # legend spacer
              ,ruler=FALSE            
              ,chrIndex = ""
              ,morpho=""
              ,karIndex = FALSE
              #,colorBorderMark="black"# color of border of marks
              ,lwd.chr = 1            # border width
              
              ,chrNameUp = TRUE       # use col. chrNameUp
              ,classChrName = "Type"  # change default title of inferior name
              ,classChrNameUp = "Chr."# change default title of upper name
              ,groupName = FALSE      # don't show group names
              
              ,OTUfont=3              # OTU name in italics
              ,OTUfamily="mono"       # font type for OTU
              
              ,leftNotes=notesdf      # data.frame with notes
              ,notesTextSize = 1.3    # font size of notes
              ,leftNotesPosX = 10.2    # horizontal pos. of formula
              ,leftNotesPosY = 0

              ,ylimBotMod = 1         # modify ylim bottom argument
              ,ylimTopMod = 0         # modify ylim top argument
              ,xlimLeftMod = 2        # modify left xlim
              ,xlimRightMod = 3       # modify right xlim
)

11.6 C. leiocarpa as Yi et al. (2018)


#
# create data.frame of chr.
#

cleiocarpaChr <- citrusSize(A=1,C=1,D=10,F=6, # Using Guerra nom.
                           OTU="C. leiocarpa",
                           shortArm=1.7
                           )

#
# add groups
#

cleiocarpaChr$group<-gsub("_.*","",cleiocarpaChr$chrName)

#
# marks data.frame
#

# CMA
cleiocarpaMarks <- citrusMarkPos(cleiocarpaChr)

# marks with overlap with CMA

# add mark of 45S rDNA in A, short arm (p)
cleiocarpaMarks <- markOverCMA(cleiocarpaMarks, # d.f. of CMA bands 
                               chrType="A",       # chr. of new mark
                               chrRegion="p",     # arm of new mark
                               markName="45S",    # name of mark
                               shrinkMark=TRUE
                               )    
# add 45S in Ds
cleiocarpaMarks <-  markOverCMA(cleiocarpaMarks, # d.f. including CMA bands
                                chrName=paste0("D_",1:4), 
                                chrRegion="q", 
                                markName="45S",
                                shrinkMark=TRUE
                                )

# creating additional data.frames of marks (non-CMA overlap)

cleiocarpaMarks_D3 <- data.frame(chrName=c("D_3","D_4"), # cr.
                                 chrRegion="q",  # arm
                                 markName="5S", 
                                 markDistCen=1.1,  # dist. to centrom.
                                 markSize=0.2,   # mark size
                                 OTU="C. leiocarpa")

#
# merge marks d.fs
#

cleiocarpaMarks <- dplyr::bind_rows(cleiocarpaMarks,    # CMA marks and overlapped 45S
                                    cleiocarpaMarks_D3, # 5S in D (no overlap)
                                    )
#
# mark style data.frame
#

# current marks
unique(cleiocarpaMarks$markName)
# [1] "CMA" "45S" "5S"

markStyleDF   <- makedfMarkColorMycolors(
  unique(cleiocarpaMarks$markName), c("darkgoldenrod1","chartreuse3","red") 
  )

# modify styles
markStyleDF$style<-c("square","dots","dots")

#
# swap chromosome arms of Ds (CMA marks originally in long arm)
#

dflist<-swapChrRegionDfSizeAndMarks(cleiocarpaChr,
                            cleiocarpaMarks,
                            paste0("D_",1:10)
                            )
cleiocarpaChr   <-dflist$dfChrSize
cleiocarpaMarks <-dflist$dfMarkPos

#
# Left notes Up data.frame
#

notesdf<- data.frame(OTU=unique(cleiocarpaChr$OTU), 
                     note= "italic('Citrus leiocarpa'),' Hort. ex Tan.' " # use with parseStr2lang
                     ) 

par(mar = rep(0,4),oma=rep(0,4) )

plotIdiograms(dfChrSize= cleiocarpaChr,     # chr. size data.frame
              dfMarkPos= cleiocarpaMarks,   # mark position data.frame 
              dfMarkColor=markStyleDF,      # mark style d.f.

              orderChr = "original",        # preserve order of chr. of d.f.
              chrId="",                     # do not add chr. names
              
              addOTUName = FALSE,           # remove name of OTU
              chrIdPatternRem="_.*",        # regex pattern for removal of names of chr.
              chrSpacing=0.2,               # separ. among chr.
              chrColor= "dodgerblue",       # chr. color
              chromatids=FALSE,             # do not use separ. chromatids
                        
              dotsAsOval = TRUE             # use oval shape instead of dots marks
              ,legendWidth = .8             # legend item width
              ,legendHeight = 3             # legend item height
              ,markLabelSpacer = 2          # legend spacer
              ,ruler=F                      # no ruler
              ,chrIndex = ""                # no chr. index
              ,morpho=""                    # no morpho.
              ,karIndex = FALSE             # no kar. ind.
              
              ,leftNotesUp=notesdf          # data.frame with notes
              ,parseStr2lang = TRUE         # use italics, see notesdf above
              ,notesTextSize = 1.3          # font size of notes
              ,leftNotesPosX = 0            # pos. left notes x axis
              ,leftNotesUpPosY = 1          # pos. left notes y axis

              ,ylimBotMod = 0               # modify ylim bottom argument
              ,xlimRightMod = 4             # modify right xlim
)

11.7 Citrus limon origin

With data from da-Costa-Silva et al. (2015), Mendes et al. (2016) and Carvalho et al. (2005)

11.7.1 Citrus reticulata

data.frame of chr. sizes


# c. reticulata ----X---- c. aurantium
#                   |
#                c. limon


# c. reticulata

#
#   chr. size - arms in pixels
#

{
citrusReticulata<-read.table(text="
chrName shortArmSize longArmSize totalTrue
f 67 91  2.65
d 61 77  2.32
c 59 78  2.18
d 61 83  2.49
d 34 63  1.87
d 50 66  1.93
d 50 83  2.28
f 42 77  2.02
f 28 67  1.70", header =T)

citrusReticulata$pseudototal <- citrusReticulata$shortArmSize+citrusReticulata$longArmSize

# pixel to micrometers
citrusReticulata$shortArmSize<- citrusReticulata$shortArmSize/(citrusReticulata$pseudototal/citrusReticulata$totalTrue)
citrusReticulata$longArmSize <- citrusReticulata$longArmSize /(citrusReticulata$pseudototal/citrusReticulata$totalTrue)

citrusReticulata$chrName<-toupper(citrusReticulata$chrName)
citrusReticulata$chrName<-make.uniqueIF(citrusReticulata$chrName)
citrusReticulata$OTU<-"C. reticulata 'Cravo'"

}

Sort chromosomes


# sort chr. by name
citrusReticulata<-citrusReticulata[order(citrusReticulata$chrName),]

# sort Ds by size
Ds<-citrusReticulata[which( citrusReticulata$chrName %in% grep("D", citrusReticulata$chrName, value=T) 
                            ),]
citrusReticulata[which( citrusReticulata$chrName %in% grep("D", citrusReticulata$chrName, value=T) 
                        ),] <- Ds[order(Ds$shortArmSize+Ds$longArmSize),]

# sort Fs by size
Fs<-citrusReticulata[which( citrusReticulata$chrName %in% grep("F", citrusReticulata$chrName, value=T) 
),]

citrusReticulata[which( citrusReticulata$chrName %in% grep("F", citrusReticulata$chrName, value=T) ),] <- 
  Fs[order(Fs$shortArmSize + Fs$longArmSize),]

# add group column to show that each one is a pair
citrusReticulata$group<-1:9

data.frame of bands


#
# c. reticulata bands
#

{
citrusReticulataMarkPosDF <- citrusMarkPos(citrusReticulata)

  # remove CMA terminal from D
  citrusReticulataMarkPosDF <- citrusReticulataMarkPosDF[-which(citrusReticulataMarkPosDF$chrName=="D_3" & 
                                                              citrusReticulataMarkPosDF$markName=="CMA" 
                                                              ),]
  
  # add marks in short arm of D
  
  Sr_D_3<-citrusReticulata[which(citrusReticulata$chrName=="D_3"),]$shortArmSize
  #45S
  citrusReticulataMarkPosDF_D45S  <- data.frame(chrName="D_3", 
                                               chrRegion="p",
                                               markName="45S",
                                               markDistCen=Sr_D_3- (.15+.15/2), 
                                               markSize=0.15,
                                               OTU=unique(citrusReticulata$OTU)
  )
  
  # CMA 
  citrusReticulataMarkPosDF_DCMA  <- data.frame(chrName="D_3", 
                                               chrRegion="p",
                                               markName="CMA",
                                               markDistCen=Sr_D_3-.3, 
                                               markSize=0.3,
                                               OTU=unique(citrusReticulata$OTU)
  )
  
  # add 45S rDNA mark in short arm  of C
  citrusReticulataMarkPosDF_C45S  <- data.frame(chrName="C", 
                                                chrRegion="p",
                                                markName="45S",
                                                markDistCen=0, 
                                                markSize=0.1,
                                                OTU=unique(citrusReticulata$OTU)
  )
  
  # fuse marks
  citrusReticulataMarkPosDF <- dplyr::bind_rows(citrusReticulataMarkPosDF,
                                               citrusReticulataMarkPosDF_D45S,
                                               citrusReticulataMarkPosDF_DCMA,
                                               citrusReticulataMarkPosDF_C45S
  )
  
  # change band sizes
  
  # D_1
  citrusReticulataMarkPosDF[which(citrusReticulataMarkPosDF$chrName=="D_1"),]$markSize<-.75
  LAD_1<-citrusReticulata[which(citrusReticulata$chrName=="D_1"),]$longArmSize
  citrusReticulataMarkPosDF[which(citrusReticulataMarkPosDF$chrName=="D_1"),]$markDistCen<-
  LAD_1-.75
  
  # C short arm
  citrusReticulataMarkPosDF[which(citrusReticulataMarkPosDF$chrName=="C" &
                                    citrusReticulataMarkPosDF$markName=="CMA" &
                                    citrusReticulataMarkPosDF$chrRegion=="p"),]$markSize<-.3
  
  SAC <- citrusReticulata[which(citrusReticulata$chrName=="C" ),]$shortArmSize
  
  citrusReticulataMarkPosDF[which(citrusReticulataMarkPosDF$chrName=="C" &
                                    citrusReticulataMarkPosDF$markName=="CMA" &
                                    citrusReticulataMarkPosDF$chrRegion=="p"
                                    ),]$markDistCen<-SAC-.3
  
  # C LONG ARM
  citrusReticulataMarkPosDF[which(citrusReticulataMarkPosDF$chrName=="C" &
                                    citrusReticulataMarkPosDF$markName=="CMA" &
                                    citrusReticulataMarkPosDF$chrRegion=="q"),]$markSize<-.4
   
  LAC <- citrusReticulata[which(citrusReticulata$chrName=="C" ),]$longArmSize
  
  citrusReticulataMarkPosDF[which(citrusReticulataMarkPosDF$chrName=="C" &
                                    citrusReticulataMarkPosDF$markName=="CMA" &
                                    citrusReticulataMarkPosDF$chrRegion=="q"
  ),]$markDistCen<- LAC-.4
  
  
  # D_2
  citrusReticulataMarkPosDF[which(citrusReticulataMarkPosDF$chrName=="D_2"),]$markSize<-.55
  LAD_2<-citrusReticulata[which(citrusReticulata$chrName=="D_2"),]$longArmSize
  citrusReticulataMarkPosDF[which(citrusReticulataMarkPosDF$chrName=="D_2"),]$markDistCen<-
    LAD_2-.55
  
  # D_4
  citrusReticulataMarkPosDF[which(citrusReticulataMarkPosDF$chrName=="D_4"),]$markSize<-.6
  LAD_4<-citrusReticulata[which(citrusReticulata$chrName=="D_4"),]$longArmSize
  citrusReticulataMarkPosDF[which(citrusReticulataMarkPosDF$chrName=="D_4"),]$markDistCen<-
    LAD_4-.6
  
  # D_5
  citrusReticulataMarkPosDF[which(citrusReticulataMarkPosDF$chrName=="D_5"),]$markSize<-.7
  LAD_5<-citrusReticulata[which(citrusReticulata$chrName=="D_5"),]$longArmSize
  citrusReticulataMarkPosDF[which(citrusReticulataMarkPosDF$chrName=="D_5"),]$markDistCen<-
    LAD_5-.7
}

11.7.2 C. aurantium ‘common’

data.frame of chr. sizes


# From Mendes et al. 2016
 
# 1a + 1b + 1C + 8D + 7F

{
  
  #
  # chr .sizes
  #
  
  citrusaurantium<-read.table(text="
chrName shortArmSize longArmSize
f   1.43333333333333    2.06666666666667
f   1.36666666666667    1.83333333333333
d   1.3 1.66666666666667
d   1.13333333333333    1.46666666666667
d   1   1.6
a   1.3 2
d   1.36666666666667    1.8
d   1.06666666666667    1.63333333333333
d   0.733333333333333   1.36666666666667
f   0.833333333333333   1.36666666666667
d   1.13333333333333    1.33333333333333
c   1.16666666666667    1.66666666666667
d   1.06666666666667    1.8
b   1   1.83333333333333
f   0.966666666666667   1.6
f   0.8 1.36666666666667
f   0.633333333333333   1.43333333333333
f   0.733333333333333   1.3
", header =TRUE)
  
  # modify chr. names
  citrusaurantium$chrName<-toupper(citrusaurantium$chrName)
  citrusaurantium$chrName<-make.uniqueIF(citrusaurantium$chrName)
  
  # add column
  citrusaurantium$OTU<-"C. aurantium 'common'"
  
}
  

Order pairs based in BAC markers (not shown here - different to 45S / 5S rDNA )

  
{
  # confirmed pairs
  customOrder<-c("A","D_3","C","D_7")
  
  customOrder<-c(customOrder,sort(setdiff(citrusaurantium$chrName,customOrder)) )
  
  # sort 
  citrusaurantium$chrName<-factor(citrusaurantium$chrName, levels=customOrder)
  citrusaurantium<-citrusaurantium[order(citrusaurantium$chrName),]
  
  
  # sort Ds by size
  
  Ds<-citrusaurantium[which( citrusaurantium$chrName %in% grep("D", citrusaurantium$chrName, value=T) &
                               !citrusaurantium$chrName %in% c("D_3","D_7") ),]
  citrusaurantium[which( citrusaurantium$chrName %in% grep("D", citrusaurantium$chrName, value=T) &
                           !citrusaurantium$chrName %in% c("D_3","D_7") ),] <- Ds[order(Ds$shortArmSize+Ds$longArmSize),]
  
  # sort Fs by size
  Fs<-citrusaurantium[which( citrusaurantium$chrName %in% grep("F", citrusaurantium$chrName, value=T) 
  ),]
  citrusaurantium[which( citrusaurantium$chrName %in% grep("F", citrusaurantium$chrName, value=T) ),] <- 
    Fs[order(Fs$shortArmSize + Fs$longArmSize),]
  
  # pairs:
  
  groups<-c(1,1,2,2)
  citrusaurantium$group<-c(groups,rep(NA,18-length(groups) ) )
  
  # secondary name
  citrusaurantium$chrNameUp<-1:18
  
}

data.frame of bands

Option 1. Write from scratch:

{
  citrusaurantiumMarkPosDF<-read.table(text="
  chrName chrRegion markName markDistCen markSize    
  A           p      CMA   0.73    0.570 
  A           p      CMA   0.00    0.350 
  A           q      CMA   1.23    0.770 
  B           p      CMA   0.00    0.350 
  B           q      CMA   0.86    0.970 
  C           p      CMA   0.74    0.430 
  C           q      CMA   1.07    0.600 
  D_1         q      CMA   0.60    1.070 
  D_2         q      CMA   0.84    0.630 
  D_3         q      CMA   1.07    0.530 
  D_4         q      CMA   1.07    0.730 
  D_5         q      CMA   0.86    0.770 
  D_7         q      CMA   0.46    0.870 
  D_8         q      CMA   0.90    0.900 
  B           p      45S   0.09    0.175 
  A           p      45S   0.09    0.175 
  D_6         p      45S   0.58    0.100 
  D_6         p      CMA   0.53    0.200
  ",header=TRUE) 
  
citrusaurantiumMarkPosDF$OTU<-"C. aurantium 'common'"
}
# this is equivalent to the following section

Option 2. Use functions:

{
  
#
# CMA bands
#
  citrusaurantiumMarkPosDF <- citrusMarkPos(citrusaurantium)

  # add 45S in B
  citrusaurantiumMarkPosDF<-markOverCMA(citrusaurantiumMarkPosDF, 
                                        chrType="B", 
                                        chrRegion="p", 
                                        markName="45S")
  
  # add 45S in A p prox
  citrusaurantiumMarkPosDF<-markOverCMA(citrusaurantiumMarkPosDF, 
                                        chrType="A", 
                                        chrRegion="p", 
                                        markName="45S")
  
  
  # D_6
  
  # change D (D_6) band from long to short
  SA_D_6<-citrusaurantium[which(citrusaurantium$chrName=="D_6"),]$shortArmSize
  
  # 45S in short
  citrusaurantiumMarkPosDF_D45S  <- data.frame(chrName="D_6", 
                                               chrRegion="p",
                                               markName="45S",
                                               markDistCen=SA_D_6-.15, 
                                               markSize=0.1,
                                               OTU=unique(citrusaurantium$OTU)
  )
  
  # CMA in short
  citrusaurantiumMarkPosDF_DCMA  <- data.frame(chrName="D_6", 
                                               chrRegion="p",
                                               markName="CMA",
                                               markDistCen=SA_D_6-.2, 
                                               markSize=0.2,
                                               OTU=unique(citrusaurantium$OTU)
  )
  
  # remove CMA terminal from D_6 long
  citrusaurantiumMarkPosDF<-citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName!="D_6"),]
  
  # change mark sizes according to publication
  
  # D_1 band
  
  # change mark size
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="D_1"),]$markSize<-1.07
  
  # arm size
  LAD_1<-citrusaurantium[which(citrusaurantium$chrName=="D_1"),]$longArmSize
  
  # change mark dist. to cen.
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="D_1"),]$markDistCen<-
    LAD_1-1.07
  
  # D_2
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="D_2"),]$markSize<-0.63
  LAD_2<-citrusaurantium[which(citrusaurantium$chrName=="D_2"),]$longArmSize
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="D_2"),]$markDistCen<-
    LAD_2-.63

  # D_3
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="D_3"),]$markSize<-0.53
  LAD_3<-citrusaurantium[which(citrusaurantium$chrName=="D_3"),]$longArmSize
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="D_3"),]$markDistCen<-
    LAD_3-.53

  # A p ter
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="A" &
                                   citrusaurantiumMarkPosDF$markDistCen==1.05),]$markSize<-0.57
  SAA<-citrusaurantium[which(citrusaurantium$chrName=="A"),]$shortArmSize
  
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="A"&
                                   citrusaurantiumMarkPosDF$markDistCen==1.05),]$markDistCen<-
  SAA-.57
  
  # A q
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="A" &
                                   citrusaurantiumMarkPosDF$chrRegion=="q"),]$markSize<-0.77
  LAA<-citrusaurantium[which(citrusaurantium$chrName=="A"),]$longArmSize
  
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="A"&
                                   citrusaurantiumMarkPosDF$chrRegion=="q"),]$markDistCen<-
    LAA-.77
  
  # D_4
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="D_4"),]$markSize<-0.73
  LAD_4<-citrusaurantium[which(citrusaurantium$chrName=="D_4"),]$longArmSize
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="D_4"),]$markDistCen<-
    LAD_4-.73

  # D_5
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="D_5"),]$markSize<-0.77
  LAD_5<-citrusaurantium[which(citrusaurantium$chrName=="D_5"),]$longArmSize
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="D_5"),]$markDistCen<-
    LAD_5-.77

  # D_7
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="D_7"),]$markSize<-0.87
  LAD_7<-citrusaurantium[which(citrusaurantium$chrName=="D_7"),]$longArmSize
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="D_7"),]$markDistCen<-
    LAD_7-.87

  # C p
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="C" &
                                   citrusaurantiumMarkPosDF$chrRegion=="p"),]$markSize<-.43
  SAC<-citrusaurantium[which(citrusaurantium$chrName=="C"),]$shortArmSize
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="C" &
                                   citrusaurantiumMarkPosDF$chrRegion=="p"),]$markDistCen<-
    SAC-.43
  
  # C q
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="C" &
                                   citrusaurantiumMarkPosDF$chrRegion=="q"),]$markSize<-.6
  LAC<-citrusaurantium[which(citrusaurantium$chrName=="C"),]$longArmSize
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="C" &
                                   citrusaurantiumMarkPosDF$chrRegion=="q"),]$markDistCen<-
    LAC-.6

  # D_8
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="D_8"),]$markSize<-0.9
  LAD_8<-citrusaurantium[which(citrusaurantium$chrName=="D_8"),]$longArmSize
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="D_8"),]$markDistCen<-
    LAD_8-.9

  # B q
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="B" &
                                   citrusaurantiumMarkPosDF$chrRegion=="q"),]$markSize<-.97
  LAB<-citrusaurantium[which(citrusaurantium$chrName=="B"),]$longArmSize
  citrusaurantiumMarkPosDF[which(citrusaurantiumMarkPosDF$chrName=="B" &
                                   citrusaurantiumMarkPosDF$chrRegion=="q"),]$markDistCen<-
    LAB-.97
  
  # fuse marks
  citrusaurantiumMarkPosDF <- dplyr::bind_rows(citrusaurantiumMarkPosDF,
                                               citrusaurantiumMarkPosDF_D45S,
                                               citrusaurantiumMarkPosDF_DCMA
  )
}

11.7.3 C. limon


# from: Carvalho 2005

# C. limon - 1B(45Sprox) + 1C + 8D + 1D(45S) + 5F + 1FL0 + 1FL+

{
    # data.frame of  chr. sizes
    
  citruslimon <- citrusSize(B=1,C=1,D=9,F=5,FL0=1,FL=1, 
                                 OTU="C. limon")
  citruslimon
  
  # modify sizes
  
  citruslimon$shortArmSize[3]<-1.1
  citruslimon$longArmSize[3]<-1.5
  
  citruslimon$shortArmSize[4:5]<-1.15
  citruslimon$longArmSize[4:5]<-1.6
  
  citruslimon$shortArmSize[6:7]<-1.1
  citruslimon$longArmSize[6:7]<-1.6
  
  citruslimon$shortArmSize[8:9]<-1.15
  citruslimon$longArmSize[8:9]<-1.65
  
  citruslimon$shortArmSize[2]<-1
  citruslimon$longArmSize[2]<-1.6
  
  citruslimon$shortArmSize[12]<-1
  citruslimon$longArmSize[12]<-1.5
  
  citruslimon$shortArmSize[10:11]<-.95
  citruslimon$longArmSize[10:11]<-1.4
  
  citruslimon$shortArmSize[13:14]<-1
  citruslimon$longArmSize[13:14]<-1.5
  
  citruslimon$shortArmSize[15:16]<-.95
  citruslimon$longArmSize[15:16]<-1.3
  
  # sort Ds by size
  
  Ds<-citruslimon[which( citruslimon$chrName %in% grep("D", citruslimon$chrName, value=T) 
  ),]
  
  citruslimon[which( citruslimon$chrName %in% grep("D", citruslimon$chrName, value=T) 
  ),] <- Ds[order(Ds$shortArmSize+Ds$longArmSize),]
  
  # sort Fs by size
  Fs<-citruslimon[which( citruslimon$chrName %in% grep("F", citruslimon$chrName, value=T) 
  ),]
  
  citruslimon[which( citruslimon$chrName %in% grep("F", citruslimon$chrName, value=T) ),] <- 
    Fs[order(Fs$shortArmSize + Fs$longArmSize),]
  
  
  # secondary chr. name
  citruslimon$chrNameUp<-1:18
  
  #
  # data.frame of CMA band pos.
  #
  
  citruslimonMarkPosDF <- citrusMarkPos(citruslimon)
  head(citruslimonMarkPosDF)
  
  # marks with overlap with CMA
  # 45S in B, short arm
  
  citruslimonMarkPosDF<-markOverCMA(citruslimonMarkPosDF, 
                                    chrType="B", 
                                    chrRegion="p", 
                                    markName="45S")
  
  # 45S in D (D_1), long arm
  citruslimonMarkPosDF<-markOverCMA(citruslimonMarkPosDF, 
                                    chrName="D_1", 
                                      chrRegion="q", 
                                      markName="45S")
    
    # add mark from scratch (no overlap with CMA)
    
  }

11.7.4 Merge data.frames from all OTUs


#
# data.frames of size - merge
#

threeSize    <-dplyr::bind_rows(citrusReticulata, citruslimon, citrusaurantium)

#
# data.frames of band pos. merge
#

threeMarkPos <-dplyr::bind_rows(citruslimonMarkPosDF, citrusaurantiumMarkPosDF, citrusReticulataMarkPosDF)


#
#   leftNotes with formulas
#

# formulas
limon      <- "1B + 1C + 9D + 5F + 1FL0 + 1FL+ [1B/45S, 1D/45S]"
aurantium  <- "1A + 1B + 1C + 8D + 7F [1A/45S,1B/45S,1D/45S]"
reticulata <- "2C + 10D + 6F [2C/45S, 2D/45S]"

leftNotesdf<- data.frame(OTU=unique(threeSize$OTU), note=c(reticulata, limon, aurantium) )

# authors
notesdf<- data.frame(OTU=unique(threeSize$OTU), note=c("da-Costa-Silva et al. (2015)","Carvalho et al. (2005)","Mendes et al. (in prep.)") )

# marks' style data.frame

markStyleDF   <- makedfMarkColorMycolors(
  unique(citrusReticulataMarkPosDF$markName), c("darkgoldenrod1","chartreuse3") 
)

markStyleDF$style<-c("square","dots")

11.7.5 Plot

{
svg("climon.svg",width=12,height=10 )
par(mar=rep(0,4),oma=rep(0,4))
plotIdiograms(dfChrSize= threeSize,   # chr. size data.frame
              dfMarkPos= threeMarkPos,# mark position data.frame (inc. cen.)
              dfMarkColor=markStyleDF,# mark style d.f.
              
              orderChr = "original",  # order of chr. as in d.f.
              chrIdPatternRem="_.*",  # pattern to remove from chr. names
              karHeight = 2,          # karyotype height
              karHeiSpace = 6,        # height + separ. among karyot.
              
              chrSpacing=.20,         # separ. among chr.
              chrColor= "dodgerblue" 
              ,distTextChr = .9       # distance text to chr.
              
              ,legendWidth = .8       # legend item width
              ,legendHeight = 3       # legend item height
              ,markLabelSpacer = 2    # legend spacer
              ,ruler=FALSE            # do not use ruler
              ,chrIndex = ""          # do not print chr. index
              ,morpho=""              # do not print morphology
              ,karIndex = FALSE       # do not print kar. index
              
              #,colorBorderMark="black"# color of border of marks
              ,lwd.chr = 1            # border width
              
              ,OTUfont=3              # OTU name in italics
              
              ,leftNotes=leftNotesdf  # data.frame with notes (formula)
              ,notesTextSize = 1.3    # font size of notes
              ,leftNotesPosX = 0      # horizontal pos. of formula
              ,leftNotesPosY = 1      # vertical pos. of formula
              ,notes = notesdf        # authors
              
              ,classGroupName = "Pair"# name for groups 
              ,chrNameUp = TRUE       # use col. chrNameUp
              ,classChrName = "Type"  # change default title of inferior name
              ,classChrNameUp = "Chr."# change default title of upper name
              
              ,ylimBotMod = 1         # modify ylim bottom argument
              ,ylimTopMod = 0         # modify ylim top argument
              ,xlimLeftMod = 2        # modify left xlim
              ,xlimRightMod = 5       # modify right xlim
              
              ,threshold=40           # fixes shrinking of scale, needed because some chr. greater than 3.5 um
              ,moveKarHor = "C. limon"# kar. to move to right
              ,mkhValue = 5           # move cariótipo para direita 
              ,anchor=TRUE            # parental structure
              ,moveAnchorV = -1       # move anchor
              ,anchorVsizeF=1         # anchor vertical size factor modifier
              ,karSepar = F           # modif. separ de karyo.
)
dev.off() # close svg
}

For a plot of GISH of Citrus, visit the GISH chapter

11.8 Citrus Functions

Details of functions can be found with:

?citrusSize 
?citrusMarkPos 
?markOverCMA

Or in: https://ferroao.gitlab.io/idiogramFISH/reference/citrusSize.html