11 Citrus
Jupyter interactive version:
11.1 C. maxima as da-Costa-Silva et al. (2019)
master data.frame of chr. size and marks
From this special data.frame citrusMaximaChrMark we will get two of the three canonical data.frames:
- One for chr. sizes (parameter
dfChrSize) - One for marks’ positions (parameter
dfMarkPos) - One (optional) for mark style (parameter
dfMarkColor)
Column chrNameUp will be used in this case for unifying the chr. names (chrName) in the 1st and 2nd 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
,leftNotesTextSize = 1.3# font size of notes
,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
,leftNotesTextSize = 1 # font size of 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
Details of functions can be found with:
?citrusSize
?citrusMarkPos
?markOverCMAOr in: https://ferroao.gitlab.io/idiogramFISH/reference/citrusSize.html
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 mattersPlot
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
,leftNotesTextSize = 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_2$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$OTU), note="1B + 11D + 4F + 2FL0") # keep spacing
}
par(mar = c(0, 0, 0, 0), oma=rep(0,4) )
library(idiogramFISH)
plotIdiograms(dfChrSize= citrusSizeDF_2, # d.f. of chr. size
dfMarkPos= citrusMarkPosDF45S_2,# d.f. of mark pos
dfMarkColor=markStyleDF, # d.f. of mark style
orderChr = "original", # chr. order as in d.f.
chrIdPatternRem = "_.*", # modif name of chr. removing this pattern
chrSpacing=.20, # separ. among chr.
chrColor= "dodgerblue"
,legendWidth = .8 # legend item width
,legendHeight = 2.5 # legend item height
,markLabelSpacer = 2 # legend spacer
,ruler=F
,chrIndex = ""
,morpho=""
,karIndex = FALSE
,chrNameUp = TRUE # use col. chrNameUp
,classChrName = "Type" # change default title of inferior name
,classChrNameUp = "Chr." # change default title of upper name
,classGroupName = "Pair" # name for groups
,leftNotes=notesdf # data.frame with notes
,leftNotesTextSize = 1.3 # font size of notes
,leftNotesPosX = 10.2 # formula horiz. pos.
,leftNotesPosY = 0
,ylimBotMod = 1 # modify ylim bottom argument
,ylimTopMod = 0 # modify ylim top argument
,xlimLeftMod = 2 # modify left xlim
,xlimRightMod = 3 # modify right xlim
)
11.5 Several karyotypes per plot
Column OTU is mandatory for several OTU.
# data.frames of size - merge
bothSize <-dplyr::bind_rows(citrusSizeDF, citrusSizeDF_2)
# data.frames of band pos. merge
bothMarkPos <-dplyr::bind_rows(citrusMarkPosDF45S, citrusMarkPosDF45S_2)
# formulas
notesdf<- data.frame(OTU=unique(bothSize$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
,leftNotes=notesdf # data.frame with notes
,leftNotesTextSize = 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
,leftNotesUpTextSize = 1.3 # font size of notes
,leftNotesUpPosX = 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 (Parental 1)
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"),]$markDistCen<-
LAD_5-.7
}11.7.2 C. aurantium ‘common’ (Parental 2)
data.frame of chr. sizes
# From Mendes et al. 2016
# 1a + 1b + 1C + 8D + 7F
{
#
# chr .sizes
#
citrusaurantium<-read.table(text="
chrName shortArmSize longArmSize
f 1.43333333333333 2.06666666666667
f 1.36666666666667 1.83333333333333
d 1.3 1.66666666666667
d 1.13333333333333 1.46666666666667
d 1 1.6
a 1.3 2
d 1.36666666666667 1.8
d 1.06666666666667 1.63333333333333
d 0.733333333333333 1.36666666666667
f 0.833333333333333 1.36666666666667
d 1.13333333333333 1.33333333333333
c 1.16666666666667 1.66666666666667
d 1.06666666666667 1.8
b 1 1.83333333333333
f 0.966666666666667 1.6
f 0.8 1.36666666666667
f 0.633333333333333 1.43333333333333
f 0.733333333333333 1.3
", header =TRUE)
# modify chr. names
citrusaurantium$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)
,leftNotesTextSize = 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= .35 # 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
