7 GISH
Jupyter interactive version:
7.1 GISH of monocentric chromosomes
You need the data.frame of chr. sizes, and a d.f. of marks
Chr. sizes:
parentalAndHybChrSize| OTU | chrName | shortArmSize | longArmSize | |
|---|---|---|---|---|
| 1 | Parental 1 | 1 | 3.2 | 4 |
| 2 | Parental 1 | 4 | 1.5 | 2 |
| 3 | Parental 1 | 5 | 4.8 | 6 |
| 4 | Parental 1 | 6 | 6.1 | 7 |
| 8 | Allopolyploid | 1 | 3.2 | 4 |
| 9 | Allopolyploid | 2 | 4.5 | 5 |
| 10 | Allopolyploid | 3 | 2.0 | 3 |
| 11 | Allopolyploid | 4 | 1.5 | 2 |
| 12 | Allopolyploid | 5 | 4.8 | 6 |
| 13 | Allopolyploid | 6 | 6.1 | 7 |
| 5 | Parental 2 | 1 | 3.2 | 4 |
| 6 | Parental 2 | 2 | 4.5 | 5 |
| 7 | Parental 2 | 3 | 2.0 | 3 |
Marks’ positions data
dfAlloParentMarks| OTU | chrName | markName | chrRegion | |
|---|---|---|---|---|
| 1 | Allopolyploid | 1 | Parental 2 | qcen |
| 17 | Allopolyploid | 1 | Parental 1 | pcen |
| 16 | Allopolyploid | 1 | Parental 1 | p |
| 2 | Allopolyploid | 1 | Parental 2 | q |
| 4 | Allopolyploid | 2 | Parental 2 | w |
| 5 | Allopolyploid | 3 | Parental 2 | w |
| 6 | Allopolyploid | 4 | Parental 1 | w |
| 7 | Allopolyploid | 5 | Parental 1 | w |
| 8 | Allopolyploid | 6 | Parental 1 | w |
| 9 | Parental 1 | 6 | Parental 1 | w |
| 10 | Parental 1 | 5 | Parental 1 | w |
| 11 | Parental 1 | 1 | Parental 1 | w |
| 12 | Parental 1 | 4 | Parental 1 | w |
| 13 | Parental 2 | 2 | Parental 2 | w |
| 14 | Parental 2 | 1 | Parental 2 | w |
| 15 | Parental 2 | 3 | Parental 2 | w |
We will use column note to add a note to the right of the karyotype of the OTU (column)
notesdf2<-read.table(text=
" OTU note
\"Parental 1\" \"Parental One\"
\"Parental 2\" \"Parental Two\"
\"Allopolyploid\" Allopolyploid ", header=TRUE, stringsAsFactors=FALSE,fill=TRUE)7.1.1 Plotting
# svg("gish.svg",width=7,height=9 )
#png("parentalAndHybChrSize.png", width=700, height=900)
# REORDER OTUs
parentalAndHybChrSize$OTU<-factor(parentalAndHybChrSize$OTU,levels=c("Parental 1", "Allopolyploid","Parental 2") )
parentalAndHybChrSize<-parentalAndHybChrSize[order(parentalAndHybChrSize$OTU),]
par(mar=rep(0,4) )
plotIdiograms(dfChrSize = parentalAndHybChrSize, # d.f. of chr. sizes
dfMarkPos = dfAlloParentMarks, # d.f. of marks' positions
cenColor = NULL, # no cen. color for GISH
karHeiSpace=5, # karyotype height including spacing
karSepar = FALSE, # equally sized (height) karyotypes
legend="" # no legend
,notes=notesdf2 # data.frame with notes NEW
#,OTUasNote=TRUE # TRY THIS (OTU name to the right)
,notesTextSize = 1.3
,notesPosX = 1.5 # space from chr. (right) to note
,ruler = FALSE
,moveKarHor = "Allopolyploid"# OTU to move to the right
,mkhValue = 7 # amount to move to right
,anchor = TRUE # show anchor for moveKarHor OTUs
,moveAnchorV = 4 # modify anchor Vertical portion position
,moveAnchorH = -1.5 # modify anchor Horizon. portion position
,ylimBotMod = 1 # ylim bottom argument mod.
,xlimRightMod = 4
); # dev.off()
7.2 GISH of holocentric chromosomes
You need the data.frame of chr. sizes, and a d.f. of marks
Chr. sizes:
parentalAndHybHoloChrSize| OTU | chrName | chrSize |
|---|---|---|
| Parental 1 | 7 | 4 |
| Parental 1 | 4 | 2 |
| Parental 1 | 5 | 6 |
| Parental 1 | 6 | 7 |
| Parental 2 | 1 | 4 |
| Parental 2 | 2 | 5 |
| Parental 2 | 3 | 3 |
| Allopolyploid | 7 | 4 |
| Allopolyploid | 2 | 5 |
| Allopolyploid | 3 | 3 |
| Allopolyploid | 4 | 2 |
| Allopolyploid | 5 | 6 |
| Allopolyploid | 6 | 7 |
Marks’ positions data
dfAlloParentMarksHolo| OTU | chrName | markName | chrRegion | |
|---|---|---|---|---|
| 1 | Allopolyploid | 7 | Parental 1 | w |
| 4 | Allopolyploid | 2 | Parental 2 | w |
| 5 | Allopolyploid | 3 | Parental 2 | w |
| 6 | Allopolyploid | 4 | Parental 1 | w |
| 7 | Allopolyploid | 5 | Parental 1 | w |
| 8 | Allopolyploid | 6 | Parental 1 | w |
| 9 | Parental 1 | 6 | Parental 1 | w |
| 10 | Parental 1 | 5 | Parental 1 | w |
| 11 | Parental 1 | 7 | Parental 1 | w |
| 12 | Parental 1 | 4 | Parental 1 | w |
| 13 | Parental 2 | 2 | Parental 2 | w |
| 14 | Parental 2 | 1 | Parental 2 | w |
| 15 | Parental 2 | 3 | Parental 2 | w |
Plotting
# svg("gish.svg",width=8,height=7 )
par(mar=c(0,0,0,0))
plotIdiograms(dfChrSize = parentalAndHybHoloChrSize, # d.f. of chr. sizes
dfMarkPos = dfAlloParentMarksHolo, # d.f. of marks' positions
chrColor = "gray", # chr. color
cenColor = NULL, # cen. color when GISH
karHeight = 3, # karyotype height without spacing
karHeiSpace=5, # karyotype height including spacing
distTextChr = 0.8 # separation among chr. and text
,ruler=FALSE # no ruler
,legend="" # no legend
,xlimRightMod = 0 # xlim right arg. modif.
,xModifier = 100 # separ. among chromatids
); # dev.off()
7.3 GISH of Citrus as Yasuda et al. (2010)
For more details on the use of Citrus functions go to chapter Citrus
Parental C. schweinfurthii: 14D + 4F (using Guerra nomenclature).
{
#
# c. schweinfurthii chr sizes d.f.
#
cschweinformula<-"14D + 4F"
require(idiogramFISH)
citrusschwein <- citrusSize(D=14,
F=4
,OTU="C. schweinfurthii"
,longArm=1.2)
#
# c. schweinfurthii CMA and GISH marks
#
citrusschweinMarkPosDF <- citrusMarkPos(citrusschwein)
#
# data.frame of genomic marks
#
citrusschweinMarkPosDF2 <- data.frame(chrName=c(paste0("D_",1:7),paste0("F_",1:2)),
chrRegion="w"
,markName="schweingenome"
,OTU=unique(citrusschwein$OTU)
)
#
# merge marks pos.
#
citrusschweinMarkPosDF <- dplyr::bind_rows(citrusschweinMarkPosDF2,citrusschweinMarkPosDF)
#
# Inversion of some chr. (D marks up)
#
csSwap <- swapChrRegionDfSizeAndMarks(citrusschwein,citrusschweinMarkPosDF,c(paste0("D_",1:14) ) )
citrusschwein <- csSwap$dfChrSize
citrusschweinMarkPosDF<- csSwap$dfMarkPos
#
# mark style
#
unique(citrusschweinMarkPosDF$markName)
{
markStyleschweinDF <- makedfMarkColorMycolors(
unique(citrusschweinMarkPosDF$markName), c("chartreuse3","darkgoldenrod1") )
}
#
# d.f. of notes
#
leftNotesschwein <- data.frame(OTU=unique(citrusschwein$OTU), note= paste0("Female gamete: 7D + 2E" ) )
leftNotesschweinUp<- data.frame(OTU=unique(citrusschwein$OTU), note= paste0(unique(citrusschwein$OTU)," (",cschweinformula,")" ) )
notesschwein<- data.frame(OTU=unique(citrusschwein$OTU), note= "Yasuda et al. (2010)" )
}
Parental ‘Nanpu’ tangor
{
cnanpuformula<-"1A + 4C + 5D + 8F" # Guerra nom.
#
# 'Nanpu' tangor chr. sizes
#
citrusnanpu <- citrusSize(A=1,C=4,D=5,F=8 #
,OTU="nanpu tangor"
,longArm=1.2)
#
# c. nanpu CMA marks
#
citrusnanpuMarkPosDF <- citrusMarkPos(citrusnanpu)
#
# d.f. of genomic marks
#
citrusnanpuMarkPosDF2 <- data.frame(chrName = c("A","C_1",paste0("D_",1:4), paste0("F_",1:3) ),
chrRegion="w"
,markName="nanpugenome"
,OTU=unique(citrusnanpu$OTU)
)
#
# merge marks pos.
#
citrusnanpuMarkPosDF <- dplyr::bind_rows(citrusnanpuMarkPosDF2,citrusnanpuMarkPosDF)
#
# mark style d.f.
#
unique(citrusnanpuMarkPosDF$markName)
{
markStylenanpuDF <- makedfMarkColorMycolors(
unique(citrusnanpuMarkPosDF$markName), c("chocolate","darkgoldenrod1") )
}
#
# invert some chr.
#
csSwap<-swapChrRegionDfSizeAndMarks(citrusnanpu,citrusnanpuMarkPosDF,c(paste0("D_",1:5) ) )
citrusnanpu <- csSwap$dfChrSize
citrusnanpuMarkPosDF <- csSwap$dfMarkPos
#
# notes data.frames
#
leftNotesnanpu <- data.frame(OTU=unique(citrusnanpu$OTU), note= paste0("Male gamete: 1A + 1C + 4D + 3E" ) )
leftNotesnanpuUp<- data.frame(OTU=unique(citrusnanpu$OTU), note= paste0("'Nanpu' tangor (",cnanpuformula,")" ) )
notesnanpu<- data.frame(OTU=unique(citrusnanpu$OTU), note= "Yasuda et al. (2010)" )
}
Merge data.frames from parentals
{
bothParentalsChr <- dplyr::bind_rows(citrusnanpu,citrusschwein)
bothParentalsMarks <- dplyr::bind_rows(citrusschweinMarkPosDF, citrusnanpuMarkPosDF)
bothPmarkStyle <- unique(dplyr::bind_rows(markStyleschweinDF, markStylenanpuDF) )
bothPleftNotesUp <- dplyr::bind_rows(leftNotesschweinUp,leftNotesnanpuUp)
bothPleftNotes <- dplyr::bind_rows(leftNotesschwein,leftNotesnanpu)
}data.frames of the hybrid
{
cschnanpuformula<-"1A + 1C + 11D + 5F"
require(idiogramFISH)
#
# hybrid chr. size
#
citrusschnanpu <- citrusSize(A=1,C=1,D=11,F=5 #
,OTU="schweinfurthii + nanpu"
,longArm=1.2)
#
# hybrid CMA marks
#
citrusschnanpuMarkPosDF <- citrusMarkPos(citrusschnanpu)
#
# invert some chr.
#
csSwap<-swapChrRegionDfSizeAndMarks(citrusschnanpu,citrusschnanpuMarkPosDF,c(paste0("D_",1:11) ) )
citrusschnanpu <- csSwap$dfChrSize
citrusschnanpuMarkPosDF<- csSwap$dfMarkPos
#
# d.f. of gish marks
#
citrusschnanpuMarkPosDF2 <- data.frame(chrName=c(paste0("D_",5:11), paste0("F_",1:2) ),
chrRegion="w"
,markName="schweingenome"
,OTU=unique(citrusschnanpu$OTU)
)
citrusschnanpuMarkPosDF3 <- data.frame(chrName=c("A","C",paste0("D_",1:4), paste0("F_",3:5) ),
chrRegion="w"
,markName="nanpugenome"
,OTU=unique(citrusschnanpu$OTU)
)
#
# merge marks
#
citrusschnanpuMarkPosDF <- dplyr::bind_rows(citrusschnanpuMarkPosDF2,citrusschnanpuMarkPosDF3,citrusschnanpuMarkPosDF)
#
# style of marks d.f.
#
unique(citrusschnanpuMarkPosDF$markName)
{
markStyleschnanpuDF <- makedfMarkColorMycolors(
unique(citrusschnanpuMarkPosDF$markName), c("chartreuse3","chocolate","darkgoldenrod1") )
}
#
# notes for hybrid
#
# italics! # rest: \" to \"
name <- paste0("italic('C. schweinfurthii'), \" × 'Nanpu' tangor (CN3) (", cschnanpuformula,")\"" )
# to parse italics, use parseStr2lang = TRUE
leftNotesschnanpuUp <- data.frame(OTU=unique(citrusschnanpu$OTU), note= name )
notesschnanpu <- data.frame(OTU=unique(citrusschnanpu$OTU), note= "'Yasuda et al. (2010)'" )
}Plot
#
# plot of parentals only
#
{
par(mar=rep(0,4), oma=rep(0,4) )
plotIdiograms(callPlot=T,
dfChrSize= bothParentalsChr, # chr. size data.frame
dfMarkPos= bothParentalsMarks, # mark position data.frame
dfMarkColor=bothPmarkStyle, # mark style d.f.
orderChr = "original" # order of chr. as in d.f.
,chrWidth = .5 # chr. width
,chrSpacing=.5 # separ. among chr.
,karHeight=4 # kar. height
,karHeiSpace=5 # anchor height
,chromatids = FALSE # don't use chromatids
,chrColor= "white" # chr. color
,ruler=FALSE # don't use ruler
,chrId="" # don't use chr. name
,chrIndex = "" # don't use chr. indices
,morpho="" # don't use morphology
,karIndex = FALSE # don't use kar. indices
,colorBorderMark="black"# color of border of marks
,addOTUName = F # do not add OTU names
,lwd.chr = 1.6 # border width
,lwd.marks=1 # border width marks
,gishCenBorder=T # cen. border of gish as mark color
,hideCenLines=1.75 # hide cen. border
,legend="" # no legend for marks
,leftNotes = bothPleftNotes # data.frame with left notes
,leftNotesUp= bothPleftNotesUp # data.frame with Up left notes
,leftNoteFontUp =3 # italics
,leftNotesTextSize = 1.3 # font size of notes
,leftNotesUpTextSize = 1.3 # font size of notes
,leftNotesPosX = 0 # horizontal pos. of left notes
,leftNotesPosY = 0 # vertical pos. of left down notes
,leftNotesUpPosX = 0 # horizontal pos. of left up notes
,leftNotesUpPosY = 2 # vertical pos. of left up notes
,verticalPlot=FALSE # horizontal plot
,karSpaceHor=3 # horizontal spacing among kar.
,karAnchorLeft = "C. schweinfurthii" # anchor to the left of
,anchor=TRUE # add anchor
,ylimBotMod = 1 # modify ylim bottom argument
,ylimTopMod = 0 # modify ylim top argument
,xlimLeftMod =0 # modify left xlim
,xlimRightMod = 2 # modify right xlim
)
}
# add plot of hybrid over parents plot
{
plotIdiograms(callPlot=FALSE, # plot over previous plot
dfChrSize= citrusschnanpu, # chr. size data.frame
dfMarkPos= citrusschnanpuMarkPosDF, # mark position data.frame
dfMarkColor=markStyleschnanpuDF, # mark style d.f.
orderChr = "original", # order of chr. as in d.f.
chrWidth = .5, # chr. width
chrSpacing=.5, # separ. among chr.
karHeight=4 # kar. height
,chromatids = FALSE # don't use chromatids
,chrColor= "white" # chr. color
,ruler=FALSE # don't use ruler
,chrId="" # don't use chr. name
,chrIndex = "" # don't use chr. indices
,morpho="" # don't use morphology
,karIndex = FALSE # don't use kar. indices
,colorBorderMark="black"# color of border of marks
,addOTUName=F # don't add OTU name
,lwd.chr = 1.6 # border width
,lwd.marks=1 # border width marks
,leftNotesUp = leftNotesschnanpuUp # up notes: name of hybrid
,parseStr2lang = TRUE # for italics, see notes data.frame
,notesTextSize = 1.3 # font size of notes
,leftNotesUpTextSize = 1.3 # font size of notes
,leftNotesPosX = 0 # horizontal pos. of notes
,leftNotesUpPosY = 2 # vertical pos. left up notes
,notes = notesschnanpu # right notes - authors
,notesPosX=3 # notes hor. pos
,ylimBotMod = 1 # modify ylim bottom argument
,ylimTopMod = -5 # modify ylim top argument
,xlimLeftMod = 0 # modify left xlim
,xlimRightMod = 2 # modify right xlim
,gishCenBorder=T # cen. border as mark color
,legend="" # no legend for marks
,hideCenLines=1.75 # hide cen. lines
,moveAllKarValueHor=9.5 # move kar. to right
,moveAllKarValueY =-10 # move kar. down
)
} # hybrid