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This guide shows how to plot groups of chromosomes, this can be used to plot heteromorphic pairs
For v. > 1.1.0
1 Load package
visit gitlab for installation instructions https://gitlab.com/ferroao/idiogramFISH
2 Adding the column group
Open your chromosome data - Chr. size - as data.frame and add column
From scratch:
# Example data.frame written in R, use
dfwithgroups<-read.table(text="
chrName shortArmSize longArmSize group
1 1 3 5 1
2 1 3.2 5.5 1
3 1 3.5 4.8 1
4 4 1 3 NA
5 5 3 5 NA
6 X 4 6 NA", header=T, stringsAsFactors=F)| chrName | shortArmSize | longArmSize | group |
|---|---|---|---|
| 1 | 3.0 | 5.0 | 1 |
| 1 | 3.2 | 5.5 | 1 |
| 1 | 3.5 | 4.8 | 1 |
| 4 | 1.0 | 3.0 | NA |
| 5 | 3.0 | 5.0 | NA |
| X | 4.0 | 6.0 | NA |
3 Plotting
You can plot without marks:
plotIdiograms(dfChrSize=dfwithgroups, # chr sizes
orderBySize = TRUE, # order chr. by size
chrColor = "gray", # chr. color
cenColor = "gray", # centromere color
chrId="original", # chr. names as in you data.frame
indexIdTextSize=1, # font size of chr. name and indices
chrIndex = FALSE, # do not add chr. indices
morpho=FALSE, # do not add chr. morphology
karIndex = FALSE, # do not add karyotype indices
chrWidth=2.5, # chromosome width
chrSpacing = 2.5, # space among chromosomes
karSpacing=1, # vertical size of karyotypes
karHeight = 1, # vertical size of karyotypes including spacing
rulerPos=-2.2, # position of ruler
ruler.tck=-0.02, # size and orientation of tick of ruler
rulerNumberPos=.5, # position of numbers of ruler
rulerNumberSize=.7, # font size of ruler
ylimBotMod = 0, # modify ylim bottom argument
xlimRightMod = 0 # modify xlim right argument
)
4 Plot heteromorphic pairs
It can be used to plot heteromorphic pairs, see pair 1
dfwithHetero<-read.table(text="
chrName shortArmSize longArmSize group
1 1A 3 5 1
2 1B 3 5 1
4 2 1 3 NA
5 3 3 5 NA
6 4 4 6 NA", header=TRUE, stringsAsFactors=FALSE)| chrName | shortArmSize | longArmSize | group | |
|---|---|---|---|---|
| 1 | 1A | 3 | 5 | 1 |
| 2 | 1B | 3 | 5 | 1 |
| 4 | 2 | 1 | 3 | NA |
| 5 | 3 | 3 | 5 | NA |
| 6 | 4 | 4 | 6 | NA |
Marks positions’ data
Open or write your mark positions as a data.frame. This data.frame has the marks present in all karyotypes with position info.
dfOfMarksHetero<-read.table(text=
" chrName markName markArm markSize markDistCen
1 1A 5S p 1 0.9
2 1B 45S p 1 0.9
3 2 CMA q 1 1.0
4 3 DAPI q 1 1.0", header=TRUE, stringsAsFactors=FALSE)| chrName | markName | markArm | markSize | markDistCen |
|---|---|---|---|---|
| 1A | 5S | p | 1 | 0.9 |
| 1B | 45S | p | 1 | 0.9 |
| 2 | CMA | q | 1 | 1.0 |
| 3 | DAPI | q | 1 | 1.0 |
Plotting of the heteromorphic pair
plotIdiograms(dfChrSize=dfwithHetero, # chr sizes
dfMarkPos=dfOfMarksHetero, # position of marks
chrColor = "gray", # colors of chr.
cenColor = "gray", # colors of centromeres
chrId="original", # chr. name in df.
indexIdTextSize=1, # font size of chr. name and indices
chrIndex = FALSE, # do not add chr. indices
morpho=FALSE, # do not add chr. morphologies
karIndex = FALSE, # do not add karyotype indices
dotRoundCorr=2, # correction factor of roundness of dots
markLabelSize=1, # font size of legends
MarkDistanceType="cen", # mark distance is to center of mark
chrWidth=2.5, # chr. width
chrSpacing = 2.5, # space among chr.
orderBySize = FALSE, # do not order chr. by size
karSpacing=1.2, # vertical size of karyotypes including spacing
rulerPos=-1.9, # position of rulers
ruler.tck=-0.02, # size and orientation of ticks of ruler
rulerNumberPos=.5, # position of numbers of ruler
rulerNumberSize=1, # font size of ruler numbers
ylimBotMod = -.2, # modify ylim bottom argument
xlimRightMod = 0 # modify xlim right argument
)
5 Holocentrics in groups
Let’s modify some data.frames to add a group
data("dfChrSizeHolo")
data("dfMarkPosHolo")
dfMarkPosHoloHetero<-dfMarkPosHolo
dfMarkPosHoloHetero$chrName<-c(3,3,"1A",2,"1B","1B")
dfChrSizeHoloHetero<-dfChrSizeHolo
dfChrSizeHoloHetero$chrName<-c("1A","1B",2,3)
# Adding the group column
dfChrSizeHoloHetero$group<-c(1,1,NA,NA)plotIdiogramsHolo(dfChrSize=dfChrSizeHoloHetero, # df of chr sizes
orderBySize = FALSE, # do not order chr. by size
dfMarkPos=dfMarkPosHoloHetero, # df of position of marks
dotRoundCorr=3, # correction of roundness of dots
chrWidth = 2.3, # chr. width
chrSpacing = 2, # chr. spacing
karIndex = FALSE, # do not add karyotype asymmetry index
indexIdTextSize=1, # font size of chr. name and indices
karHeight = 1.4, # vertical size of karyotypes
addOTUName=FALSE, # do not add name of OTUs
legend="aside", # position of legend to the right
markLabelSize=1, # font size of legend
markLabelSpacer=4, # space among chr. and legend
rulerNumberSize=1, # font size of ruler
rulerPos=-2.2, # position of ruler
ruler.tck=-0.03, # size and orientation of ticks
rulerNumberPos=.9, # position of rulers' numbers
xlimLeftMod=2.2, # modify left argument of xlim
xlimRightMod=15, # modify right argument of xlim
ylimBotMod=.3 # modifiy bottom argument of ylim
)
Creating a new data.frame for holocentrics
dfChrSizeHoloGroup<-data.frame(chrName=c(1,1,1,1,2,3,4),
chrSize=c(3.1,3.2,3.3,3.4,4,5,6),
group=c(1,1,1,1,NA,NA,NA)
)| chrName | chrSize | group |
|---|---|---|
| 1 | 3.1 | 1 |
| 1 | 3.2 | 1 |
| 1 | 3.3 | 1 |
| 1 | 3.4 | 1 |
| 2 | 4.0 | NA |
| 3 | 5.0 | NA |
| 4 | 6.0 | NA |
plotIdiogramsHolo(dfChrSize=dfChrSizeHoloGroup, # data.frame of chr sizes
orderBySize = FALSE, # do not order chr. by size
karIndex = FALSE, # do not add karyotype indices
chrWidth = 2, # chr. width
chrSpacing = 2, # space among chr.
indexIdTextSize=1, # font size of chr. names and indices
OTUTextSize=1, # font size of OTU names
karHeight = 1.4, # karyotype rel. height
rulerNumberSize=1, # font size of ruler
rulerPos=-2.2, # position of ruler
ruler.tck=-0.03, # size and orientation of ticks of ruler
rulerNumberPos=.9, # position of number of ruler
xlimLeftMod=2.2, # modify left argument of xlim
xlimRightMod=10, # modify right argument of xlim
ylimBotMod=.3 # modify bottom argument of ylim
)