4 Human karyotype

4.1 Karyotype of 400 bands

Organize chr. in rows using column OTU. (Adler, 1994)

library(idiogramFISH)
# Chromosome sizes for human
head(humChr) 
chrName group shortArmSize longArmSize
1 A 5.600 5.890
2 A 4.245 6.715
3 A 4.220 4.720
4 B 2.240 6.165
5 B 2.110 5.920
6 C 2.880 4.835
FstRow<-length(which(humChr$group %in% c("A","B") ) )        # groups in 1st row
SndRow<-length(which(humChr$group %in% "C" ) )               # groups in second row
TrdRow<-length(which(humChr$group %in% c("D","E") ) )        # groups in third row
FrtRow<-length(which(humChr$group %in% c("F","G","sex") ) )  # groups in forth row

OTUdf<-data.frame(OTU=c(rep("otu1",FstRow),
                        rep("otu2",SndRow),
                        rep("otu3",TrdRow),
                        rep("otu4",FrtRow)
), stringsAsFactors=FALSE # c
) # df

OTUdf$chrName<-humChr$chrName

humChr$OTU<-OTUdf$OTU

Add OTU info. to data.frame of marks’ position

# data.frame with marks' position
head(humMarkPos)  
chrName markName chrRegion markDistCen markSize
2 1 chr1p36.3 p 5.290 0.310
3 1 chr1p36.2 p 5.100 0.190
4 1 chr1p36.1 p 4.680 0.420
5 1 chr1p35 p 4.435 0.245
6 1 chr1p34.3 p 4.270 0.165
7 1 chr1p34.2 p 4.110 0.160
humMarkPos$OTU<-OTUdf$OTU[match(humMarkPos$chrName, OTUdf$chrName)]

This is the data.frame of mark characteristics

head(humMarkColor)
markName markColor style
2 chr1p36.3 white square
3 chr1p36.2 black square
4 chr1p36.1 white square
5 chr1p35 black square
6 chr1p34.3 white square
7 chr1p34.2 black square

Plot

# fig.width=10, fig.height=28
par(mar=rep(0,4))
plotIdiograms(humChr,                     # data.frame of chromosome size (in package)
              dfMarkPos = humMarkPos,     # df of mark positions  (in package)
              dfMarkColor = humMarkColor, # df of mark characteristics (in package)
              
              addOTUName = FALSE,         # do not add name of OTU
              karHeight = 6,              # vertical size of kar.
              karHeiSpace = 7,            # vertical spacing among OTU
              chrWidth = .4,              # chr. width
              chrSpacing = .6,            # space among chr.
              
              amoSepar = 2,               # reduce distance among OTUs
              karIndex = FALSE,           # do not add karyotype indices
              distTextChr = 1.5,          # distance from chr. to text.
              
              chrColor = "black",         # chr. color
              chrIndex = "",              # do not add chromosome indices
              morpho = "",                # do not add morphological categories

              centromereSize = 0,         # apparent centromere size
              
              squareness = 10,             # squareness of chr. and marks
              legend = "inline",          # mark labels next to chr.
              markLabelSize = .5,         # size of legend font
              colorBorderMark = "black",  # force color of border of marks 
              pattern= "chr[0-9XY]+",     # REGEX pattern to remove from name of marks
              indexIdTextSize = 2,        # font size of chr name and indices
              lwd.chr=.5,                 # width of chr and mark borders
              
              ruler= FALSE,

              xlimRightMod = 0,           # space to the right of karyotype
              ylimBotMod = -.6            # modify ylim of bottom
              # ,asp=1                    # y x aspect
              )

4.2 Robertsonian Translocations - function robert

This procedure transforms the data of long arms of the chromosomes 13 and 14 from data.frames of chr. and marks in a derivative (Robertson, 1916).

We can do any Robertsonian translocation using:

chrt13q14q<-robert(humChr,humMarkPos,13,14,"q","q")

# which produces a list of two data.frames:

# 1. chr. sizes
dfChrSizeDer<-chrt13q14q$dfChrSizeDer
# remove the group column
dfChrSizeDer<-dfChrSizeDer[ , !(names(dfChrSizeDer) %in% "group")]

# 2. marks' positions
dfMarkPosDer<-chrt13q14q$dfMarkPosDer

head(dfMarkPosDer)
chrName markName chrRegion markDistCen markSize OTU
613 t(13;14)(q10:q10) chr14q11.1 p 0.000 0.125 otu3
713 t(13;14)(q10:q10) chr14q11.2 p 0.125 0.330 otu3
813 t(13;14)(q10:q10) chr14q12 p 0.455 0.335 otu3
913 t(13;14)(q10:q10) chr14q13 p 0.790 0.305 otu3
1013 t(13;14)(q10:q10) chr14q21 p 1.095 0.600 otu3
1113 t(13;14)(q10:q10) chr14q22 p 1.695 0.330 otu3

plot of t(13;14)

par(mar=c(0,2,.5,0))

plotIdiograms(dfChrSizeDer,               # data.frame of chromosome size
              dfMarkPos = dfMarkPosDer,   # df of mark positions
              dfMarkColor = humMarkColor, # df of mark characteristics (in package)

              addOTUName = FALSE,         # do not add name of OTU
              karIndex = FALSE,           # do not add karyotype indices
              morpho = "",                # do not add morphological categories
              chrIndex = "",              # do not add chromosome indices
              
              chrColor = "black",         # chr. color
              chrWidth = 1,               # chromosome width
              karHeight = 9,              # kar. height without space
              centromereSize = 0,         # apparent centromere size
              squareness = 7,              # squareness of chr. and marks

              markLabelSize = .5,         # size of legend font
              legend = "inline",          # mark labels next to chr.
              pattern= "chr[0-9XY]+",     # REGEX pattern to remove from name of marks
              distTextChr = 6,            # distance from chr. to text.
              indexIdTextSize = 2,        # font size of chr name and indices
              lwd.chr=.5,                 # width of chr and mark borders
              colorBorderMark = "black",  # force color of border of marks 
              
              ruler= FALSE
              
              ,xlimLeftMod = 4            # space to the right of karyotype
              # ,asp=1                    # aspect ratio y x
)

References

Robertson WRB. 1916. Chromosome studies. I. Taxonomic relationships shown in the chromosomes of tettigidae and acrididae: V-shaped chromosomes and their significance in acrididae, locustidae, and gryllidae: Chromosomes and variation Journal of Morphology, 27(2): 179–331. https://onlinelibrary.wiley.com/doi/abs/10.1002/jmor.1050270202