Chapter 5 Multiple OTUs


Jupyter interactive version:

Colab (online) Github   Raw
5 Multiple OTUs link Raw


5.1 Example with several species (OTUs) - mono.

To illustrate this, we will load some data.frames from the package

  • Chromosome sizes
require(idiogramFISH)
head(bigdfOfChrSize,15)
OTU chrName shortArmSize longArmSize
Species 1 1 1.5 2.0
Species 1 2 2.0 2.5
Species 1 3 1.0 2.0
Species 2 1 3.0 4.0
Species 2 2 4.0 5.0
Species 2 3 2.0 3.0
Species 2 X 1.0 2.0
Species 2 4 3.0 4.0
Species 3 1 3.2 4.0
Species 3 2 4.5 5.0
Species 3 3 2.0 3.0
Species 3 4 1.5 2.0
Species 3 5 4.8 6.0
Species 3 6 6.1 7.0
Species 4 1 1.5 2.0
  • Mark characteristics, does not require OTU
  • df optional for ver > 1.0.0
data("dfMarkColor")
markName markColor style
5S red dots
45S chartreuse3 square
DAPI blue square
CMA darkgoldenrod1 square
  • Mark position
data("bigdfOfMarks")
OTU chrName markName chrRegion markDistCen markSize
Species 1 1 5S p 0.5 1
Species 1 1 45S q 0.5 1
Species 1 2 45S p 1.0 1
Species 1 3 DAPI q 1.0 1
Species 3 3 5S p 1.0 1
Species 3 3 DAPI q 1.0 1
Species 3 4 45S p NA NA
Species 3 4 DAPI q 1.0 1
Species 3 5 CMA q 2.0 1
Species 3 6 5S q 0.5 1
Species 2 1 DAPI cen NA NA
Species 2 4 CMA cen NA NA

Plotting

# png("bigdfOfChrSize.png", width=650, height=1300)
par(mar = c(0, 0, 0, 0))
plotIdiograms(dfChrSize  =bigdfOfChrSize,# chr. sizes
              dfMarkColor=dfMarkColor,   # mark characteristics, optional in dev version. see above. 
              dfMarkPos  =bigdfOfMarks,  # mark positions (inc. cen. marks)

              karHeight=2.5,             # karyotype rel. height
              karHeiSpace=6,             # karyotype vertical size with spacing
              chrWidth = .35,            # chr. width
              amoSepar = 2,              # Vertical separation of kar. when karSepar = TRUE
              
              squareness = 4,            # squareness of chr. vertices
              distTextChr=.8,            # distance of chr. to text
              chrIndex = "AR",           # add arm ratio only. For v. >=1.12
              nameChrIndexPos = 3,
              morpho="Guerra",           # add chr. morphology by Guerra, see above. For v. >=1.12
              indexIdTextSize=.6,        # font size of indices and chr. name
              OTUTextSize=.9,            # font size of OTU names
              
              markLabelSize=.7,          # font size of legend
              fixCenBorder = TRUE,       # use chrColor as border color of cen. or cen. marks
              legendHeight = 2,          # height of labels
              
              rulerPos=-1,               # position of ruler
              ruler.tck=-0.004,          # size and orient. of ticks in ruler
              rulerNumberPos=.4,         # position of numbers of ruler
              rulerNumberSize=.4,        # font size of ruler
              xPosRulerTitle = 5,        # ruler units pos.
              rulerTitleSize=.5,         # ruler font size of units (title)

              xlimRightMod = 3,          # modify xlim left argument 
              xlimLeftMod = 2,           # modify xlim left argument 
              ylimBotMod = 0,            # modify ylim bottom argument
              ylimTopMod = -.3           # modify ylim top argument
); # dev.off() # for png()

5.2 Example with several species (OTUs) - holo.

To illustrate this, we will load some data.frames from the package

  • Chromosome sizes
data(bigdfChrSizeHolo)
OTU chrName chrSize
species one 1 5.1
species one 2 5.0
species one 3 4.9
species one 4 5.2
species two 1 3.0
species two 2 4.0
species two 3 2.0
species two 4 5.0
species three 1 1.5
species three 2 2.0
species three 3 6.0
species three 4 8.0
  • Mark characteristics, does not require OTU
  • d.f optional for ver. > 1.0.0
data(dfMarkColor) 
markName markColor style
5S red dots
45S chartreuse3 square
DAPI blue square
CMA darkgoldenrod1 square
  • Mark position
data(bigdfMarkPosHolo)
OTU chrName markName markPos markSize
species two 3 5S 1.0 0.5
species two 3 DAPI 2.0 0.5
species two 1 45S 2.0 0.5
species two 2 DAPI 2.0 0.5
species two 4 CMA 2.0 0.5
species two 4 5S 0.5 0.5

Plotting

library(idiogramFISH)

# fig.width=6, fig.height=6
png("bigdfChrSizeHolo.png", width=600, height=600)
par(mar=rep(0,4)) 

plotIdiograms(dfChrSize=bigdfChrSizeHolo, # chr. size data.frame
              dfMarkColor=dfMarkColor,    # df of mark style
              dfMarkPos=bigdfMarkPosHolo, # df of marks' position
              
              markDistType="cen",         # measure towards center of mark
              squareness=6,               # vertices squareness of chr. and marks 
              
              karHeiSpace = 4,            # karyotype height including spacing
              karSepar=TRUE,              # reduce vertical space among karyotypes 
              amoSepar = 1,               # separation among karyotypes
              distTextChr=.5,             # distance text to chr.
              
              legendWidth = 1             # width of legend labels
              
              ,chrId="simple",            # numbering of chr., not using "original" name
              
              indexIdTextSize=.9,         # font size of chr names and indices
              markLabelSize=.9,           # font size of legends
              
              rulerPos=0,                 # position of ruler
              rulerNumberSize=.9,         # font size of ruler
              ruler.tck= -.004,           # tick length and orient.
              xPosRulerTitle = 3,         # position of ruler units (title)
              
              ylimBotMod=.4               # modify ylim bottom argument
              ,xModifier = 50             # separation among chromatids
)
dev.off()