5 Multiple OTUs

Jupyter interactive version:

5.1 Example with several species (OTUs) - mono.

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

  • Chromosome sizes
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(dfMarkColorIn) 
markName markColor style
5S red dots
45S chartreuse3 square
DAPI blue square
CMA darkgoldenrod1 square
proteinD darkgreen inProtein
  • Mark position
data(bigdfMarkPosHolo2)
OTU chrName markName markPos markSize chrRegion
species two 3 5S 1.0 0.5 NA
species two 3 DAPI 1.5 0.5 NA
species two 1 45S 2.0 0.5 NA
species two 2 DAPI 2.0 0.5 NA
species two 4 CMA 2.0 0.5 NA
species two 4 5S 0.5 0.5 NA
species one 1 proteinD NA NA w
species one 2 proteinD NA NA w
species one 3 proteinD NA NA w
species one 4 proteinD NA NA w
species two 1 proteinD NA NA w
species two 2 proteinD NA NA w
species two 3 proteinD NA NA w
species two 4 proteinD NA NA w
species three 1 proteinD NA NA w
species three 2 proteinD NA NA w
species three 3 proteinD NA NA w
species three 4 proteinD NA NA w

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 = dfMarkColorIn,   # df of mark style
  dfMarkPos = bigdfMarkPosHolo2, # 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()