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()