idiogramFISH (version 2.0.0)

citrusSize: FUNCTIONS: citrusSize, citrusMarkPos, markOverCMA

Description

Helper function to create data.frames with chr. size and mark size data for Citrus based on categories in Carvalho et al. (2005)

Special behaviour while plotting: normally you will get chr. names as: B_1, B_2, etc. to remove _*, use chrIdPatternRem='_.*' in plotIdiograms. However, for FL+ and FL0, this conversion is automatic. So, in plot you will never see FL0_1, FL0_2, for example.

Usage

citrusSize(
  A = 0,
  B = 0,
  C = 0,
  D = 0,
  E = 0,
  F = 0,
  FL = 0,
  FL0 = 0,
  G = 0,
  shortArm = 1.2,
  longArm = 1.7,
  shortArmFL = 1.3,
  longArmFL = 1.8,
  OTU = "OTU 1"
)
citrusMarkPos(
  chrSizeDf,
  mSizePter = 0.25,
  mSizeQter = 0.35,
  mSizePprox = 0.35,
  mOther = 0.25,
  markName = "CMA"
)
markOverCMA(
  citrusMarkPosDF,
  chrType = "B",
  chrName,
  chrRegion = "p",
  markName = "45S",
  shrinkMark = TRUE
)

Arguments

A

number of A to calculate (citrusSize)

B

number of B to calculate (citrusSize)

C

number of C to calculate (citrusSize)

D

number of D to calculate (citrusSize)

E

number of E to calculate (citrusSize)

F

number of F to calculate (citrusSize)

FL

number of FL+ to calculate (citrusSize)

FL0

number of FL0 to calculate (citrusSize)

G

number of G to calculate (citrusSize)

shortArm

for A to G (not FL) (citrusSize)

longArm

for A to G (not FL) (citrusSize)

shortArmFL

for FL (citrusSize)

longArmFL

for FL (citrusSize)

OTU

name of species (citrusSize)

chrSizeDf

data.frame created with citrusSize function (citrusMarkPos)

mSizePter

numeric, default size for P(short) ter (terminal) bands. 0.25 (default) (citrusMarkPos)

mSizeQter

numeric, default size for Q(long) ter (terminal) bands. 0.35 (default) (citrusMarkPos)

mSizePprox

numeric, default size for P prox (proximal) bands. 0.35 (default) (citrusMarkPos)

mOther

numeric, default size for other bands. 0.25 (default) (citrusMarkPos)

markName

character, default name of mark "CMA", or "45S", respectively. (citrusMarkPos,markOverCMA)

citrusMarkPosDF

data.frame, with CMA marks (markOverCMA)

chrType

character, defaults to "B", chr. type to duplicate mark (markOverCMA)

chrName

character, defaults to "B", chr. name(s) to duplicate mark (markOverCMA)

chrRegion

character, arm, defaults to "p". for mark duplication (markOverCMA)

shrinkMark

boolean, shrink new mark to be created (markOverCMA)

Value

data.frame

data.frame

data.frame

References

Carvalho, R., Soares Filho, W. S., Brasileiro-Vidal, A. C., & Guerra, M. (2005). The relationships among lemons, limes and citron: A chromosomal comparison. Cytogenetic and Genome Research, 109(1<U+2013>3), 276<U+2013>282. https://doi.org/10.1159/000082410

Examples

# NOT RUN {
citrusSizeDF <- citrusSize(B=1,D=11,F=4,FL0=2,OTU="C. jambhiri")
suppressMessages(
plotIdiograms(citrusSizeDF,
              indexIdTextSize=.4,# font size
              rulerNumberSize=.4,# font size
              rulerTitleSize=.4, # font size
              rulerPos =-.5,     # ruler pos.
              xPosRulerTitle =1.5,     # ruler title pos.
              orderChr="original"# order of chr. as in d.f.
              )
              )
citrusSizeDF2 <- citrusSize(B=2,D=10,F=4,FL0=1,
FL=1,         # equivalent to FL+
OTU="C. limettioides")


suppressMessages(
 plotIdiograms(citrusSizeDF2,     # FL^NA error corrected in 1.15.4
               indexIdTextSize=.4,# font size
               rulerNumberSize=.4,# font size
               rulerTitleSize=.4, # font size
               rulerPos =-.5,     # ruler pos.
               xPosRulerTitle =1.5,     # ruler title pos.
               orderChr="original"# order of chr. as in d.f.
 )
)

citrusMarkPosDF <- citrusMarkPos(citrusSizeDF)
suppressMessages(
plotIdiograms(dfChrSize= citrusSizeDF,      # chr. size data.frame
              dfMarkPos= citrusMarkPosDF,# mark position data.frame (inc. cen.)
              ruler=FALSE,               # remove
              chrIndex=FALSE,            # remove
              morpho=FALSE,              # remove
              karIndex=FALSE,            # remove
              indexIdTextSize=.4,        # font size
              xlimRightMod=4,            # xlim mod.
              orderChr="original",       # order chr. as in d.f.
              chrColor="blue",           # chr. color
              legendHeight=3             # legend item height
              )
              )
citrusMarkPosDF45S<-markOverCMA(citrusMarkPosDF, chrType="B", chrRegion="p", markName="45S")
suppressMessages(
plotIdiograms(dfChrSize= citrusSizeDF, # chr. size data.frame
              dfMarkPos= citrusMarkPosDF45S,# mark position data.frame (inc. cen.)
              ruler=FALSE,             # remove ruler
              chrIndex=FALSE,          # remove index
              morpho=FALSE,            # remove morphol.
              karIndex=FALSE,          # remove
              indexIdTextSize=.4,      # font size chr.
              xlimRightMod=4,          # modify xlim
              orderChr="original",     # as in d.f.
              chrColor="blue",
              legendHeight=5,          # height of legend item
              colorBorderMark="black", # mark border color
              OTUfont=3                # italics
              )
              )
# }