citrusSize: FUNCTIONS: citrusSize, citrusMarkPos, markOverCMA

In idiogramFISH: Shiny App. Idiograms with Marks and Karyotype Indices

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(1-3), 276-282. https://doi.org/10.1159/000082410

Examples

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
)
)

idiogramFISH documentation built on Aug. 22, 2023, 5:08 p.m.