citrusSize | R Documentation |
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.
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 )
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 |
mSizePter |
numeric, default size for P(short) ter (terminal) bands. |
mSizeQter |
numeric, default size for Q(long) ter (terminal) bands. |
mSizePprox |
numeric, default size for P prox (proximal) bands. |
mOther |
numeric, default size for other bands. |
markName |
character, default name of mark |
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) |
data.frame
data.frame
data.frame
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
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 ) )
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