Chapter 13 Functions

Here you will find how to modify the characteristics of your plots. Default values in parentheses

13.1 Function plotIdiograms

Karyotypes

dfChrSize: mandatory data.frame, with columns: OTU (optional), chrName (mandatory), shortArmSize, longArmSize for monocen. or chrSize for holocen.

defaultFontFamily: character. use this as the font family. No default value.

revOTUs: (FALSE) If TRUE, reverses the order of OTUs in data.frame dfChrSize

verticalPlot: boolean, when TRUE karyotypes are plotted vertically, otherwise, horizontally. Defaults to TRUE

karHeight: (2) Vertical size of karyotypes considering only chromosomes. for ex karHeight = 1

karHeiSpace: (2.5) Vertical size of karyotypes including spacer. for ex karHeiSpace = 1.2

karSpaceHor: numeric, separation among horizontal karyotypes. When verticalPlot=FALSE. Defaults to 0

karSepar: (TRUE) If TRUE reduces the space among karyotypes. FALSE = equally sized karyotypes or TRUE = equally spaced karyotypes. Incompatible with addMissingOTUAfter

amoSepar: (9) For karSepar = TRUE, if zero, no space among karyotypes. Amount of separation. if overlap, increase this and karHeiSpace

addMissingOTUAfter: (NA) character vector, Pass to this parameter a vector of OTUs after which empty spaces (ghost karyotypes) must be added. See missOUTspacings and the phylogeny chapter

addMissingOTUBefore: character, when you want to add space (ghost OTUs) before one or several OTUs, pass the names of OTUs after the desired space in a character vector i.e. c("species one","species five")

missOTUspacings: (0) numeric vector. With the same length of addMissingOTUAfter. Pass to this parameter the number of ghost karyotypes following the OTUs passed to addMissingOTUAfter. See the phylogeny chapter

moveKarHor: character, OTUs’ names of karyotypes that should be moved horizontally. See mkhValue

mkhValue: numeric, value to move kar. hor. See moveKarHor

karAnchorLeft: character, OTUs’ names of karyotypes to the right of your desired anchor. For verticalPlot=FALSE

karAnchorRight: character, OTUs’ add anchor to the right of this OTU (names of karyotypes). For verticalPlot=FALSE

moveAllKarValueHor: numeric, similar to mkhValue, but affects all karyotypes.

moveAllKarValueY: numeric, similar to moveAllKarValueHor, but affects y axis.

n: (50) numeric, number of vertices for the rounded corners

markN: numeric, vertices number for round corners of marks

propWidth: boolean, defaults to FALSE. Diminishes chr. width with increasing number of OTUs. For backwards compatibility

Indices

chrIndex: ("both") character, add arm ratio with "AR" and centromeric index with "CI", or "both" (Default), or "" for none to each chromosome (Levan et al., 1964). See armRatioCIalso.

chrSize: boolean, when TRUE adds total chr size under each chr. Defautls to FALSE

chrNameUp: boolean, when TRUE adds secondary chromosome name from col. chrNameUp over chrs. Defaults to FALSE

nsmall: numeric, rounding decimals for chrSize parameter. Defaults to 1

chrSizeMbp: boolean, when TRUE adds total Mbp chr. size to each chr. provided, there is a Mbp column in dfChrSize data.frame. Defaults to FALSE. If data in columns shortArmSize, or col. chrSize is in millions (“Mbp”). Use chrSize=TRUE not this one (not column Mbp, you don’t need this).

morpho: ("both") character, if "both" (default) prints the Guerra (1986) and Levan (1964) classif. of cen. position. , use also "Guerra" or "Levan" or "" for none. See ?armRatioCI also (function).

nameChrIndexPos: (2) Modify position of name (CI, AR) of chr. indices, numeric value.

karIndex: (TRUE) boolean. Adds karyotype indices A (intra - cen) and A2 (inter - size) (Romero-Zarco, 1986; Watanabe et al., 1999). Disable with karIndex = FALSE

karIndexPos: (0.5) numeric. Modify position of karyotype indices, to the left or right

indexIdTextSize: font size of chr. and kar. indices and chromosome name

distTextChr: Vertical distance from indices (text) to the chromosome.

markPer: character, name of mark to calculate % of mark in chr. and add it to plot. See perAsFraction

perAsFraction: boolean, when TRUE % is shown as fraction. Defaults to FALSE. See markPer

showMarkPos: boolean, adds position of marks under karyotype (fraction 0-1) when TRUE. Defaults to FALSE

bToRemove: character, bands to remove from calc. of pos.

Anchor

anchor: boolean, when TRUE, plots a parent progeny structure in karyotypes in moveKarHor

anchorText: character, text to add to anchor structure near symbol. See anchor. Defaults to ""

anchorTextMoveX: numeric, for vertical plots with anchorText move text in X axis. Defaults to 0.5

anchorTextMoveY: numeric, for horizontal plots with anchorText move text in Y axis. Defaults to 1

anchorTextMParental: character, designed to fill with a character object the space left of a missing parental in the anchor structure.

anchorTextMoveParenX: numeric, for plots with anchorTextMParental move text in X axis. Defaults to 0

anchorTextMoveParenY: numeric, for plots with anchorTextMParental move text in Y axis. Defaults to 0

anchorLineLty: numeric, type of line in anchor, corresponds to lty. Defaults to 1

anchorVsizeF numeric, factor to modify vertical size of anchor 0.5 (default). Size itself is equal to karHeiSpace

moveAnchorV: numeric, displace anchor vertical portion to right or left. See anchor

moveAnchorH: numeric, displace anchor horizontal portion to right or left. See anchor

pchAnchor: numeric, symbol for anchor, see ?points and anchor

moveKarHor: character, OTUs’ names of karyotypes that should be moved horizontally. See mkhValue

mkhValue: numeric, value to move kar. hor. See moveKarHor

Notes

notes: data.frame with columns OTU and note for adding notes to each OTU, they appear to the right of the karyotype

leftNotes: data.frame with columns OTU and note for adding notes to each OTU, they appear to the left of the karyotype

leftNotesUp: data.frame, (to the left), similar to leftNotes, but intended for placement over kar.

notesTextSize: (0.4) numeric, font size of notes, see notes

notesPosX: (0.5) numeric, moves right notes in the x axis

leftNotesPosX: (0.5) numeric, moves left notes in the x axis

notesPosY: numeric, move right notes down or up (y axis)

leftNotesPosY: numeric, move leftNotes down or up (y axis)

leftNotesUpPosY: numeric, move leftNotesUp down or up (y axis)

noteFont: numeric 1 for normal, 2 for bold, 3 for italics, 4 for bold-italics. See notes

leftNoteFont: numeric 1 for normal, 2 for bold, 3 for italics, 4 for bold-italics. See leftNotes

leftNoteFontUp: numeric 1 for normal, 2 for bold, 3 for italics, 4 for bold-italics. See leftNotesUp

parseTypes: boolean, parse in notes the Citrus chr. types names. Creates subindex pos. for FL. Defaults to TRUE

parseStr2lang: bolean, parse string in notes with function str2lang(paste0("paste(",note,")") ) for ex: "italic('C. sinensis'), ' Author'". See notes, leftNotes,leftNotesUp.

Units

MbThreshold: (10000) numeric. If chrSize > 10000 will be considered Mb. See MbUnit

threshold: (35) This is the max. value allowed for the main two significative digits, otherwise scale will shrink. For example, after 35 μm (Default), apparent size will be 3.5 (not 35) and scale interval will change. See ceilingFactor: you may have to use -1 for it. Introduced in 1.13

MbUnit: (Mb) character, text of units of title when MbThreshold met and OTU not in specialOTUNames. Introduced in 1.13. See specialyTitle

yTitle: (μm) character, units for common title.

specialyTitle: character, title of ruler if OTU is in specialOTUNames. Will not apply if MbThreshold met. In that case use MbUnit

specialOTUNames: character vector, normally title of ruler is μm or Mb (big numbers). Use this param. to be able to put a different unit in ruler title. See specialyTitle

classMbName: character, name of “chromosome” when in Mbp. Defaults to "Pm". See MbUnit

classcMName: character, name of “chromosome” when OTU in specialOTUNames. Defaults to "L.G."

classChrName: character, name of “chromosome” when in micrometers (apparently). Defaults to "Chr.". See specialOTUnames, classMbName, classcMName

classChrNameUp: character, name of “chromosome” for col. "chrNameUp". Defaults to "Type"

classGroupName: character, name of groups. Defaults to ""

OTU names

addOTUName: (TRUE) If TRUE adds name of species (OTU) under karyotype

OTUTextSize: (1) font size of OTU names, except when OTUasNote=TRUE see notesTextSize

OTUfont: numeric, 1 for normal, 2 for bold, 3 for italics, 4 for bold-italics

OTUfamily: character, font family for OTU name.

OTUasNote: (FALSE) See also notes. If TRUE OTU name is written to the right, as notes.

OTUasLeftNote: boolean, when TRUE adds OTU (species) name to the left-up

Chromosomes

chrNameUp: boolean, when TRUE adds secondary chromosome name from col. chrNameUp over chrs. Defaults to FALSE

orderBySize: deprecated

roundness: deprecated, See squareness

orderChr: ("size") size sorts chromosomes from the largest to the smallest. Other options: original, name, group (requires group column)

chrId: ("original") If you want to rename chromosomes from 1 to n use chrId = "simple". For original names use chrId = "original". For no names use chrId = ""

chrIdPatternRem: character, regex pattern to remove from chr. names

indexIdTextSize: (1) font size of chr. and kar. indices and chromosome name

distTextChr: (1) Vertical distance from name (text) of chromosome to the chromosome.

chrWidth: (0.5) Determines the width of chromosomes

chrSpacing: (0.5) Determines the horizontal spacing among chromosomes

chrColor: ("gray") Determines the color of chromosomes

squareness: (4) Make squared or rounded vertices for chromosomes. Smaller numbers = more rounded

lwd.chr: (0.5) thickness of border of chr., some marks; ruler. Also thick of cM marks when lwd.cM absent

Groups

groupSepar: numeric, factor for affecting chr. spacing chrSpacing among groups. Defaults to 0.5

groupUp: boolean, when TRUE, when groups present, they appear over the chr. name. Defaults to FALSE

groupName boolean, when TRUE (default), shows group names. When FALSE only line

Centromeres

centromereSize: Apparent size of centromeres. Automatic when absent.

cenColor: Determines the color of centromeres. if GISH use NULL. Defaults to chrColor

fixCenBorder: boolean, when TRUE uses chrColor as centromere (and cen. mark) border color. See also cenColor, chrColor, colorBorderMark, borderOfWhiteMarks. No default value.

roundedCen: deprecated, see cenFormat

cenFormat: character, when "triangle", cen. has triangular aspect. When "rounded", it has rounded aspect (Default). "inProtein" for using the mark with style of same name.

cenFactor: numeric, modifies any cen. mark and cen. size. Defaults to 1

Chromatids

chromatids: boolean, when TRUE shows separated chromatids. Defaults to TRUE

arrowsBothChrt: boolean, when TRUE (default) (for chromatids=TRUE) shows upArrow, downArrow styles of marks in both chromatids when arrowsToSide=TRUE.

holocenNotAsChromatids: boolean, when TRUE and chromatids=TRUE does not plot holocen kar. with chromatids. Defaults to FALSE. A value of TRUE modifies excHoloFrArrToSide to TRUE always.

xModifier: numeric, for chromatids=TRUE, separation among chromatids. Quotient for chrWidth. Defaults to 12 : chrWidth/12

xModMonoHoloRate: numeric, factor to shrink xModifier for holocen. 5 means 5 times smaller (quotient).

Marks

dfMarkPos: pass to this argument the name of the data.frame of positions of marks. Currently includes GISH and centromeric marks (cen). See previous chapters. columns: OTU (opt), chrName, markName (name of site), chrRegion (for monocen. and opt for whole arm (w) in holocen.), markDistCen (for monocen.), markPos (for holocen.), markSize; column chrRegion: use p for short arm, q for long arm, cen for centromeric mark and w for whole chr. mark; column markDistCen: use distance from centromere to mark, not necessary for cen. marks (cen), w, p, q (when whole arm). See also param. markDistType

dfMarkColor: pass to this argument the name of the data.frame of marks characteristics, see previous chapters. Not mandatory for plotting marks. Specifying colors and style for marks (sites); columns: markName, markColor, style. style accepts: "square","squareLeft", "dots", "cM", "cMLeft","cenStyle", "upArrow", "downArrow", "exProtein". (if column style missing all (except 5S) are plotted as in param. defaultStyleMark). “cM” introduced in 1.13

roundness: Deprecated.

squareness: (4) Squared or rounded vertices when marks of the “square” style (defined in data.frame passed to dfMarkColor). Affects chromosomes also. Smaller numbers = more rounded

dfCenMarks: Only for centromereSize > 0, pass to this argument the name of data.frame of centromeric marks. Currently included in dfMarkPos. See previous chapters.

defaultStyleMark: character, default style of mark, only used when style column of dfMarkColor data.frame is missing or in absence of this data.frame. Use "square" (default),"squareLeft", "dots", "cM", "cMLeft","cenStyle", "upArrow", "downArrow".

markDistType: ("beg") If you measure your marks to the beginning of mark use markDistType = "beg", if to the center of the mark, use "cen".

origin: ("b") If you measure your mark from the bottom of chromosome use origin = "b", or "t" from top. Applies to holocentrics. (monocentrics marks are measured from centromere)

efZero: numeric, internal, numbers below this one will be considered as zero, for comparison purposes. Defaults to 1e-5

cMBeginCenter: boolean, start position of cM and cMLeft marks. If TRUE, starts in the center (width) of chr. . Defaults to FALSE

protruding: (0.2) numeric, when style of mark is “cM,” “upArrow,” “downArrow” (inline), fraction of chrWidth to stretch marker.

startPos: numeric, factor to increase separation of exProtein marks to chromosome. Defaults to 0

pMarkFac: numeric, fraction of chr. size for exProtein style marks. Defaults to 0.25

dotRoundCorr: numeric, to be deprecated, requires useXYfactor=TRUE corrects roundness of dots and vertices of chromosomes. When style of sites = dots, an increase in this, makes the horizontal radius of the dot smaller. Use asp=1 instead

useXYfactor : boolean, for backwards compatibility, for using dotRoundCorr. Defaults to FALSE

useOneDot: boolean, use one dot instead of two in style of marks dots. Defaults to FALSE

dotsAsOval: boolean, use oval instead of two dots in style of marks dots. Defaults to FALSE. See useOneDot. Not useful for chromatids=TRUE or circularPlot=TRUE

markN: numeric, vertices number for round corners of marks

Color

mycolors: optional, character vector with colors’ names, which are associated automatically with marks according to their order in the data.frame of position of marks. See this ordering with unique(dfMarkPos$markName). Argument example: mycolors = c("red","chartreuse3","dodgerblue"). Not mandatory for plotting marks, package has default colors.

defCenStyleCol: character, color of outer part of cenStyle marks. Defaults to white

Borders

chrBorderColor: character, color for border of chromosomes, defaults to chrColor

gishCenBorder: boolean, when TRUE, cen. mark border color is the same as mark color, ignoring colorBorderMark. No default.

hideCenLines: numeric, factor to multiply line width (lwd) used for covering cen. border, when chrColor is white or when gishCenBorder=TRUE

borderOfWhiteMarks: (TRUE) boolean, when TRUE uses black border for white marks. See dfMarkColor. Does not apply to marks with cenStyle

colorBorderMark: character, without default, pass a name of a color to use as border of marks. See borderOfWhiteMarks

fixCenBorder: boolean, when TRUE uses chrColor as centromere (and cen. mark) border color. See also cenColor, chrColor, colorBorderMark, borderOfWhiteMarks. No default value.

lwd.chr: (0.5) width of border lines for chr. and marks when related param. absent.

lwd.mimicCen: thickness of lines of cenStyle marks; affects only lateral borders. Defaults to lwd.chr

lwd.marks: thickness of most marks. Except cM marks and centr. related marks. See lwd.chr, lwd.cM

lwd.cM: thickness of cM marks. Defaults to lwd.chr

Arrows

excHoloFrArrToSide: boolean, when arrowsToSide=TRUE, excludes holocen. from this behaviour, plotting a centered arrow only.

arrowhead numeric, proportion of head of arrow (mark styles: upArrow,downArrow). Defaults to 0.3

shrinkArrow numeric, proportion, shrinks body of arrow. Defaults to 0.3333

arrowheadWidthShrink numeric, proportion, shrinks head of arrow. Defaults to 0.1

arrowsToSide boolean, when FALSE use a centered arrow, instead of an arrow next to chr. margins. Defaults to TRUE. See arrowsBothChrt

arrowsBothChrt: boolean, when TRUE (default) (for chromatids=TRUE) shows upArrow, downArrow styles of marks in both chromatids when arrowsToSide=TRUE.

cMBeginCenter: boolean, start position of cM and cMLeft marks. If TRUE, starts in the center (width) of chr. . Defaults to FALSE

protruding: (0.2) numeric, when style of mark is “cM,” “upArrow,” “downArrow” (inline), fraction of chrWidth to stretch marker.

Labels

This parameters have to do with the legends

pattern: ("") REGEX pattern to eliminate from the marks name when plotting. See human karyotype chapter for example.

legend: ("aside") If you wanto to plot the names of marks near each chromosome use legend = "inline", to the right of karyotypes use legend = "aside", otherwise use legend = "" for no legend. See markLabelSpacer

remSimiMarkLeg: boolean, when legend="aside", if you use pattern, you can have several marks with same name. When TRUE this remove this pseudoduplicates from legend. Be sure that this pseudoduplicates have the same color, otherwise you should use FALSE (default).

bannedMarkName: character, character string or vector with mark names to be removed from plot. Not the marks but the labels. See bMarkNameAside

bMarkNameAside: boolean, when TRUE and legend="inline", shows marks in bannedMarkName as legend="aside" would do. See bannedMarkName

forbiddenMark: character, character string or vector with mark names to be removed from plot. Not the marks but the labels.

legendWidth: (1.7) numeric, factor to modify the width of the square and dots of legend. For legend="aside".

legendHeight: (NA) numeric, factor to modify the height of the square and dots of legend. For legend="aside".

markLabelSize: (1) Determines the size of text of the legend.

markLabelSpacer: (1) When legend = "aside" determines the separation of legends from the karyotype right side

legendYcoord: numeric, modify Y position of legend when legend="aside"

markNewLine: character, character to split mark Names into different lines. Applies to square marks. Defaults to NA

mylheight: numeric, for markNewLine!=NA; is equivalent to lheight of par: “The line height multiplier. The height of a line of text (used to vertically space multi-line text) is found by multiplying the character height both by the current character expansion and by the line height multiplier.” Defaults to 0.7.

Rulers

ruler: (TRUE) When TRUE displays ruler to the left of karyotype, when FALSE shows no ruler

rulerPos: (-0.5) Absolute position of ruler, corresponds to “pos” argument of the function axis of R plots

rulerPosMod: Deprecated

ruler.tck: (-0.02) tick size of ruler, corresponds to “tck” argument of axis function

rulerNumberPos: (0.5) numeric, Modify position of numbers of ruler

rulerNumberSize: (1) Size of number’s font in ruler

rulerInterval: numeric, intervals in ruler. No default, automatic. Introduced in 1.13

rulerIntervalcM: numeric, intervals in ruler of OTU in specialOTUNames. No default. Introduced in 1.13

rulerIntervalMb: numeric, intervals in ruler of OTU with data in Mb (>MbThreshold) and absent from specialOTUNames. No default. Introduced in 1.13

ceilingFactor: (0) numeric, affects number of decimals for ceiling. Affects max. value of ruler. When threshold is greater than 35 this may have to be negative. Introduced in 1.13

xPosRulerTitle: (2.6) Modifies the horizontal position of the title of rulers (Mb, etc). Moves to left from 1st chr. in chrSpacing times

yPosRulerTitle: numeric, affects vertical position of ruler title. Defaults to 0

rulerTitleSize: Font size of units (title).

useMinorTicks: boolean, display minor ticks between labeled ticks in ruler. See miniTickFactor. Defaults to FALSE. (ticks without label)

miniTickFactor: numeric, number of minor ticks for each labeled tick. See useMinorTicks. Defaults to 10

Margins

You can establish margins with par as in any R plot, and also with this parameters. These works as a quick fix to increase desired size of plot when some elements are outside of margins:

xlimLeftMod: (1) modifies xlim left (first) component of the plot as in any “R-plot”

xlimRightMod: (2) xlim (right) modification by adding space to the right of idiograms

ylimBotMod: (0.2) modify ylim bottom component of plot adding more space

ylimTopMod: (0.2) modify ylim top component of plot adding more space.

callPlot: boolean, create new plot in your device. Defaults to TRUE

asp: numeric, y x aspect of plot. Defautls to 1

… accepts other arguments for the plot. See ?plot

Circular plot

circularPlot: boolean, if TRUE chromosomes are plotted in concentric circles. Defaults to FALSE. See verticalPlot

shrinkFactor: numeric, for circularPlot=TRUE percentage of usage of circle. Defaults to 0.9

separFactor: numeric, for circularPlot=TRUE modify separation of concentric karyotypes. Defaults to 1.5

labelSpacing: numeric, for circularPlot=TRUE. Spacing of mark labels. Defaults to 0.7

labelOutwards: boolean, inline labels projected outwards

chrLabelSpacing: numeric, for circularPlot=TRUE. Spacing of chr. labels. Defaults to 0.5

radius: numeric, for circularPlot=TRUE. Affects radius of karyotypes. Defaults to 0.5

rotation: numeric, anti-clockwise rotation, defaults to 0.5 which rotates first chr. from top to -90 degrees. (-0.5*π = 9 o’clock)

circleCenter: numeric, for circularPlot=TRUE. Affects coordinates of center of circles. Affects legend="aside" position.

circleCenterY: numeric, for circularPlot=TRUE. Affects coordinates of center of circles. Affects legend="aside" position.

13.2 Function robert

chr1: name of chr. See ?robert

chr2: name of chr. ?robert

arm1: arm of chr1 to be included ?robert

arm2: arm of chr2 to be included ?robert

13.3 Function genBankReadIF

filename.gb: name of file to read, downloaded from genBank, or name of genbank object produced with rentrez::entrez_fetch(db="nuccore", id="theID", rettype="gbwithparts", retmode = "text")

13.4 Function namesToColumns

marksDf: data.frame with columns: markName,style,markPos

dfChrSize: data.frame, size of chr. Same of plot.

markType: (c("downArrow","upArrow","cMLeft","cM")), character, mark to arrange in columns

amountofSpaces: (13) numeric, number of characters for each column

colNumber: (2) numeric, number of columns

protruding: (0.5) numeric, same as plot, minimal protruding for arrow marks, equivalent to cM protruding

protrudingInt: (0.5) numeric, spacing of columns in terms of width of chr. percent 1 = 100%. Defaults to 0.5

circularPlot: (TRUE) boolean, use TRUE for circular plots. Use FALSE otherwise

rotation: (0.5) numeric, same as plot, anti-clockwise rotation, defaults to 0.5 which rotates chr. from top to -90 degrees. (-0.5*π )

defaultStyleMark: ("square") character, if some data in column style missing fill with this one. Defaults to “square”

orderBySize: Deprecated

orderChr: (size) character, when "size", sorts chromosomes by total length from the largest to the smallest. "original": preserves d.f. order. "name": sorts alphabetically; "group": sorts by group name; "chrNameUp": sorts according to column chrNameUp. See chrNameUp

halfModDown: (NA) numeric, for circ. plots, when plotting several chromosomes in a circular plot, using a small value 0.05 corrects for alignment problems of downArrows, cMLeft labels. Defaults to NA

halfModUp: (NA) numeric, for circ. plots, when plotting several chromosomes in a circular plot, using a small value 0.05 corrects for alignment problems of upArrows, cM labels. Defaults to NA

rotatMod: (0) numeric, for circ. plots, when rotation != 0 (diff.), corrects alignment of labels. Defaults to 0

13.5 Function citrusSize

A: number of A to calculate

B: number of B to calculate

C: number of C to calculate

D: number of D to calculate

E: number of E to calculate

F: number of F to calculate

FL: number of FL+ to calculate

FL0: number of FL0 to calculate

G: number of G to calculate

shortArm: for A to G (not FL)

longArm: for A to G (not FL)

shortArmFL: for FL

longArmFL: for FL

OTU: name of species

13.6 Function citrusMarkPos

chrSizeDf: data.frame created with citrusSize function

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

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

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

mOther: numeric, default size for other bands. 0.25 (default)

markName: character, default name of mark “CMA,” or “45S,” respectively. (citrusMarkPos,markOverCMA)

13.7 Function markOverCMA

markName: character, default name of mark “CMA,” or “45S,” respectively.

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 to duplicate mark (markOverCMA)

chrRegion: character, arm, defaults to “p.” for mark duplication (markOverCMA)

13.8 Other functions

Use ?function

armRatioCI(dfChrSize)

swapChrRegionDfSizeAndMarks(dfChrSize, dfMarkPos, chrNamesToSwap)

asymmetry(dfChrSize)

asymmetryA2(dfChrSize)

13.9 helper functions for ggplot

mapChr <- mapGGChr(dfChrSizeHolo)

mapChrMark <- mapGGChrMark(dfChrSizeHolo,dfMarkPosHolo)