plotIdiograms {idiogramFISH}

Plot idiograms of karyotypes/genomes with and without centromere

Description

This function reads a data.frame passed to dfChrSize with columns: chrName (mono/holo) and shortArmSize and longArmSize for monocentrics or a column chrSize for holocentrics and produces a plot of idiograms. If more than one species, a column named OTU is needed.

Optionally, it reads another data.frame passed to dfMarkPos with the position of marks (sites). Examples: markposDFs. Another data.frame for mark characteristics can be used dfMarkColor or a character vector passed to mycolors

Usage

 plotIdiograms( dfChrSize, defaultFontFamily, revOTUs = FALSE,
 karHeight = 2, karHeiSpace = 2.5, karSepar = TRUE, amoSepar = 10,
 addMissingOTUAfter = NA, addMissingOTUBefore = NA, missOTUspacings = 0,
 moveKarHor = "", moveAllKarValueHor = 0, moveAllKarValueY = 0,
 karAnchorLeft = "", karAnchorRight = "", anchor = FALSE, anchorLineLty = 1,
 anchorText = "", anchorTextMParental, anchorTextMoveX = 0.5,
 anchorTextMoveY = 1, anchorTextMoveParenX = 0, anchorTextMoveParenY = 0,
 anchorVsizeF = 0.5, anchorHsizeF = 1, pchAnchor = 23, moveAnchorV = 0,
 moveAnchorH = 0, mkhValue = 0.5, n = 50, markN = 25, notes, leftNotes,
 leftNotesUp, notesTextSize = 1, leftNotesTextSize = 1, leftNotesUpTextSize = 1,
 notesLeft, notesPosX = 0.5, notesPosY = 0, leftNotesPosX = 0.5,
 leftNotesPosY = 0, leftNotesUpPosX = 0.5, leftNotesUpPosY = 0, noteFont = 1,
 leftNoteFont = 1, leftNoteFontUp = 1, parseTypes = TRUE, parseStr2lang = FALSE,
 propWidth = FALSE, MbThreshold = 10000, threshold = 35, MbUnit = "Mb",
 yTitle = "µm", specialyTitle = "cM", specialOTUNames = "", addOTUName = TRUE,
 OTUTextSize = 1, OTUfont, OTUfamily = "", OTUasNote = FALSE,
 OTUasLeftNote = FALSE, orderChr = "size", chrId = "original",
 classMbName = "Pm.", classcMName = "L.G.", classChrName = "Chr.",
 classChrNameUp = "Type", classGroupName = "", chrNameUp = FALSE,
 chrIdPatternRem, indexIdTextSize = 1, distTextChr = 1, groupUp = FALSE,
 groupName = TRUE, groupSepar = 0.5, chromatids = TRUE, arrowsBothChrt = TRUE,
 holocenNotAsChromatids = FALSE, excHoloFrArrToSide = FALSE, xModifier = 12,
 xModMonoHoloRate = 1, chrWidth = 0.5, chrSpacing = 0.5, specialChrWidth = 0.3,
 specialChrSpacing = 0.7, chrColor = "gray", chrBorderColor, centromereSize = 0,
 autoCenSize = TRUE, cenColor, fixCenBorder = NULL, gishCenBorder = FALSE,
 hideCenLines = 1.75, roundedCen, cenFormat = "rounded", cenFactor = 1,
 squareness = 4, lwd.chr = 0.5, lwd.cM, lwd.marks = 99, dfMarkPos,
 defaultStyleMark = "square", markDistType = "beg", protruding = 0.2,
 startPos = 0, pMarkFac = 0.25, origin = "b", efZero = 1e-05,
 cMBeginCenter = FALSE, arrowhead = 0.3, shrinkArrow = 0.3333,
 arrowheadWidthShrink = 0.1, arrowsToSide = TRUE, useOneDot = FALSE,
 dotsAsOval = FALSE, dfMarkColor, mycolors, alpha_val = 1,
 borderOfWhiteMarks = TRUE, colorBorderMark = "", lwd.mimicCen, defCenStyleCol,
 pattern = "", legend = "aside", remSimiMarkLeg = TRUE, bannedMarkName,
 bMarkNameAside = FALSE, forbiddenMark, legendWidth = 1.7, legendHeight = NA,
 markLabelSize = 1, markLabelSpacer = 1, legendYcoord = 0, markNewLine = NA,
 mylheight = 0.7, chrSize = FALSE, nsmall = 1, chrSizeMbp = FALSE, markPer = "",
 showMarkPos = FALSE, bToRemove = "", perAsFraction = FALSE, chrIndex = "both",
 morpho = "both", nameChrIndexPos = 2, karIndex = TRUE, karIndexPos = 0.5,
 ruler = TRUE, useMinorTicks = FALSE, miniTickFactor = 10, rulerPos = 0,
 ruler.tck = -0.02, rulerNumberPos = 0.5, rulerNumberSize = 1,
 collapseCen = TRUE, rulerInterval = 0, rulerIntervalcM = 0,
 rulerIntervalMb = 0, ceilingFactor = 0, xPosRulerTitle = 2.6,
 yPosRulerTitle = 0, rulerTitleSize = 1, xlimLeftMod = 1, xlimRightMod = 2,
 ylimBotMod = 0.2, ylimTopMod = 0.2, callPlot = TRUE, asp = 1,
 circularPlot = FALSE, verticalPlot = TRUE, karSpaceHor = 0, shrinkFactor = 0.9,
 separFactor = 1.5, labelSpacing = 0.7, labelOutwards = FALSE,
 chrLabelSpacing = 0.5, radius = 0.5, rotation = 0.5, circleCenter = 1,
 circleCenterY = 1, OTUlabelSpacing = 0.3, OTUsrt = 0, OTUplacing = "first",
 OTULabelSpacerx = 0, OTULabelSpacery = 0, OTUcentered = TRUE, OTUjustif = 0,
 OTUlegendHeight = NA, roundness, ... 
)

Arguments

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

boolean, The order of species is the one in the main data.frame, use TRUE to reverse

karHeight

numeric, vertical size of karyotypes. See also karHeiSpace. Defaults to 2

karHeiSpace

numeric, vertical size of karyotypes including spacing. Use with karSepar=FALSE. Proportional to karHeight, if overlap, increase. Defautl value 2.5

karSepar

boolean, reduce distance among karyotypes FALSE = equally sized karyotypes or TRUE = equally spaced karyotypes. Incompatible with addMissingOTUAfter

amoSepar

numeric, depends on karSepar=TRUE, if zero your karyotypes will have no distance among them, if overlap, increase this and karHeiSpace

addMissingOTUAfter

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

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

numeric, when you use addMissingOTUAfter this numeric vector should have the same length and corresponds to the number of free spaces (ghost OTUs) to add after each OTU respectively

moveKarHor

character, OTUs' names of karyotypes that should be moved horizontally. See mkhValue

moveAllKarValueHor

numeric, similar to mkhValue, but affects all karyotypes.

moveAllKarValueY

numeric, similar to moveAllKarValueHor, but affects y axis.

karAnchorLeft

character, OTUs' add anchor to the left of this OTU names of karyotypes. For verticalPlot=FALSE

karAnchorRight

character, OTUs' add anchor to the right of this OTU names of karyotypes. For verticalPlot=FALSE

anchor

boolean, when TRUE, plots a parent progeny structure in karyotypes in moveKarHor. Or a horizontal anchor to the left/right of karAnchorLeft, karAnchorRight when verticalPlot=FALSE

anchorLineLty

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

anchorText

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

anchorTextMParental

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

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

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

anchorVsizeF

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

anchorHsizeF

numeric, factor to modify horizontal size of anchor 1 (default).

pchAnchor

numeric, symbol for anchor, see ?points and anchor

moveAnchorV

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

moveAnchorH

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

mkhValue

numeric, value to move kar. hor. See moveKarHor

n

numeric vertices number for round corners

markN

numeric vertices number for round corners of marks

notes

data.frame, or csv file name in quotes, (shown to the right of kar.), with columns OTU and note for adding notes to each OTU, they appear to the right of chromosomes

leftNotes

data.frame, or csv file name in quotes (shown to the left), with columns OTU and note for adding notes to each OTU, they appear to the left of chromosomes

leftNotesUp

data.frame, or csv file name in quotes, (shown to the left-up), similar to leftNotes, but intended for placement over chr.

notesTextSize

numeric, font size of notes, see notes

leftNotesTextSize

numeric, font size of notes, see leftNotes

leftNotesUpTextSize

numeric, font size of notes, see leftNotesUp

notesLeft

deprecated, use a data.frame for leftNotes

notesPosX

numeric, move right notes to the right or left (x axis)

notesPosY

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

leftNotesPosX

numeric, move left notes to the right or left (x axis)

leftNotesPosY

numeric, move left notes (leftNotes) down or up (y axis)

leftNotesUpPosX

numeric, move up left notes to the right or left (x axis)

leftNotesUpPosY

numeric, move up left notes (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. Incompatible with parseStr2lang

parseStr2lang

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

propWidth

boolean, defaults to FALSE. Diminishes chr. width with increasing number of OTUs

MbThreshold

numeric, if greater than this number (defaults to 10000), MbUnit will apply and specialyTitle will not.

threshold

this is the max. value allowed for the main two significative digits, otherwise scale will shrink. For example, after 35 \mu m (Default), apparent size will be 3.5 and scale interval will change. See also ceilingFactor, you may have to use -1. Introduced in 1.13

MbUnit

character, text of units of title when MbThreshold met and OTU not in specialOTUNames. See specialyTitle Defaults to "Mb", but anything can be used. Introduced in 1.13. See specialyTitle

yTitle

character, units for common title. Defaults to \mu m

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 micrometer or Mb (big numbers). Use this param. to be able to put a different unit in ruler title. See "specialyTitle"

addOTUName

boolean, when TRUE adds OTU (species) name to karyotype

OTUTextSize

numeric, font size of OTU name (species). Defaults to 1. When OTUasNote is TRUE, use notesTextSize instead

OTUfont

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

OTUfamily

character, font family for OTU name.

OTUasNote

boolean, when TRUE adds OTU (species) name to the right, see notes

OTUasLeftNote

boolean, when TRUE adds OTU (species) name to the left-up, see leftNotesUp

orderChr

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

chrId

character, print name of chromosome, "original" uses the original name in OTU column of dfChrSize, "simple" (just 1 to ...) or "none".

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 ""

chrNameUp

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

chrIdPatternRem

character, regex pattern to remove from chr. names

indexIdTextSize

numeric, font size of chr. and kar. indices and chromosome name. Defaults to 1

distTextChr

numeric, distance from name of chromosome to chromosome, also affects vertical separation of indices. Defaults to 1

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

groupSepar

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

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.

excHoloFrArrToSide

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

xModifier

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

xModMonoHoloRate

numeric, factor to shrink chromatid separ. for holocen. 5 means 5 times smaller (quotient).

chrWidth

numeric, relative chromosome width. Defaults to 0.5

chrSpacing

numeric, horizontal spacing among chromosomes, see also chrWidth. Defaults to 0.5

specialChrWidth

numeric, relative chromosome width. Defaults to 0.5 for OTUs in specialOTUNames

specialChrSpacing

numeric, horizontal spacing among chromosomes for OTUs in specialOTUNames, see also chrWidth. Defaults to 0.5

chrColor

character, main color for chromosomes. Defaults to "gray"

chrBorderColor

character, color for border of chromosomes, defaults to chrColor

centromereSize

numeric, optional, this establishes the apparent size of cen. in the plot in \mum. See autoCenSize=TRUE. Default: 0. Use with autoCenSize=FALSE

autoCenSize

boolean, when TRUE ignores centromereSize

cenColor

character, color for centromeres, if GISH use NULL or NA. 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. When chrColor is "white" this turns into "black".

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

roundedCen

deprecated, see cenFormat

cenFormat

boolean, 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

squareness

numeric, shape of vertices of chromosomes and square marks, higher values more squared. Defaults to 4

lwd.chr

thickness of border of chr., some marks and ruler. Thick of cM marks when lwd.cM absent and other marks when lwd.marks absent. Defaults to 0.5

lwd.cM

thickness of cM marks. Defaults to lwd.chr

lwd.marks

thickness of most marks. Except cM marks and centr. related marks. See lwd.chr, lwd.cM. Defaults to lwd.chr value when 99

dfMarkPos

data.frame of marks (sites): 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

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

character, if "cen" = the distance you provided in data.frame (dfMarkPos) column markDistCen or markPos is to the center of the mark, if "beg" = the distance you provided is to the beginning of the mark (Default)

protruding

numeric, when style of mark is "cM", fraction of chrWidth to stretch marker. Defaults to 0.2. Introduced in 1.13

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

origin

For non-monocentric chr. (for holocentrics only) Use "b" (default) if distance to mark in ("markPos" column in "dfMarkPos") data.frame measured from bottom of chromosome, use "t" for distance to mark from top of chr.

efZero

numeric, 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

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 (TRUE, default). See arrowsBothChrt

useOneDot

boolean, use one dot instead of two in style of marks dots. Defaults to FALSE. Not useful for chromatids=TRUE

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

dfMarkColor

data.frame, optional, 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).

mycolors

character vector, optional, i.e. c("blue", "red", "green") for specifying color of marks in order of appearance. if diverges with number of marks will be recycled if dfMarkColor present, mycolors will be ignored. To know the order of your marks use something like: unique(dfMarkPos$markName)

alpha_val

numeric vector, make marks transparent, accepts values from 0 to 1, @see scales::alpha

borderOfWhiteMarks

boolean, if TRUE (Default) uses black border for white marks. See dfMarkColor. Does not apply to marks with style cenStyle

colorBorderMark

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

lwd.mimicCen

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

defCenStyleCol

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

pattern

REGEX pattern to remove from names of marks

legend

character, "none" for no legend; "inline" prints labels near chromosomes; "aside" prints legend to the right of karyotypes (default). 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.

bannedMarkName

character, character string or vector with mark names to be removed from plot. Not the marks but the labels. Except when bMarkNameAside is used.

bMarkNameAside

boolean, when TRUE and legend="inline", shows marks in bannedMarkName as legend="aside".

forbiddenMark

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

legendWidth

numeric, factor to increase width of squares and of legend. Defaults to 1.7

legendHeight

numeric, factor to increase height of squares and dots of legend. Automatic.

markLabelSize

numeric, only if legend != (not) "", size of the font of labels of marks (legend). Defaults to 1

markLabelSpacer

numeric, only if legend="aside", space from the rightmost chr. to legend. Defaults to 1

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.

chrSize

boolean, when TRUE adds total chr size under each chr. 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).

markPer

character vector, name of mark(s) to calculate % of mark in chr. and add it to plot. See perAsFraction

showMarkPos

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

bToRemove

character vector, bands to remove from calc. of pos., when showMarkPos = TRUE

perAsFraction

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

chrIndex

character, add arm ratio with "AR" and centromeric index with "CI", or "both" (Default), or "none" for none

morpho

character, when "both" (default) prints the Guerra and Levan classif of cen. position, use also "Guerra" or "Levan" or "none" for none. See also ?armRatioCI.

nameChrIndexPos

numeric, modify position of name of chr. indices

karIndex

logical, add karyotype indices A (intrachromosomal - centromere pos.) and A2 (interchromosomal asymmetry, variation among chromosome sizes)

karIndexPos

numeric, move karyotype index. Defaults to 0.5

ruler

boolean, display ruler to the left of karyotype, when FALSE no ruler

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

rulerPos

numeric, absolute position of ruler, corresponds to pos argument of axis R plot

ruler.tck

numeric, tick size of ruler, corresponds to tck argument of axis R plot. Defaults to -0.02

rulerNumberPos

numeric, modify position of numbers of ruler. Defaults to 0.5

rulerNumberSize

numeric, size of number's font in ruler. Defaults to 1

collapseCen

boolean, avoid spacing in ruler between short arm and long arm.

rulerInterval

numeric, intervals in ruler. No default, automatic.

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. Usa data in millions

ceilingFactor

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

xPosRulerTitle

numeric, modify position of ruler title. See yTitle, specialyTitle, MbUnit. Defaults to 2.6. A value of 2.6 means 2.6 times the value of chrSpacing to the left, from the first chr.

yPosRulerTitle

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

rulerTitleSize

numeric font size of units of ruler. See also xPosRulerTitle

xlimLeftMod

numeric, modifies xlim left argument of plot

xlimRightMod

numeric, xlim right side modification by adding space to the right of idiograms. Defaults to 2

ylimBotMod

numeric, modify ylim bottom argument of plot

ylimTopMod

numeric, modify ylim top argument of plot

callPlot

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

asp

numeric, y x aspect of plot. Defaults to 1

circularPlot

boolean, if TRUE chromosomes/karyotypes are plotted in concentric circles. Defaults to FALSE

verticalPlot

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

karSpaceHor

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

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 chr. from top to -90 degrees. (-0.5*\pi )

circleCenter

numeric, for circularPlot=TRUE. Coordinate X of center of circles. Affects legend="aside" position. Defaults to 1

circleCenterY

numeric, for circularPlot=TRUE. Coordinate Y of center of circles. Affects legend="aside" position. Defaults to 1

OTUlabelSpacing

numeric, for circularPlot=TRUE. Spacing for OTU names. Defaults to 0.3

OTUsrt

numeric, for circularPlot=TRUE. Angle to use for OTU names. Defaults to 0

OTUplacing

character, for circularPlot=TRUE. location of OTU name. Defaults to "first" plots name near first chr. "number" places number near 1st chr. and index and name to the right or center. "simple" place name to the right or center without numbering. See also OTUcentered

OTULabelSpacerx

numeric, for circularPlot=TRUE and OTUplacing="number" or "simple". Modifies x names position

OTULabelSpacery

numeric, for circularPlot=TRUE and OTUplacing="number" or "simple". Modifies y names position

OTUcentered

boolean, for circularPlot=TRUE and OTUplacing="number" or "simple". OTU name in center of circle when TRUE, otherwise, to the right.

OTUjustif

numeric, for circularPlot=TRUE and OTUplacing="number" or "simple". Justification of OTU name. 0 = left (Default); use 0.5 for centered. See ?text -> adj

OTUlegendHeight

numeric, for circularPlot=TRUE and OTUplacing="number" or "simple". Modifies y names separation

roundness

deprecated, use squareness

...

accepts other arguments for the plot, see, ?plot

Value

plot

See Also

asymmetry

armRatioCI

chrbasicdatamono

chrbasicdataHolo

markposDFs

markdataholo

dfMarkColor

Examples

data(dfOfChrSize)
plotIdiograms(dfOfChrSize, ylimBotMod = .75, rulerPos = -.5)
plotIdiograms(dfOfChrSize, circularPlot = TRUE, chrLabelSpacing = 1)
plotIdiograms(dfChrSizeHolo, rulerPos = -.5)