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 armRatioCI
also.
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., when showMarkPos = TRUE
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
anchorHsizeF
: numeric, factor to modify horizontal size of anchor 1
(default).
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 or .csv name in quotes with columns OTU
and note
for adding notes to each OTU, they appear to the right of the karyotype
leftNotes
: data.frame or .csv name in quotes with columns OTU
and note
for adding notes to each OTU, they appear to the left of the karyotype
leftNotesUp
: data.frame or .csv name in quotes (to the left), similar to leftNotes
, but intended for placement over kar.
notesTextSize
: (0.4
) numeric, font size of notes, see notes
leftNotesTextSize
: numeric, font size of notes, see leftNotes
leftNotesUpTextSize
: numeric, font size of notes, see leftNotesUp
notesPosX
: (0.5
) numeric, moves right notes in the x axis
notesPosY
: numeric, move right notes down or up (y axis)
leftNotesPosX
: (0.5
) numeric, moves left notes in the x axis
leftNotesPosY
: numeric, move leftNotes
down or up (y axis)
leftNotesUpPosX
: numeric, move up left notes to the right or left (x 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
: boolean, 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
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
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
Centromeres
autoCenSize
boolean, when TRUE
ignores centromereSize
centromereSize
: Apparent size of centromeres. Requires autoCenSize = FALSE
cenColor
: Determines the color of centromeres. if GISH use NULL
. Defaults to chrColor
collapseCen
boolean, avoid spacing in ruler between short arm and long arm.
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
).
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 the pattern
arg., you can get 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. 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.
rulerIntervalcM
: numeric, intervals in ruler of OTU in specialOTUNames
.
rulerIntervalMb
: numeric, intervals in ruler of OTU with data in Mb (>MbThreshold
) and absent from specialOTUNames
.
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.
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)