idiogramFISH (version 2.0.0)

yVertoHor: FUNCTIONS: yVertoHor, xHortoVer, xHortoVerRoundCen, xHortoVerDots, mapCircle, mapRadius, transYList, mapOTUnames, addOTUnames, applyMapCircle, intercalate, drawPlot, drawPlotMark, drawPlotMarkLine, drawCen, circLabelMark, circPlotDots, plotChrNames, addChrNameAttrMark, addChrNameAttrMarkDots, xMarkMap, xMarkMapLeft, markMapPer, markMapPercM, markMapPerDots, radDotsPer, centerMarkMapPer, transyListMark, transyListCen, transRadDots, transyListMarkDots, oneDot, OTUlabelsright

Description

FUNCTIONS: yVertoHor, xHortoVer, xHortoVerRoundCen, xHortoVerDots, mapCircle, mapRadius, transYList, mapOTUnames, addOTUnames, applyMapCircle, intercalate, drawPlot, drawPlotMark, drawPlotMarkLine, drawCen, circLabelMark, circPlotDots, plotChrNames, addChrNameAttrMark, addChrNameAttrMarkDots, xMarkMap, xMarkMapLeft, markMapPer, markMapPercM, markMapPerDots, radDotsPer, centerMarkMapPer, transyListMark, transyListCen, transRadDots, transyListMarkDots, oneDot, OTUlabelsright

Usage

yVertoHor(y, monocenNames)

Arguments

y

list, chr coords.

monocenNames

character, vector with names of OTUs

ylist

y coords

x

only d.f. of this cen. type

r3

modifier of pos.

circleCenterY

numeric

cenBorder

character, cen border color

cenColor2

character, cen. color

cfunction

character, name of function to apply

lwd.chr

numeric, width of line

chrColor

character, chr. color

chrId

character, type of chr. name

chrNames

list, resulting from applyMapCircle

chrWidth

character, chr. width

circleCenter

numeric, modify center of circle of chr.

circleMaps

list, resulting from applyMapCircle

circleMapsMarksCr

list, resulting from applyMapCircle

circleMapsOTUname

list, resulting from applyMapCircle

colBorderCr

character, border color

colCr

character color of mark

dfMarkColorInternal

data.frame of mark charact.

diffXRounded

numeric, difference of chr. width to rounded corner

firstXchrEach

list, first element from xlistNewChr

firstYchrEach

list, first element from xlistNewChr

fixCenBorder2

boolean, change cen border

indexIdTextSize

numeric, text size

labelSpacing

numeric, spacing of labels to chr. or mark.

parparlistOfdfMarkPosDataCen

list, of d.f.s of marks

listOfdfMarkPos

list, of d.f.s of marks

listOfdfMarkPosSq

list, of d.f.s of marks

mapCircle

function name

markDistType

character, type of distance to mark

markLabelSize

numeric, size of mark label

n

numeric, number of vertices

OTUplacing

boolean use number instead of OTU name

OTUlabelSpacing

numeric, spacing for OTU name

OTUsrt

numeric, angle for OTU name

OTUTextSize

numeric, font size of OTU

pattern

character, regex pattern to remove from mark names

position

numeric, indexer for karyotype position

radius

numeric, radius

rad

list, list of radius for dots marks

radiusMap

function, map radius in circle

radPerCr

list, radius percentages

separFactor

numeric, separation of kar. in circle

shrinkFactor

numeric, percentage in decimal of whole chr.

unlist

boolean, for unlisting x or y coordinates

xfactor

numeric, modify y x aspect

xlist

list, x coordinates

xlistMarkCen

list, marks

xlistNew

list, transformed coordinates

xlistNewCen

list, transformed coordinates

xlistNewChr

list, transformed coordinates

xMark

list, mark coords.

xMarkCr

list, mark coords.

xMarkList

list, mark coords.

xRounded

list, transformed coords.

ylistNew

list, chr coords.

ylistNewCen

list, chr coords.

ylistNewChr

list, chr coords.

ylistTrans

list, trans .chr coords.

ylistTransChr

list, trans .chr coords.

yMark

list, mark coords.

yMarkCen

list, mark coords.

yMarkPer

list, mark coords in percentage.

OTUlegendHeight

numeric

labelOutwards

srt

Value

plot