Title: Shiny App. Idiograms with Marks and Karyotype Indices
Version: 2.0.13
Date: 2023-08-21
Description: Plot idiograms of karyotypes, plasmids, circular chr. having a set of data.frames for chromosome data and optionally mark data. Two styles of chromosomes can be used: without or with visible chromatids. Supports micrometers, cM and Mb or any unit. Three styles of centromeres are available: triangle, rounded and inProtein; and six styles of marks are available: square (squareLeft), dots, cM (cMLeft), cenStyle, upArrow (downArrow), exProtein (inProtein); its legend (label) can be drawn inline or to the right of karyotypes. Idiograms can also be plotted in concentric circles. It is possible to calculate chromosome indices by Levan et al. (1964) <doi:10.1111/j.1601-5223.1964.tb01953.x>, karyotype indices of Watanabe et al. (1999) <doi:10.1007/PL00013869> and Romero-Zarco (1986) <doi:10.2307/1221906> and classify chromosomes by morphology Guerra (1986) and Levan et al. (1964).
Depends: R (≥ 3.5)
Imports: rlang, crayon, plyr, dplyr, tidyr, scales
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
Encoding: UTF-8
LazyData: true
Suggests: rentrez, ggplot2, ggpubr, ggtree, phytools, treeio, rmdformats, knitr, kableExtra, rvcheck, badger, rmarkdown, RCurl, shiny, shinydashboard, rhandsontable, gtools, rclipboard, clipr, shinyjs
VignetteBuilder: rmdformats, knitr, kableExtra, rmarkdown, RCurl, rvcheck, badger, rentrez
SystemRequirements: pandoc (>= 2.0)
URL: https://ferroao.gitlab.io/manualidiogramfish/, https://ferroao.gitlab.io/idiogramfishhelppages
BugReports: https://gitlab.com/ferroao/idiogramFISH/-/issues
RoxygenNote: 7.2.3
NeedsCompilation: no
Packaged: 2023-08-22 15:15:44 UTC; fernando
Author: Fernando Roa [aut, cre], Mariana PC Telles [ctb]
Maintainer: Fernando Roa <froao@unal.edu.co>
Repository: CRAN
Date/Publication: 2023-08-22 16:50:02 UTC

idiogramFISH: Shiny App. Idiograms with Marks and Karyotype Indices

Description

logo

Plot idiograms of karyotypes, plasmids, circular chr. having a set of data.frames for chromosome data and optionally mark data. Two styles of chromosomes can be used: without or with visible chromatids. Supports micrometers, cM and Mb or any unit. Three styles of centromeres are available: triangle, rounded and inProtein; and six styles of marks are available: square (squareLeft), dots, cM (cMLeft), cenStyle, upArrow (downArrow), exProtein (inProtein); its legend (label) can be drawn inline or to the right of karyotypes. Idiograms can also be plotted in concentric circles. It is possible to calculate chromosome indices by Levan et al. (1964) doi:10.1111/j.1601-5223.1964.tb01953.x, karyotype indices of Watanabe et al. (1999) doi:10.1007/PL00013869 and Romero-Zarco (1986) doi:10.2307/1221906 and classify chromosomes by morphology Guerra (1986) and Levan et al. (1964).

Author(s)

Maintainer: Fernando Roa froao@unal.edu.co

Other contributors:

See Also

Useful links:

addAttributesDfChrSize

Description

returns all cols. as character

Usage

addAttributesDfChrSize(
  listOfdfChromSize,
  threshold,
  specialOTUNames,
  centromereSize,
  MbThreshold,
  cenFactor,
  chrWidth,
  specialChrWidth,
  squareness,
  modifyChr = TRUE,
  mymessage = TRUE
)

Value

list of data.frames

This is an internal function that adds notes

Description

This is an internal function that adds notes

Usage

addNotes(
  notes,
  listOfdfChromSizenoNA,
  groupName,
  indexCount,
  morphoCount,
  xmnoNA,
  ymnoNA,
  distTextChr,
  chrIdCount,
  notesPosX,
  notesPosY,
  notesTextSize,
  defaultFontFamily2,
  OTUasNote,
  OTUfont,
  OTUfamily,
  downNote,
  rightN,
  leftNoteFont,
  leftNoteFontUp,
  noteFont,
  parseTypes,
  parseStr2lang
)

Arguments

notes

x component of polygon

listOfdfChromSizenoNA

y component of polygon

groupName

y of chr

indexCount

colors for marks

morphoCount

list of df. of mark pos.

xmnoNA

thick of border line

ymnoNA

boolean

distTextChr

numeric

chrIdCount

numeric

notesPosX

numeric

notesPosY

numeric

notesTextSize

numeric

defaultFontFamily2

character, regex

downNote

numeric

Value

plot

FUNCTIONS armRatioCI and swapChrRegionDfSizeAndMarks.

Description

armRatioCI: reads a data.frame and produces AR (arm ratio), CI (centromeric index) , Guerra and Levan classifications.

swapChrRegionDfSizeAndMarks: reads data.frames to swap arms

Usage

armRatioCI(dfChrSize, rnumeric = FALSE)

swapChrRegionDfSizeAndMarks(dfChrSize, dfMarkPos, chrNamesToSwap)

Arguments

dfChrSize

name of data.frame with columns: shortArmSize, longArmSize

rnumeric

boolean, returns only numeric AR, CI

dfMarkPos

name of data.frame of marks

chrNamesToSwap

name of chr. names to swap arms

Value

data.frame (armRatioCI)

list of data.frames (swapChrRegionDfSizeAndMarks)

References

LEVAN A, FREDGA K, SANDBERG AA (1964) NOMENCLATURE FOR CENTROMERIC POSITION ON CHROMOSOMES. Hereditas 52:201-220.

Guerra. 1986. Reviewing the chromosome nomenclature of Levan et al. Braz. Jour. Gen. Vol IX, 4, 741-743

See Also

chrbasicdatamono

Examples

armRatioCI(dfOfChrSize)
armRatioCI(bigdfOfChrSize)

swapChrRegionDfSizeAndMarks(dfOfChrSize, dfOfMarks, "1")

arrowPlotMark This is an internal function that plot marks

Description

It returns a plot

Usage

arrowPlotMark(
  squareness,
  xMark,
  yMark,
  dfMarkColorInt,
  listOfdfMarkPosArrow,
  chrWidth,
  n,
  lwd.chr,
  circularPlot,
  y,
  x,
  markLabelSize,
  separFactor,
  labelSpacing,
  circleCenter,
  circleCenterY,
  radius,
  ylistTransChr,
  rotation,
  arrowheadWidthShrink,
  alpha_val
)

Arguments

squareness

squareness of vertices <

xMark

x component of polygon

yMark

yMark component of polygon

dfMarkColorInt

colors for marks

listOfdfMarkPosArrow

list of df. of mark pos.

chrWidth

numeric, width of chr.

n

numeric, to define vertices of rounded portions

lwd.chr

thick of border line

circularPlot

boolean TRUE for circ.

y

list, y coords.

markLabelSize

numeric, font size

separFactor

numeric, sep. kars.

labelSpacing

numeric, spacing

circleCenter

numeric

circleCenterY

numeric

radius

numeric

ylistTransChr

list, transf. coords.

rotation

rotate*

Value

plot

FUNCTIONS asymmetry and asymmetryA2.

Description

asymmetry: calculates karyotype asymmetry A and A2.

asymmetryA2: calculates karyotype asymmetry A2

This functions read a data.frame with columns: shortArmSize and longArmSize

If several species present, use column OTU.

It returns a list with the A and A2 indices

A = \frac{\sum_{i=1}^{n} \frac{longArm_{i} - shortArm_{i}}{CL_{i}} }{n}

A: Watanabe et al. (1999) asymmetry of karyotype ranging from 0 (symmetric) to 1 (asymmetric)

A_{2} = \frac{sCL}{xCL}

(s = std dev, CL = chr. length, x = mean) (Romero-Zarco 1986)

related to:

CV_{CL} = A_{2} * 100

(CV = coeff. var.) (Paszko 2006)

Usage

asymmetry(dfChrSize, asDf = FALSE)

asymmetryA2(dfChrSize)

Arguments

dfChrSize

name of data.frame

asDf

boolean, return d.f. instead of list

Value

list

References

Watanabe K, Yahara T, Denda T, Kosuge K. 1999. Chromosomal evolution in the genus Brachyscome (Asteraceae, Astereae): Statistical tests regarding correlation between changes in karyotype and habit using phylogenetic information. Journal of Plant Research 112: 145-161. 10.1007/PL00013869

A2: Romero-Zarco. 1986. A New Method for Estimating Karyotype Asymmetry. Taxon Vol. 35, No. 3 pp. 526-530

Paszko B. 2006. A critical review and a new proposal of karyotype asymmetry indices. Plant Syst Evol 258:39-48.

See Also

chrbasicdatamono

chrbasicdatamono

chrbasicdataHolo

Examples

asymmetry(dfOfChrSize)
myAlist <- asymmetry(bigdfOfChrSize)
as.data.frame(myAlist)
asymmetryA2(dfOfChrSize)
as.data.frame(asymmetryA2(bigdfOfChrSize))
asymmetryA2(dfChrSizeHolo)
as.data.frame(asymmetryA2(bigdfChrSizeHolo))

This is an internal function that eliminates factors

Description

It returns a data.frames

Usage

cMPlotMark(
  bannedMarkName,
  xMark,
  yMark,
  y,
  x,
  dfMarkColorInt,
  listOfdfMarkPoscM,
  lwd.cM,
  circularPlot,
  radius,
  circleCenter,
  circleCenterY,
  separFactor,
  markLabelSize,
  pattern,
  n,
  labelSpacing,
  chrWidth,
  ylistTransChr,
  rotation,
  labelOutwards,
  alpha_val
)

Arguments

xMark

x component of polygon

yMark

y component of polygon

y

y of chr

dfMarkColorInt

colors for marks

listOfdfMarkPoscM

list of df. of mark pos.

lwd.cM

thick of border line

circularPlot

boolean

radius

numeric

circleCenter

numeric

circleCenterY

numeric

separFactor

numeric

markLabelSize

numeric

pattern

character, regex

n

numeric

labelSpacing

numeric

chrWidth

numeric, chr. width

ylistTransChr

list

rotation

rotation

labelOutwards

srt

alpha_val

numeric

Value

plot

checkArmHolocenError This is an internal function that makes list of d.fs

Description

checkArmHolocenError This is an internal function that makes list of d.fs

Usage

checkArmHolocenError(listOfdfArmGISHInternal, CenTypeNames)

Arguments

listOfdfArmGISHInternal

df list

CenTypeNames

character vector

Value

list

Function to check names of OTUs (species) among data.frames

Description

This function reads two data.frames the one with chromosome sizes, and one df with data of marks (sites) both have to have the column chrName and if several species, OTU. The functions returns a filtered list with 1. data.frame of chrSizes, 2. data.frame of marks, 3. mark names 4. max mark size.

Usage

checkNameChrDfMarks(listChrSize, listOfdfMarks)

Arguments

listChrSize

list of data.frames, with columns: OTU (optional), chrName, for chr. with cen.: shortArmSize, longArmSize, for holoc.: chrSize

listOfdfMarks

list of data.frames of marks (sites): OTU (opt / mandat. if in dfChrSize), chrName markName markSize, for chr. with cen.: chrRegion (p,q) markDistCen, for holoc: markPos

Value

list

Chr. basic data Holo.

Description

dfChrSizeHolo: Example data for holocentrics for 1 species

bigdfChrSizeHolo: Example data for holocentrics for several species, OTU

parentalAndHybHoloChrSize: Example data for holocentrics for several species, OTU

bigdfOfChrSize3Mb: Example data in Mb without chr. arms for three species, OTU

Usage

dfChrSizeHolo

bigdfChrSizeHolo

parentalAndHybHoloChrSize

bigdfOfChrSize3Mb

Format

data.frame with columns:

OTU

grouping OTU (species), optional if only one OTU

chrName

name of chromosome

chrSize

size of chromosome, micrometers or Mb

group

chromosome group, optional

chrNameUp

optional name over kar.

Mbp

optional name to show size in Mbp, use only when chrSize is not in Mbp

An object of class data.frame with 12 rows and 3 columns.

An object of class data.frame with 13 rows and 3 columns.

An object of class data.frame with 14 rows and 3 columns.

See Also

asymmetryA2

plotIdiograms

markdataholo

Chr. basic data Monocen.

Description

dfOfChrSize: Example data for monocentrics

bigdfOfChrSize: Example data for monocentrics for several species, OTU

humChr: Data for human karyotype, measured from Adler (1994)

allChrSizeSample: Example data for monocentrics for several species, OTU

parentalAndHybChrSize: Example data for monocentrics for GISH

traspadf: Example data for Tradescantia (Rhoeo) spathacea (Golczyk et al. 2005)

Usage

dfOfChrSize

bigdfOfChrSize

humChr

allChrSizeSample

parentalAndHybChrSize

traspadf

Format

data.frame with columns:

OTU

OTU, species, optional if only one OTU (species)

chrName

name of chromosome

shortArmSize

size of short arm, micrometers

longArmSize

size of long arm, micrometers

group

chr group, optional

chrNameUp

optional name over kar.

Mbp

optional name to show size in Mbp, use only when shortArmSize is not in Mbp

An object of class data.frame with 50 rows and 4 columns.

An object of class data.frame with 24 rows and 4 columns.

An object of class data.frame with 75 rows and 4 columns.

An object of class data.frame with 13 rows and 4 columns.

An object of class data.frame with 12 rows and 4 columns.

Source

http://www.pathology.washington.edu/research/cytopages/idiograms/human/

References

Adler 1994. Idiogram Album. http://www.pathology.washington.edu/research/cytopages/idiograms/human/

Golczyk H, Hasterok R, Joachimiak AJ (2005) FISH-aimed karyotyping and characterization of Renner complexes in permanent heterozygote Rhoeo spathacea. Genome 48:145-153.

See Also

plotIdiograms

armRatioCI

asymmetry

markposDFs

FUNCTIONS: citrusSize, citrusMarkPos, markOverCMA

Description

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.

Usage

 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
)

Arguments

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 citrusSize function (citrusMarkPos)

mSizePter

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

mSizeQter

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

mSizePprox

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

mOther

numeric, default size for other bands. 0.25 (default) (citrusMarkPos)

markName

character, default name of mark "CMA", or "45S", respectively. (citrusMarkPos,markOverCMA)

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)

Value

data.frame

data.frame

data.frame

References

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

Examples

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
)
)

Function to do ceiling at different levels

Description

This function reads number to round

Usage

customCeiling(x, customDecimals = 1)

Arguments

x

number to round

customDecimals

desired decimal positions

Value

numeric

Mark characteristics

Description

style column does not apply to cen. marks, only color.

dfMarkColor: Example General data for marks NOT position

humMarkColor: human bands' characteristics, from Adler (1994)

mydfMaColor: mark characteristics used in vignette of phylogeny

dfMarkColor5S25S: mark characteristics used in circular plot vignette

dfMarkColorIn: mark characteristics

Usage

dfMarkColor

humMarkColor

mydfMaColor

dfMarkColor5S25S

dfMarkColorIn

Format

dfMarkColor a data.frame with columns:

markName

name of mark

markColor

use R colors

style

character, use square or dots, optional

protruding

numeric, modifies aspect of cM/cMLeft marks, see parameter protruding in plotIdiograms, optional

An object of class data.frame with 395 rows and 3 columns.

An object of class data.frame with 6 rows and 3 columns.

An object of class data.frame with 2 rows and 3 columns.

An object of class data.frame with 5 rows and 3 columns.

Source

http://www.pathology.washington.edu/research/cytopages/idiograms/human/

References

Adler 1994. Idiogram Album. URL: http://www.pathology.washington.edu/research/cytopages/idiograms/human/

See Also

plotIdiograms

markposDFs

markdataholo

dfToListColumn This is an internal function that makes list of d.fs

Description

dfToListColumn This is an internal function that makes list of d.fs

Usage

dfToListColumn(dfLookColumn, columnToSplit = "OTU")

Arguments

dfLookColumn

df with or without Column to list

columnToSplit

character, column name to split

Value

list

filterExtraOTU This is an internal function that filters list of d.f. of marks

Description

It returns rulers (axis)

Usage

filterExtraOTU(listOfdfChromSize, listOfdfMarkPosCenType)

Arguments

listOfdfChromSize

list of all d.f. of chr.

listOfdfMarkPosCenType

only d.f. of this cen. type

Value

data.frame

This function fixes duplicated names when no marks

Description

It returns a list of data.frames

Usage

fixChrNameDupDF(list1dfChromSize, mybooleanChrName)

Arguments

list1dfChromSize

list of 1 df of chr size

mybooleanChrName

test for absence of marks

Value

list

FUNCTION genBankReadIF

Description

genBankReadIF: creates a list of data.frames from a genbank format file or a rentrez object

Requires tidyr

Usage

genBankReadIF(filename.gb, forbiddenFields = "translation")

Arguments

filename.gb

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

forbiddenFields

names of field of feature (CDS, gene) to ignore, separated by |. Defaults to "translation"

Value

list

This is an internal function that inserts in vector or list

Description

It returns list or vector

Usage

insertInList(list, pos, elems)

Arguments

list

vector or list

pos

index to insert in

elems

elements to be inserted

Value

list or vector

FUNCTION make.uniqueIF

Description

make.uniqueIF: produces unique strings from duplicated

Usage

make.uniqueIF(string, sep = "_", letter = FALSE)

Arguments

string

name of char. vector

sep

separator

letter

boolean, use numbers when FALSE

Value

character vector

Examples

make.uniqueIF(c(1, 1, 2, 2))

These are internal functions that eliminate factors

Description

It returns a data.frame

Usage

makeNumCols(df)

Arguments

df

data.frame

Value

data.frame

makeVectorNames This is an internal function that makes a vector of names

Description

makeVectorNames This is an internal function that makes a vector of names

Usage

makeVectorNames(namedList, attr, selector)

Arguments

namedList

original list

attr

attribute

selector

value of attribute

Value

character vector

Function to automatically make a data.frame of Marks' characterisitcs

Description

This function reads character vector with marks names

It returns a data.frame with color and style for each mark

Usage

makedfMarkColor(
  dfMarkColor,
  markNames,
  colorstoremove = NA,
  defaultStyleMark = "square",
  reserveDF
)

Arguments

dfMarkColor

d.f of marks to use

markNames

names of marks

colorstoremove

remove this colors from the result

defaultStyleMark

character vector with default style "square" "cM" "dots"

Value

data.frame

FUNCTION to make a data.frame of Marks' characterisitcs

Description

This function reads character vector with marks names, a character vector of prohibited colors and a custom list of colors to be associated with the mark names

It returns a data.frame with color and style for each mark

Usage

makedfMarkColorMycolors(
  markNames,
  mycolors,
  colorstoremove = NULL,
  defaultStyleMark = "square"
)

Arguments

markNames

names of marks

mycolors

character vector of names of colors

colorstoremove

character vector of colors to remove from mycolors. Default NULL

defaultStyleMark

character vector with default style "square". Other options: "squareLeft", "cM" "cMLeft", "dots", "upArrow", "downArrow", "cenStyle"

Value

data.frame

FUNCTIONS mapGGChr and mapGGChrMark (for ggplot)

Description

Currently works for holocentrics when only one OTU. See vignette.

mapGGChr: reads a data.frame and produces coordinates for ggplot of chr.

mapGGChrMark: reads data.frames and produces data.frames for ggplot of chr. and marks

Usage

mapGGChr(dfChrSize, chrSpacing = 0.5, squareness = 4, n = 50)

mapGGChrMark(dfChrSize, dfMarkPos, chrSpacing = 0.5, squareness = 4, n = 50)

Arguments

dfChrSize

character, name of data.frame with columns: chrSize

chrSpacing

numeric, 1 - chrSpacing will be the width of chr.

squareness

numeric, squareness

n

numeric, vertices number for rounded portions

dfMarkPos

(mapGGChrMark) name of data.frame of marks

Value

list

list

mapXY This is an internal function that creates coords for chr. or arms or marks

Description

mapXY This is an internal function that creates coords for chr. or arms or marks

Usage

mapXY(
  start,
  end,
  y,
  yMod,
  x,
  yfactor,
  r2,
  pts_1,
  pts_2,
  pts_3,
  pts_4,
  chrt = FALSE
)

Arguments

start

1st index

end

last index

y

y coords

yMod

y coords modified because of squareness

x

x coords

yfactor

y x factor

r2

radius

pts_1

points of squareness

pts_2

points of squareness

pts_3

points of squareness

pts_4

points of squareness

Value

list

mapXYCenMimic This is an internal function that creates coords for chr. or arms or marks

Description

mapXYCenMimic This is an internal function that creates coords for chr. or arms or marks

Usage

mapXYCenMimic(start, end, y, x, yfactor, r2, pts, cenFormat = "triangle")

Arguments

start

1st index

end

last index

y

y coords

yfactor

y x factor

r2

r2ius

pts

points of squareness

cenFormat

boolean

Value

list

markDistCenGISHfix This is an internal function that fixes markDistCen when GISH

Description

markDistCenGISHfix This is an internal function that fixes markDistCen when GISH

Usage

markDistCenGISHfix(
  dfArmGISHInternalMonocen,
  dfChrSizeInternal,
  columnArmSize,
  markDistType,
  listOfdfChromSize,
  addR2 = TRUE
)

Arguments

dfArmGISHInternalMonocen

df of GISH OF ARM

dfChrSizeInternal

d.f. of chr. size

columnArmSize

column rel. to arm.

markDistType

character

Value

data.frame

Mark Positional data - Holocen.

Description

When several OTUs, some can be monocen. and others holocen. Marks distance for monocen. are measured from cen. and for holocen. from top or bottom depending on param origin. See vignettes.

bigdfMarkPosHolo: Example data for mark position of holocentrics with column OTU

dfMarkPosHolo: Example data for mark position of holocentrics

dfAlloParentMarksHolo: Example data for mark position of GISH

bigdfOfMarks3Mb: Example data for mark position in Mb

bigdfMarkPosHolo2: Example data for mark position

Usage

bigdfMarkPosHolo

dfMarkPosHolo

dfAlloParentMarksHolo

bigdfOfMarks3Mb

bigdfMarkPosHolo2

Format

data.frame with columns:

OTU

OTU, species, optional

chrName

name of chromosome

markName

name of mark

markPos

position from bottom or top (see parameter origin in plotIdiograms)

markSize

size of mark in micrometers or Mb

An object of class data.frame with 6 rows and 4 columns.

An object of class data.frame with 13 rows and 4 columns.

An object of class data.frame with 12 rows and 5 columns.

An object of class data.frame with 18 rows and 6 columns.

See Also

markposDFs

plotIdiograms

chrbasicdataHolo

Mark Positional data - monocentrics

Description

When several OTUs, some can be monocen. and others holocen. Marks distance for monocen. are measured from cen. and for holocen. from top or bottom depending on param origin. See vignettes.

bigdfOfMarks: Example data for mark position with column OTU

dfOfMarks: Example data for marks' position

dfOfMarks2: Marks' position including cen. marks

humMarkPos: human karyotype bands' (marks) positions, measured from Adler (1994)

allMarksSample: Example data for marks' position

dfAlloParentMarks: Example data for mark position of GISH of monocen.

traspaMarks: T. spathacea (Rhoeo) marks' positions, from Golczyk et al. (2005)

Usage

bigdfOfMarks

dfOfMarks

dfOfMarks2

humMarkPos

allMarksSample

dfAlloParentMarks

traspaMarks

Format

bigdfOfMarks a data.frame with columns:

OTU

OTU, species, mandatory if in dfChrSize

chrName

name of chromosome

markName

name of mark

chrRegion

use p for short arm, q for long arm, and cen for centromeric

markDistCen

distance of mark to centromere (not for cen)

markSize

size of mark (not for cen)

An object of class data.frame with 4 rows and 5 columns.

An object of class data.frame with 6 rows and 5 columns.

An object of class data.frame with 395 rows and 5 columns.

An object of class data.frame with 43 rows and 6 columns.

An object of class data.frame with 16 rows and 4 columns.

An object of class data.frame with 18 rows and 7 columns.

Source

Washington U

References

Adler 1994. Idiogram Album. URL: Washington U.

Golczyk H, Hasterok R, Joachimiak AJ (2005) FISH-aimed karyotyping and characterization of Renner complexes in permanent heterozygote Rhoeo spathacea. Genome 48:145-153.

See Also

markdataholo

plotIdiograms

chrbasicdatamono

dfMarkColor

mimicCenPlotMark This is an internal function that plot marks

Description

It returns a plot

Usage

mimicCenPlotMark(
  squareness,
  xMark,
  yMark,
  defCenStyleCol,
  listOfdfMarkPosCenStyle,
  chrWidth,
  specialChrWidth,
  yfactor,
  n,
  lwd.mimicCen,
  listOfdfChromSize,
  circularPlot,
  y,
  markLabelSize,
  separFactor,
  labelSpacing,
  circleCenter,
  circleCenterY,
  radius,
  ylistTransChr,
  rotation,
  labelOutwards,
  yMarkLine,
  xMarkRightLine,
  xMarkLeftLine,
  x,
  cenFormat = "triangle",
  pts
)

Arguments

squareness

squareness of vertices <

xMark

x component of polygon

yMark

yMark component of polygon

listOfdfMarkPosCenStyle

list of df. of mark pos.

chrWidth

numeric, width of chr.

specialChrWidth

numeric, width of chr.

yfactor

yMark distortion based on canvas proportion

n

numeric, to define vertices of rounded portions

listOfdfChromSize

chr size df list

circularPlot

boolean TRUE for circ.

y

list, y coords.

markLabelSize

numeric, font size

separFactor

numeric, sep. kars.

labelSpacing

numeric, spacing

circleCenter

numeric

circleCenterY

numeric

radius

numeric

ylistTransChr

list, transf. coords.

rotation

rotate

labelOutwards

srt

Value

plot

FUNCTION that modifies marks' names into columns

Description

Reads a data.frame with marks' of styles downArrow,upArrow,cM,cMLeft positions. It separates names in columns, avoiding overlap when multiple close names

Exceptionally this function requires the column style in the data.frame of marks' positions.

Returns a data.frame

Usage

 namesToColumns( marksDf, dfChrSize, markType = c("downArrow", "upArrow",
 "cMLeft", "cM"), amountofSpaces = 13, colNumber = 2, protruding = 0.2,
 protrudingInt = 0.5, circularPlot = TRUE, rotation = 0.5,
 defaultStyleMark = "square", orderChr = "size", halfModDown = NA,
 halfModUp = NA, rotatMod = 0 
)

Arguments

marksDf

data.frame with columns: markName,style,markPos

dfChrSize

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

markType

character, use c("downArrow","upArrow","cM","cMLeft") or a subset

amountofSpaces

numeric, number of spaces for each column

colNumber

numeric, number of columns

protruding

numeric, same as plot, minimal protruding for arrow marks, equivalent to cM protruding

protrudingInt

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

circularPlot

boolean, use TRUE for circular plots. Use FALSE otherwise

rotation

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

defaultStyleMark

character, if some data in column style missing fill with this one. Defaults to "square"

orderChr

character, replaces orderBySize - deprecated 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

halfModDown

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

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

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

Value

data.frame

newOrderColumn This is an internal function that adds neworder column to listOfdfChromSizeCenType

Description

It returns rulers (axis)

Usage

newOrderColumn(listOfdfChromSize, listOfdfChromSizeCenType)

Arguments

listOfdfChromSize

list of all d.f. of chr.

listOfdfChromSizeCenType

only d.f. of this cen. type

Value

data.frame

FUNCTION perMark

Description

calculates fraction (%) of chromosome for each mark

Usage

perMark(dfMarkPos, listOfdfChromSize, result = "list", bToRemove = "")

Arguments

dfMarkPos

data.frame, of marks' position

listOfdfChromSize

list of data.frames or data.frame of chr. sizes.

result

character, type of return, "data.frame" or "list"

bToRemove

character vector, bands to ignore

Value

list

Examples

load(system.file("shinyApps", "iBoard/www/rda/monoholoCS.rda", package = "idiogramFISH"))
load(system.file("shinyApps", "iBoard/www/rda/monoholoMarks.rda", package = "idiogramFISH"))
monoholoMarks2 <- fillMarkInfo(monoholoMarks, monoholoCS)
perMark(monoholoMarks2, monoholoCS, result = "data.frame")

plotDotMarks This is an internal function that plot dot marks

Description

It returns a plot

Usage

plotDotMarks(
  bannedMarkName,
  xMarkCr,
  yMarkCr,
  rad,
  radX,
  colCr,
  n,
  xfactor,
  colBorderCr,
  circularPlot,
  y,
  x,
  radius,
  circleCenter,
  circleCenterY,
  separFactor,
  chrWidth,
  listOfdfMarkPosCr,
  markLabelSize,
  pattern,
  labelSpacing,
  useOneDot,
  legend,
  ylistTransChr,
  rotation,
  labelOutwards,
  dotsAsOval,
  alpha_val = 1
)

Arguments

xMarkCr

x coords

yMarkCr

y coords

rad

radius

colCr

color

n

vertices number

xfactor

aspect

colBorderCr

border color

circularPlot

boolean

y

y of chr.

x

x of chr.

radius

numeric

circleCenter

numeric

circleCenterY

numeric

separFactor

numeric

chrWidth

numeric

listOfdfMarkPosCr

list of d.f.

markLabelSize

numeric

pattern

numeric

labelSpacing

numeric

useOneDot

boolean

legend

character

ylistTransChr

list of trans. coords

rotation

rotation

labelOutwards

srt

Value

plot

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)

sqPlotMarkCP This is an internal function that plot marks

Description

It returns a plot

Usage

plotSqMarks(
  chromatidsCheck_1,
  chromatidsCheck_2,
  circularPlot,
  squareness,
  xMarkSq,
  yMarkSq,
  dfMarkColorInt,
  lwd.marks2,
  listMarkPosSq,
  listChrSize,
  specialChrWidth,
  chrWidth,
  yfactor,
  markN,
  ptsl,
  bannedMarkName3,
  y,
  markLabelSize,
  pattern,
  separFactor,
  labelSpacing,
  circleCenter,
  circleCenterY,
  radius,
  legend,
  ylistTransChrSimple,
  rotation,
  labelOutwards,
  x,
  xModifierMH,
  pts,
  alpha_val = 1
)

Arguments

circularPlot

boolean TRUE for circ.

squareness

squareness of vertices <

dfMarkColorInt

colors for marks

listMarkPosSq

list of df. of mark pos.

listChrSize

chr size df list

specialChrWidth

numeric, width of chr.

chrWidth

numeric, width of chr.

yfactor

yMark distortion based on canvas proportion

y

list, y coords.

markLabelSize

numeric, font size

pattern

character, regex

separFactor

numeric, sep. kars.

labelSpacing

numeric, spacing

circleCenter

numeric

circleCenterY

numeric

radius

numeric

legend

character

rotation

rotate

labelOutwards

srt

Value

plot

This is an internal function to plot labels to the right, when "aside" for its position

Description

It returns a graphic element with the legends

Usage

plotlabelsright(
  maxx,
  y,
  markLabelSpacer,
  chrWidth,
  dfMarkColorInt,
  allMarkMaxSize,
  normalizeToOne,
  markLabelSize,
  xfactor,
  legendWidth,
  legendHeight,
  n,
  pattern,
  legendYcoord,
  useOneDot,
  dotsAsOval,
  circularPlot
)

Arguments

y

The y axis coordinates of chromosomes

markLabelSpacer

distance from right chr to legend

chrWidth

chr widht

dfMarkColorInt

data.frame of mark characteristics

allMarkMaxSize

maximum size of marks

normalizeToOne

transformation value of karyotype height

markLabelSize

font size of legends

xfactor

relative proportion of x vs y axes

legendWidth

factor to increase width of legend squares and dots

legendHeight

factor to increase height of legend squares and dots

n

numeric, vertices for round parts

pattern

character, regex to remove from markNames

legendYcoord

numeric modify Y position of legend

useOneDot

boolean, when TRUE plots only one dot

Value

Returns a graphics element

FUNCTION posCalc and fillMarkInfo

Description

calculates position of marks in fraction of (%) chromosome units (0-1)

Usage

posCalc(
  dfMarkPos,
  listOfdfChromSize,
  bToRemove = "",
  markDistType = "beg",
  origin = "b",
  showBandList = FALSE,
  result = "tibble"
)

fillMarkInfo2(dfMarkPos, dfChrSize)

fillMarkInfo(dfMarkPos, dfChrSize, markDistType = "beg", origin = "b")

Arguments

dfMarkPos

data.frame of marks' position

listOfdfChromSize

list (for posCalc) or data.frames of chr. sizes.

bToRemove

character, bands to remove from calc. of pos.

markDistType

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)

origin

character, 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.

showBandList

boolean, show row of all bands in tibble, see "result"

result

character, use "tibble" to get results in tibble, "data.frame", or other string results in a list

dfChrSize

data.frame of chr. sizes

Value

list, tibble

data.frame of marks

data.frame of marks

Examples

load(system.file("shinyApps", "iBoard/www/rda/monoholoCS.rda", package = "idiogramFISH"))
load(system.file("shinyApps", "iBoard/www/rda/monoholoMarks.rda", package = "idiogramFISH"))
monoholoMarks2 <- fillMarkInfo(monoholoMarks, monoholoCS)
posCalc(monoholoMarks2, monoholoCS, result = "data.frame")

removeNAFromList This is an internal function that removes NA from list

Description

It returns rulers (axis)

Usage

removeNAFromList(noNA, areNA)

Arguments

noNA

original list

areNA

which are NA

Value

list

FUNCTION to produce a Robertsonian translocation

Description

This function reads a data.frame with chr. sizes chrbasicdatamono and another with marks' positions, markposDFs and gets as arguments two chr. names and two arms, respectively.

It returns a list with two data.frames. One with the chr. size of the resulting translocation and another with the marks' positions for the derivative chr.

Usage

robert(dfChrSize, dfMarkPos, chr1, chr2, arm1, arm2)

Arguments

dfChrSize

name of data.frame of chr. sizes

dfMarkPos

name of data.frame of chr marks' positions

chr1

name of chr.

chr2

name of chr.

arm1

arm of chr1 to be included

arm2

arm of chr2 to be included

Value

list

References

Robertson, W. R. B. (1916). Chromosome studies. I. Taxonomic relationships shown in the chromosomes of Tettigidae and Acrididae: V-shaped chromosomes and their significance in Acrididae, Locustidae, and Gryllidae: chromosomes and variation. Journal of Morphology, 27(2), 179-331.

Examples

data(humChr)
data(humMarkPos)
chrt13q14q <- robert(humChr, humMarkPos, 13, 14, "q", "q")

rulerPlot This is an internal function that plots rulers

Description

It returns rulers (axis)

Usage

rulerPlot(
  ycoord,
  listOfdfChromSize,
  listOfdfChromSizeCenType,
  fromZerotoMax,
  rulerNumberSize,
  rulerPos,
  ruler.tck,
  lwd.chr,
  moveKarHor2,
  mkhValue,
  useMinorTicks,
  miniTickFactor,
  verticalPlot,
  moveAllKarValueHor
)

Arguments

ycoord

y coords

listOfdfChromSize

list of all d.f chr size

listOfdfChromSizeCenType

only d.f. of this cen. type

fromZerotoMax

intervals

rulerNumberSize

font

rulerPos

pos. of ruler

ruler.tck

tick size and orient.

Value

axis

rulerTitle This is an internal function that plots rulers

Description

It returns rulers (axis)

Usage

rulerTitle(
  xmnoNA,
  ymnoNA,
  chrSpacing,
  yPosRulerTitle,
  listOfdfChromSizeCenType,
  MbUnit,
  specialyTitle,
  yTitle,
  xPosRulerTitle,
  rulerTitleSize,
  verticalPlot
)

Arguments

xmnoNA

x coords

ymnoNA

y coords

chrSpacing

chr. spacing

listOfdfChromSizeCenType

only d.f. of this cen. type

MbUnit

intervals

specialyTitle

modifier of pos.

yTitle

pos. of ruler

xPosRulerTitle

font

rulerTitleSize

font size

Value

plot

FUNCTION runBoard

Description

runBoard: run shinyApp

Usage

runBoard(installAll = FALSE)

Arguments

installAll

boolean, when TRUE dependences are installed without asking. Defaults to FALSE

Value

shiny

textLabel This is an internal function that plot labels of cM marks

Description

It returns a plot

Usage

textLabel(
  xMark,
  yMark,
  listChrSizeText1,
  listOfdfMarkPos,
  specialChrSpacing,
  chrSpacing,
  markLabelSize,
  pattern,
  bannedMarkName,
  isCentromeric = FALSE,
  markNewLine2,
  mylheight2,
  xsize = 0
)

Arguments

xMark

x coords

yMark

y coords

listOfdfMarkPos

color

specialChrSpacing

vertices number

chrSpacing

aspect

markLabelSize

size of mark label font

pattern

pattern to remove from mark name

isCentromeric

use TRUE for cen. marks

Value

plotted text

textLabelDots This is an internal function that plot labels of cM marks

Description

It returns a plot

Usage

textLabelDots(
  xMarkCr,
  yMarkCr,
  listOfdfChromSize,
  listOfdfMarkPosCr,
  specialChrSpacing,
  chrSpacing,
  markLabelSize,
  pattern,
  bannedMarkName,
  xBoundariesQuar
)

Arguments

listOfdfChromSize

radius

listOfdfMarkPosCr

color

specialChrSpacing

vertices number

chrSpacing

aspect

markLabelSize

size of mark label font

pattern

pattern to remove from mark name

xBoundariesQuar

x size

Value

plotted text

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

Value

plot