Package 'idiogramFISH' reference manual

Title:	Shiny App. Idiograms with Marks and Karyotype Indices
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).
Authors:	Fernando Roa [aut, cre], Mariana PC Telles [ctb]
Maintainer:	Fernando Roa <[email protected]>
License:	GPL (>= 2)
Version:	2.0.13.9000
Built:	2024-11-03 04:53:27 UTC
Source:	https://gitlab.com/ferroao/idiogramfish

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)
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

Examples

armRatioCI(dfOfChrSize)
armRatioCI(bigdfOfChrSize)

swapChrRegionDfSizeAndMarks(dfOfChrSize, dfOfMarks, "1")
armRatioCI(dfOfChrSize)
armRatioCI(bigdfOfChrSize)

swapChrRegionDfSizeAndMarks(dfOfChrSize, dfOfMarks, "1")

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)
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.

Examples

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

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
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.

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
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.

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
)
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

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
)
)
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
)
)

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
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/

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")
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

FUNCTION make.uniqueIF

Description

make.uniqueIF: produces unique strings from duplicated

Usage

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

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

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"
)
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)
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

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
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.

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
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.

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 
)
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

FUNCTION perMark

Description

calculates fraction (%) of chromosome for each mark

Usage

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

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")

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, ... 
)
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 $\mu$ m. 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

Examples

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

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")
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

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")

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")

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)
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")

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

FUNCTION runBoard

Description

runBoard: run shinyApp

Usage

runBoard(installAll = FALSE)
runBoard(installAll = FALSE)

Arguments

installAll

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

Value

shiny

Package 'idiogramFISH'

Help Index

FUNCTIONS armRatioCI and swapChrRegionDfSizeAndMarks.

Description

Usage

Arguments

Value

References

See Also

Examples

FUNCTIONS asymmetry and asymmetryA2.

Description

Usage

Arguments

Value

References

See Also

Examples

Chr. basic data Holo.

Description

Usage

Format

See Also

Chr. basic data Monocen.

Description

Usage

Format

Source

References

See Also

FUNCTIONS: citrusSize, citrusMarkPos, markOverCMA

Description

Usage

Arguments

Value

References

Examples

Mark characteristics

Description

Usage

Format

Source

References

See Also

FUNCTION genBankReadIF

Description

Usage

Arguments

Value

FUNCTION make.uniqueIF

Description

Usage

Arguments

Value

Examples

FUNCTION to make a data.frame of Marks' characterisitcs

Description

Usage

Arguments

Value

FUNCTIONS mapGGChr and mapGGChrMark (for ggplot)

Description

Usage

Arguments

Value

Mark Positional data - Holocen.

Description

Usage

Format

See Also

Mark Positional data - monocentrics

Description

Usage

Format

Source

References

See Also

FUNCTION that modifies marks' names into columns

Description

Usage