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idiogramFISHIdiograms with Marks and Karyotype Indices

The goal of idiogramFISH is to plot idiograms of several karyotypes having a set of dataframes for chromosome data and optionally marks’ data (plotIdiograms) (Roa and Telles, 2019). Marks can have square or dot form, its legend (label) can be drawn inline or to the right of karyotypes. It is possible to calculate also chromosome and karyotype indexes and classify chromosomes by morphology (Levan et al., 1964; Guerra, 1986; Romero-Zarco, 1986; Watanabe et al., 1999).

IdiogramFISH was written in R(R Core Team, 2019) and also uses crayon package (Csárdi, 2017). Manuals were written with R-packages bookdown, knitr, badger, pkgdown and Rmarkdown (Allaire et al., 2019; Wickham and Hesselberth, 2019; Xie, 2019a, 2019b; Yu, 2019)

Installation

You can install idiogramFISH from CRAN with:

install.packages("idiogramFISH")

Or the devel version of idiogramFISH

From gitlab with devtools (Wickham et al., 2019)

Attention windows users, please install Rtools

# This installs package devtools, necessary for installing the dev version
install.packages("devtools")

url <- "https://gitlab.com/ferroao/idiogramFISH"
# Linux with vignettes and Windows R-32bits
devtools::install_git(url = url,build_vignettes = TRUE, force=T)
# Windows R-64bits and Mac with vignettes
devtools::install_git(url = url, build_opts=c("--no-resave-data","--no-manual") )
Or install it in terminal:
# clone repository:
git clone "https://gitlab.com/ferroao/idiogramFISH"

R CMD build idiogramFISH
# install
R CMD INSTALL idiogramFISH_*.tar.gz

What’s new in gitlab?

ver. > 1.0.0

Releases:

https://gitlab.com/ferroao/idiogramFISH/-/releases

Need help?

Manual in Bookdown style

https://ferroao.gitlab.io/manualidiogramfish/

Documentation in Pkgdown style

https://ferroao.gitlab.io/idiogramFISH

Vignettes:

Online:

Monocentrics
Holocentrics
Groups of chromosomes
Alongside Phylogeny
Human karyotype

Launch vignettes from R

browseVignettes("idiogramFISH") 

Basic examples

1 how to plot a karyotype:

Define your plotting window size with something like par(pin=c(10,6))

# fig.width=8, fig.height=6

library(idiogramFISH)
# load some package dataframes
data(dfOfChrSize) # chromsome data
data(dfMarkColor) # mark general data
data(dfOfMarks2)  # mark position data (inc. cen.)

# svg("testing.svg",width=14,height=8 )
plotIdiograms(dfChrSize=dfOfChrSize,    # data.frame of chr. size
              dfMarkColor=dfMarkColor,  # d.f of mark style                 < == Optional for ver. > 1.0.0
              dfMarkPos=dfOfMarks2,     # df of mark positions (includes cen. marks)
              
              dotRoundCorr=2,           # correction of dots when non-circular
              
              chrWidth=2.5,             # width of chromosome
              chrSpacing = 2.5,         # horizontal space among chromosomes
              karHeiSpace=1.6,          # vertical size of karyotype including space
              
              indexIdTextSize=1,        # font size of chr names and indices
              markLabelSize=1,          # font size of legends
              
              rulerPos=-1.9,            # position of rulers
              ruler.tck=-0.02,          # size and orientation of ruler ticks
              rulerNumberPos=.5,        # position of numbers of rulers
              rulerNumberSize=1         # font size of rulers
              ,legend="aside"           # try this
              ,legendWidth=1            # width of legend
)
# dev.off() # close svg()

Let’s explore the dataframes for monocentrics:

dfOfChrSize
chrNameshortArmSizelongArmSize
134
245
323
X12
dfMarkColor
markNamemarkColorstyle
5Sreddots
45Sgreensquare
DAPIbluesquare
CMAyellowsquare
dfOfMarks2
chrNamemarkNamemarkArmmarkSizemarkDistCen
15Sp10.5
145Sq10.5
X45Sp11.0
3DAPIq11.0
1DAPIcenNANA
XCMAcenNANA

2 How to plot a karyotype of holocentrics:

function plotIdiogramsHolo deprecated after ver. > 1.5.1

library(idiogramFISH)
# load some saved dataframes
data(dfChrSizeHolo, dfMarkColor, dfMarkPosHolo)

# plotIdiogramsHolo is deprecated

# svg("testing.svg",width=14,height=8 )
plotIdiograms(dfChrSize=dfChrSizeHolo, # data.frame of chr. size
                  dfMarkColor=dfMarkColor, # df of mark style
                  dfMarkPos=dfMarkPosHolo, # df of mark positions
                  addOTUName=FALSE,        # do not add OTU names
                  
                  dotRoundCorr=2.5,        # correction of roundness of dots (marks)  
                  chrWidth=1.5,            # chr. width
                  indexIdTextSize=1,       # font size of chr. name and indices
                  legend="aside" ,         # legend of marks to the right of plot
                  markLabelSize=1,         # font size of mark labels (legend)
                  
                  rulerNumberSize=1,       # font size of ruler
                  rulerPos=-.7,            # position of ruler
                  ruler.tck=-0.04,         # size and orientation of ruler ticks
                  rulerNumberPos=.9,       # position of numbers of rulers
                  
                  xlimLeftMod=1,           # modify xlim left argument of plot
                  xlimRightMod=10,         # modify xlim right argument of plot
                  ylimBotMod=.2            # modify ylim bottom argument of plot
                  ,legendHeight=.5         # height of legend labels
                  ,legendWidth = 1.2)      # width of legend labels
# dev.off() # close svg()

Let’s explore the dataframes for holocentrics:

dfChrSizeHolo
chrNamechrSize
13
24
32
45
dfMarkColor
markNamemarkColorstyle
5Sreddots
45Sgreensquare
DAPIbluesquare
CMAyellowsquare
dfMarkPosHolo
chrNamemarkNamemarkPosmarkSize
35S1.00.5
3DAPI2.00.5
145S2.00.5
2DAPI2.00.5
4CMA2.00.5
45S0.50.5

3. Plotting both mono. and holo.

Available only for ver. > 1.5.1

Merge data.frames with plyr (Wickham, 2016)

# chromsome data, if only 1 species, column OTU is optional
require(plyr)
dfOfChrSize$OTU   <- "Species mono"
dfChrSizeHolo$OTU <- "Species holo"
 
monoholoCS <- plyr::rbind.fill(dfOfChrSize,dfChrSizeHolo)

dfOfMarks2$OTU     <-"Species mono"
dfOfMarks2[which(dfOfMarks2$markName=="5S"),]$markSize<-.7
dfMarkPosHolo$OTU <-"Species holo"

monoholoMarks <- plyr::rbind.fill(dfOfMarks2,dfMarkPosHolo)
library(idiogramFISH)
# load some saved dataframes

# function plotIdiogramsHolo deprecated for ver. > 1.5.1
par(mar=rep(0,4))

# svg("testing.svg",width=14,height=10 )
plotIdiograms(dfChrSize  = monoholoCS,   # data.frame of chr. size
              dfMarkColor= dfMarkColor,  # df of mark style
              dfMarkPos  = monoholoMarks,# df of mark positions, includes cen. marks
 
              roundness = 8,             # vertices roundness
              dotRoundCorr=1.5,          # correction of roundness of dots (marks)  
              
              addOTUName = TRUE,         # add OTU names
              OTUTextSize = 1,           # OTU name font size
              
              chrWidth=1.5,              # chr. width
              indexIdTextSize=1,         # font size of chr. name and indices
              
              legend="aside" ,           # legend of marks to the right of plot
              markLabelSize=1,           # font size of mark labels (legend)
              legendHeight=.5,           # height of legend labels
              legendWidth = 1,           # width of legend labels

              rulerNumberSize=1,         # font size of ruler
              rulerPos= -1.8,            # position of ruler
              ruler.tck=-0.02,           # size and orientation of ruler ticks
              rulerNumberPos=.9,         # position of numbers of rulers
              
              xlimLeftMod=4,             # modify xlim left argument of plot
              xlimRightMod=10,           # modify xlim right argument of plot
              ylimBotMod=-.2             # modify ylim bottom argument of plot
)
#dev.off() # close svg()

Citation

To cite idiogramFISH in publications, please use:

Roa F, Telles MPC. 2019. idiogramFISH: Idiograms with Marks and Karyotype Indices, Universidade Federal de Goiás. Brazil. R-package. https://ferroao.gitlab.io/manualidiogramfish/

Authors

Fernando Roa
Mariana Telles

References

Allaire J, Xie Y, McPherson J, Luraschi J, Ushey K, Atkins A, Wickham H, Cheng J, Chang W, Iannone R. 2019. Rmarkdown: Dynamic documents for r. https://CRAN.R-project.org/package=rmarkdown

Csárdi G. 2017. Crayon: Colored terminal output. https://CRAN.R-project.org/package=crayon

Guerra M. 1986. Reviewing the chromosome nomenclature of Levan et al. Brazilian Journal of Genetics, 9(4): 741–743

Levan A, Fredga K, Sandberg AA. 1964. Nomenclature for centromeric position on chromosomes Hereditas, 52(2): 201–220. https://doi.org/10.1111/j.1601-5223.1964.tb01953.x

R Core Team. 2019. R: A language and environment for statistical computing R Foundation for Statistical Computing: Vienna, Austria. https://www.R-project.org/

Roa F, Telles MP. 2019. idiogramFISH: Idiograms with marks and karyotype indices Universidade Federal de Goiás: UFG, Goiânia. https://ferroao.gitlab.io/manualidiogramfish/

Romero-Zarco C. 1986. A new method for estimating karyotype asymmetry Taxon, 35(3): 526–530. https://onlinelibrary.wiley.com/doi/abs/10.2307/1221906

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, 145–161. http://link.springer.com/article/10.1007/PL00013869

Wickham H. 2016. Plyr: Tools for splitting, applying and combining data. https://CRAN.R-project.org/package=plyr

Wickham H, Hesselberth J. 2019. Pkgdown: Make static html documentation for a package. https://CRAN.R-project.org/package=pkgdown

Wickham H, Hester J, Chang W. 2019. Devtools: Tools to make developing r packages easier. https://CRAN.R-project.org/package=devtools

Xie Y. 2019a. Bookdown: Authoring books and technical documents with r markdown. https://github.com/rstudio/bookdown

Xie Y. 2019b. Knitr: A general-purpose package for dynamic report generation in r. https://CRAN.R-project.org/package=knitr

Yu G. 2019. Badger: Badge for r package. https://CRAN.R-project.org/package=badger

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Install

install.packages('idiogramFISH')

Monthly Downloads

997

Version

1.7.1

License

GPL (>= 2)

Maintainer

Last Published

October 20th, 2019

Functions in idiogramFISH (1.7.1)