idiogramFISH

Idiograms with Marks and Karyotype Indices

The goal of idiogramFISH is to plot idiograms of several karyotypes having a set of data.frames for chromosome data and optionally marks’ data (plotIdiograms) (Roa and PC Telles, 2020). 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 (Romero-Zarco, 1986; Watanabe et al., 1999) and classify chromosomes by morphology (Levan et al., 1964; Guerra, 1986).

IdiogramFISH was written in R (R Core Team, 2019) and also uses crayon (Csárdi, 2017), plyr (Wickham, 2011) and dplyr packages (Wickham et al., 2019a). Documentation was written with R-packages roxygen2 (Wickham et al., 2018), usethis (Wickham and Bryan, 2019), bookdown (Xie, 2016), knitr (Xie, 2015), pkgdown (Wickham and Hesselberth, 2019), Rmarkdown (Xie et al., 2018), rvcheck (Yu, 2019a), badger (Yu, 2019b), kableExtra (Zhu, 2019), prettydoc (Qiu, 2019) and RCurl (Temple Lang and CRAN team, 2019). For some vignette figures, packages phytools (Revell, 2012), ggtree (Yu et al., 2018), ggplot2 (Wickham, 2016) and ggpubr (Kassambara, 2019) were used.

Installation

You can install idiogramFISH from CRAN with:

install.packages("idiogramFISH")

Or the devel version of idiogramFISH

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

Attention windows users, please install Rtools and git.

Vignettes use a lua filter, so you need pandoc ver. > 2. rmarkdown::pandoc_version()

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

url <- "https://gitlab.com/ferroao/idiogramFISH"

# Necessary packages for vignettes:
list.of.packages <- c(
    "knitr",
    "kableExtra",
    "prettydoc",
    "rmarkdown",
    "RCurl",
    "rvcheck",
    "badger"
    )
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)

# Linux with vignettes and Windows
devtools::install_git(url = url,build_vignettes = TRUE, force=TRUE)

# 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 for the installed version:

browseVignettes("idiogramFISH")
packageVersion("idiogramFISH")

Basic examples

1 How to plot a karyotype:

Define your plotting window size with something like par(pin=c(10,6)), or with svg(), png(), etc. Add chromosome morphology according to Guerra (1986) or (Levan et al., 1964)

library(idiogramFISH)

data(dfOfChrSize) # chromsome data
data(dfMarkColor) # mark general data
data(dfOfMarks2)  # mark position data (inc. cen.)

# svg("testing.svg",width=11,height=4.5 )

opar <- par(no.readonly = TRUE)      # make a copy of current settings
par(mar = c(0, 0, 0, 0), omi=rep(0,4), oma=rep(0,4) )

plotIdiograms(dfChrSize=dfOfChrSize,    # data.frame of chr. size
              dfMarkColor=dfMarkColor,  # d.f of mark style <- Optional
              dfMarkPos=dfOfMarks2,     # df of mark positions (includes cen. marks)
              
              morpho="Guerra",          # chr. morpho. classif. (Guerra, Levan, both, "" ) ver. >= 1.12 only
              chrIndex="CI",            # cen. pos. (CI, AR, both, "" ) ver. >= 1.12 only
              
              rulerPos=-.9,             # position of rulers
              ruler.tck=-0.01,          # size and orientation of ruler ticks
              rulerNumberSize=.8        # font size of rulers
              
              ,legendWidth=1            # width of legend items
              ,distTextChr = .5         # chr. text separation
              
              ,xlimLeftMod = 2          # xlim left param.
              ,ylimBotMod = 0           # modify ylim bottom argument
              ,ylimTopMod = 0           # modify ylim top argument
              ,asp=1                    # y/x aspect, see ?plot
)

# par(opar)
# dev.off() # close svg()

Let’s explore the data.frames for monocentrics:

dfOfChrSize

dfMarkColor

p, q and w marks can have empty columns markDistCen and markSize since v. 1.9.1 to plot whole arms (p, q) and whole chr. w.

dfOfMarks2

2 How to plot a karyotype of holocentrics:

function plotIdiogramsHolo deprecated after ver. > 1.5.1

library(idiogramFISH)

# load some package data.frames
data(dfChrSizeHolo, dfMarkColor, dfMarkPosHolo)

# plotIdiogramsHolo is deprecated
par(mar = c(0, 0, 0, 0), omi=rep(0,4), oma=rep(0,4) )
# 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
              
              distTextChr = .5,        # chr. name distance to chr.
              
              rulerPos=-.9,            # position of ruler
              rulerNumberPos=.9,       # position of numbers of rulers
              
              xlimLeftMod=2,           # modify xlim left argument of plot
              ylimBotMod=.2            # modify ylim bottom argument of plot
              ,legendHeight=.5         # height of legend labels
              ,legendWidth = 1.2       # width of legend labels
              ,asp=1)                  # y/x aspect

# dev.off() # close svg()

Let’s explore the data.frames for holocentrics:

dfChrSizeHolo

dfMarkColor

dfMarkPosHolo

3. Plotting both mono. and holo.

Available only for ver. > 1.5.1

Merge data.frames with plyr (Wickham, 2011)

# 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 data.frames

# 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 = 4,             # vertices roundness
              addOTUName = TRUE,         # add OTU names
              distTextChr = .5,          # separ. among chr. and text and among chr. name and indices
              
              karHeiSpace = 3,           # karyotype height inc. spacing
              karIndexPos = .2,          # move karyotype index
              
              legendHeight= 1,           # height of legend labels
              legendWidth = 1,           # width of legend labels
              
              rulerPos= -0.5,            # position of ruler
              ruler.tck=-0.02,           # size and orientation of ruler ticks
              rulerNumberPos=.9,         # position of numbers of rulers
              
              xlimLeftMod=1,             # modify xlim left argument of plot
              xlimRightMod=3,            # modify xlim right argument of plot
              ylimBotMod= .2             # modify ylim bottom argument of plot
              ,asp=1                     # y x aspect ratio
)

#dev.off() # close svg()

4. Plotting GISH results

Available only for ver. > 1.8.3

library(idiogramFISH)
# load some saved data.frames

par(mar=rep(0,4))

# svg("allo.svg",width=10,height=9 )

par(mar = c(0, 0, 0, 0), omi=rep(0,4), oma=rep(0,4) )

plotIdiograms(dfChrSize = parentalAndHybChrSize,  # d.f. of chr. sizes
              dfMarkPos = dfAlloParentMarks,      # d.f. of marks' positions
              cenColor  = NULL                    # cen. color when GISH
              
              ,karHeiSpace=5,                     # karyotype height including spacing
              karSepar = FALSE,                   # equally sized karyotypes       
              
              rulerPos=-1,                        # ruler position
              ruler.tck= -0.002,                  # ruler tick orientation and length
              rulerNumberSize=.5                  # ruler font size
              ,legend=""                          # no legend
              ,asp=1                              # y x aspect ratio

              ,ylimBotMod = 1                     # modifiy ylim bottom argument
              ,xlimRightMod = 0                   # modify xlim right argument
              
)

#dev.off() # close svg()

Let’s explore the data.frames for GISH:

parentalAndHybChrSize

Use p for short arm, q for long arm, and w for whole chromosome mark.

dfAlloParentMarks

Citation

To cite idiogramFISH in publications, please use:

Roa F, Telles MPC (2020) idiogramFISH: Idiograms with Marks and Karyotype Indices, Universidade Federal de Goiás. Brazil. R-package. version 1.12.1 https://ferroao.gitlab.io/manualidiogramfish/. doi:10.5281/zenodo.3579417

To write citation to file:

sink("idiogramFISH.bib")
toBibtex(citation("idiogramFISH"))
sink()

Authors

Fernando Roa
Mariana PC Telles

References

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. https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1601-5223.1964.tb01953.x

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, 112: 145–161. http://link.springer.com/article/10.1007/PL00013869

R-packages references

Csárdi G. 2017. Crayon: Colored terminal output. R package version 1.3.4. https://CRAN.R-project.org/package=crayon

Kassambara A. 2019. Ggpubr: ’Ggplot2’ based publication ready plots. R package version 0.2.3. https://CRAN.R-project.org/package=ggpubr

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

Revell LJ. 2012. Phytools: An r package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution, 3: 217–223. https://besjournals.onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2011.00169.x

Roa F, PC Telles M. 2020. idiogramFISH: Idiograms with marks and karyotype indices Universidade Federal de Goiás, UFG, Goiânia. R-package. version 1.12.1. https://doi.org/10.5281/zenodo.3579417. https://ferroao.gitlab.io/manualidiogramfish/

Wickham H. 2011. The split-apply-combine strategy for data analysis Journal of Statistical Software, 40(1): 1–29. http://www.jstatsoft.org/v40/i01/

Wickham H. 2016. Ggplot2: Elegant graphics for data analysis Springer-Verlag New York. https://ggplot2.tidyverse.org

Wickham H, François R, Henry L, Müller K. 2019a. Dplyr: A grammar of data manipulation. R package version 0.8.3. https://CRAN.R-project.org/package=dplyr

Wickham H, Hester J, Chang W. 2019b. Devtools: Tools to make developing r packages easier. R package version 2.2.1. https://CRAN.R-project.org/package=devtools

Yu G, Lam TT-Y, Zhu H, Guan Y. 2018. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution, 35(2): 3041–3043. https://doi.org/10.1093/molbev/msy194. https://academic.oup.com/mbe/article/35/12/3041/5142656

Documentation references

Qiu Y. 2019. Prettydoc: Creating pretty documents from r markdown. R package version 0.3.0. https://CRAN.R-project.org/package=prettydoc

Temple Lang D, CRAN team. 2019. RCurl: General network (http/ftp/...) client interface for r. R package version 1.95-4.12. https://CRAN.R-project.org/package=RCurl

Wickham H, Bryan J. 2019. Usethis: Automate package and project setup. R package version 1.5.1. https://CRAN.R-project.org/package=usethis

Wickham H, Danenberg P, Eugster M. 2018. Roxygen2: In-line documentation for r. R package version 6.1.1. https://CRAN.R-project.org/package=roxygen2

Wickham H, Hesselberth J. 2019. Pkgdown: Make static html documentation for a package. R package version 1.4.1. https://CRAN.R-project.org/package=pkgdown

Xie Y. 2015. Dynamic documents with R and knitr Chapman; Hall/CRC, Boca Raton, Florida. ISBN 978-1498716963. http://yihui.name/knitr/

Xie Y. 2016. Bookdown: Authoring books and technical documents with R markdown Chapman; Hall/CRC, Boca Raton, Florida. ISBN 978-1138700109. https://github.com/rstudio/bookdown

Xie Y, Allaire J, Grolemund G. 2018. R markdown: The definitive guide Chapman; Hall/CRC, Boca Raton, Florida. ISBN 9781138359338. https://bookdown.org/yihui/rmarkdown

Yu G. 2019a. Rvcheck: R/package version check. R package version 0.1.6. https://CRAN.R-project.org/package=rvcheck

Yu G. 2019b. Badger: Badge for r package. R package version 0.0.6. https://CRAN.R-project.org/package=badger

Zhu H. 2019. KableExtra: Construct complex table with ’kable’ and pipe syntax. R package version 1.1.0. https://CRAN.R-project.org/package=kableExtra