Idiograms with Marks and Karyotype Indices
The goal of idiogramFISH is to plot idiograms of karyotypes, plasmids and circ. chr. having a set of data.frames for chromosome data and optionally marks’ data (plotIdiograms function) (Roa and PC Telles, 2020). Idiograms can also be plotted in concentric circles. Separated chromatids can be visible when not in a circular plot.
Six styles of marks are available: square (squareLeft), dots, cM (cMLeft), cenStyle, upArrow, downArrow; 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 chromosome morphology in the categories of Levan (1964), and Guerra (1986).
IdiogramFISH was written in R (R Core Team, 2019) and also uses crayon (Csárdi, 2017), tidyr (Wickham and Henry, 2020) 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), rmdformats (Barnier, 2020) and RCurl (Temple Lang and CRAN team, 2019). For some vignette figures, packages rentrez (Winter, 2017), plyr (Wickham, 2011), 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( "plyr", "knitr", "kableExtra", "rmdformats", "rmarkdown", "RCurl", "rvcheck", "badger", "rentrez" ) 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") )
Need help?
Vignettes:
Online:
Launch vignettes from R for the installed version:
packageVersion("idiogramFISH") browseVignettes("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.) dfOfMarks2[which(dfOfMarks2$markName=="5S"),]$markSize<-0.8 # modif. of mark size # column Mbp not for plotting purposes dfOfChrSize$Mbp<-(dfOfChrSize$shortArmSize+dfOfChrSize$longArmSize)*100 # svg("testing.svg",width=11,height=4.5 ) opar <- par(no.readonly = TRUE) # make a copy of current settings if you want to restore them later #par(opar) # recover par par(mar=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) karHeight=5, # kar. height chrWidth = 1.2, # chr. width chrSpacing = 1, # space among chr. morpho="Guerra", # chr. morpho. classif. (Guerra, Levan, both, "" ) ver. >= 1.12 only chrIndex="CI", # cen. pos. (CI, AR, both, "" ) ver. >= 1.12 only chrSize = TRUE, # add chr. sizes under chr. chrSizeMbp = TRUE, # add Mbp sizes under chr. (see above) rulerPos= 0, # position of ruler ruler.tck=-0.01, # size and orientation of ruler ticks rulerNumberSize=.8 # font size of rulers ,xPosRulerTitle = 3 # ruler units (title) pos. ,legendWidth=1 # width of legend items ,fixCenBorder = TRUE # use chrColor as border color of cen. or cen. marks ,distTextChr = 1.2 # chr. text separation ,xlimLeftMod = 2 # xlim left param. ,ylimBotMod = 0 # modify ylim bottom argument ,ylimTopMod = 0 # modify ylim top argument ); # dev.off() # close svg()
Let’s explore the data.frames for monocentrics:
| chrName | shortArmSize | longArmSize | Mbp |
|---|---|---|---|
| 1 | 3 | 4 | 700 |
| 2 | 4 | 5 | 900 |
| 3 | 2 | 3 | 500 |
| X | 1 | 2 | 300 |
| markName | markColor | style |
|---|---|---|
| 5S | red | dots |
| 45S | chartreuse3 | square |
| DAPI | blue | square |
| CMA | darkgoldenrod1 | square |
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.
| chrName | markName | chrRegion | markSize | markDistCen |
|---|---|---|---|---|
| 1 | 5S | p | 0.8 | 0.5 |
| 1 | 45S | q | 1.0 | 0.5 |
| X | 45S | p | NA | NA |
| 3 | DAPI | q | 1.0 | 1.0 |
| 1 | DAPI | cen | NA | NA |
| X | CMA | cen | NA | NA |
2 How to plot a karyotype of holocentrics:
library(idiogramFISH) # column Mbp not for plotting purposes dfChrSizeHolo$Mbp<-dfChrSizeHolo$chrSize*100 # svg("testing.svg",width=14,height=8 ) par(mar = c(0, 0, 0, 0), omi=rep(0,4) ) plotIdiograms(dfChrSize =dfChrSizeHolo, # data.frame of chr. size dfMarkColor=dfMarkColor, # df of mark style dfMarkPos =dfMarkPosHolo, # df of mark positions addOTUName=FALSE, # do not add OTU names distTextChr = 1, # chr. name distance to chr. chrSize = TRUE, # show chr. size under chr. chrSizeMbp = TRUE, # show chr. size in Mbp under chr. requires Mbp column rulerPos=-.4, # position of ruler rulerNumberPos=.9, # position of numbers of rulers xPosRulerTitle= 4.5 # ruler units (title) horizon. pos. ,xlimLeftMod=2 # modify xlim left argument of plot ,ylimBotMod=.2 # modify ylim bottom argument of plot ,legendHeight=.5 # height of legend labels ,legendWidth = 1.2 # width of legend labels ,xModifier = .025 # separ. among chromatids ); # dev.off() # close svg()
Let’s explore the data.frames for holocentrics:
| chrName | chrSize | Mbp |
|---|---|---|
| 1 | 3 | 300 |
| 2 | 4 | 400 |
| 3 | 2 | 200 |
| 4 | 5 | 500 |
| markName | markColor | style |
|---|---|---|
| 5S | red | dots |
| 45S | chartreuse3 | square |
| DAPI | blue | square |
| CMA | darkgoldenrod1 | square |
| chrName | markName | markPos | markSize |
|---|---|---|---|
| 3 | 5S | 1.0 | 0.5 |
| 3 | DAPI | 1.5 | 0.5 |
| 1 | 45S | 2.0 | 0.5 |
| 2 | DAPI | 2.0 | 0.5 |
| 4 | CMA | 2.0 | 0.5 |
| 4 | 5S | 0.5 | 0.5 |
3. Plotting both mono. and holo.
See vignettes for a circular version.
Merge data.frames with plyr (Wickham, 2011)
# chromsome data, if only 1 species, column OTU is optional require(plyr) dfOfChrSize$OTU <- "Species mono" dfChrSizeHolo$OTU <- "Species holo" monoholoCS <- plyr::rbind.fill(dfOfChrSize,dfChrSizeHolo) dfOfMarks2$OTU <-"Species mono" dfMarkPosHolo$OTU <-"Species holo" monoholoMarks <- plyr::rbind.fill(dfOfMarks2,dfMarkPosHolo) monoholoMarks[which(monoholoMarks$markName=="5S"),]$markSize<-.5 monoholoMarks chrName markName chrRegion markSize markDistCen OTU markPos 1 1 5S p 0.5 0.5 Species mono NA 2 1 45S q 1.0 0.5 Species mono NA 3 X 45S p NA NA Species mono NA 4 3 DAPI q 1.0 1.0 Species mono NA 5 1 DAPI cen NA NA Species mono NA 6 X CMA cen NA NA Species mono NA 7 3 5S <NA> 0.5 NA Species holo 1.0 8 3 DAPI <NA> 0.5 NA Species holo 1.5 9 1 45S <NA> 0.5 NA Species holo 2.0 10 2 DAPI <NA> 0.5 NA Species holo 2.0 11 4 CMA <NA> 0.5 NA Species holo 2.0 12 4 5S <NA> 0.5 NA Species holo 0.5
library(idiogramFISH) # svg("testing.svg",width=10,height=6 ) par(mar=rep(0,4)) plotIdiograms(dfChrSize = monoholoCS, # data.frame of chr. size dfMarkColor= dfMarkColor, # df of mark style dfMarkPos = monoholoMarks,# df of mark positions, includes cen. marks chrSize = TRUE, # show chr. size under chr. squareness = 4, # vertices squareness roundedCen = FALSE, # triangular cen. addOTUName = TRUE, # add OTU names OTUTextSize = .7, # font size of OTU distTextChr = 0.7, # separ. among chr. and text and among chr. name and indices karHeiSpace = 4, # karyotype height inc. spacing karIndexPos = .2, # move karyotype index legendHeight= 1, # height of legend labels legendWidth = 1, # width of legend labels fixCenBorder = TRUE, # use chrColor as border color of cen. or cen. marks rulerPos= 0, # position of ruler ruler.tck=-0.02, # size and orientation of ruler ticks rulerNumberPos=.9, # position of numbers of rulers xPosRulerTitle= 4, # ruler units (title) pos. xlimLeftMod=1, # modify xlim left argument of plot xlimRightMod=3, # modify xlim right argument of plot ylimBotMod= .2 # modify ylim bottom argument of plot ,chromatids=FALSE # do not show separ. chromatids # for Circular Plot, add: # ,circularPlot = TRUE # circularPlot # ,shrinkFactor = .9 # percentage 1 = 100% of circle with chr. # ,circleCenter = 3 # X coordinate of circleCenter (affects legend pos.) # ,chrLabelSpacing = .9 # chr. names spacing # ,OTUsrt = 0 # angle for OTU name (or number) # ,OTUplacing = "number" # Use number and legend instead of name # ,OTULabelSpacerx = -1.6 # modify position of OTU label, when OTUplacing="number" or "simple" # ,OTUlegendHeight = 1.5 # space among OTU names when in legend - OTUplacing ); # dev.off() # close svg()
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 1.16.6 https://ferroao.gitlab.io/manualidiogramfish/. doi:10.5281/zenodo.3579417
To write citation to file:
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. https://link.springer.com/article/10.1007/PL00013869
R-packages references
Barnier J. 2020. Rmdformats: HTML output formats and templates for ’rmarkdown’ documents. R package version 0.3.7. https://CRAN.R-project.org/package=rmdformats
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. https://www.jstatsoft.org/article/view/v040i01
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, Henry L. 2020. Tidyr: Tidy messy data. R package version 1.0.2. https://CRAN.R-project.org/package=tidyr
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
Winter DJ. 2017. rentrez: An r package for the ncbi eUtils api The R Journal, 9(2): 520–526
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
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. https://yihui.org/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 JJ, 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