idiogramFISH: Shiny App. Idiograms with Marks and Karyotype Indices

Introduction

The goal of idiogramFISH functions or shiny-app is to plot karyotypes, plasmids and circular chr. having a set of data.frames for chromosome data and optionally marks’ data (Roa and PC Telles, 2021). Karyotypes can also be plotted in concentric circles.

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).

Six styles of marks are available: square (squareLeft), dots, cM (cMLeft), cenStyle, upArrow (downArrow), exProtein (inProtein) (column style in dfMarkColor data.frame); its legend (label) (parameter legend) can be drawn inline or to the right of karyotypes. Three styles of centromere are available: rounded, triangle and inProtein (cenFormat parameter). Chromosome regions (column chrRegion in dfMarkPos data.frame) for monocentrics are p, q, cen, pcen, qcen. The last three cannot accommodate most mark styles, but can be colored. The region w can be used both in monocentrics and holocentrics.

IdiogramFISH was written in R (R Core Team, 2019) and also uses crayon (Csárdi, 2017), tidyr (Wickham and Henry, 2020), plyr (Wickham, 2011) and dplyr packages (Wickham et al., 2019). 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), phytools (Revell, 2012), ggtree (Yu et al., 2018), ggplot2 (Wickham, 2016) and ggpubr (Kassambara, 2019) were used.

In addition, the shiny app runBoard() uses shiny (Chang et al., 2021), shinydashboard (Chang and Borges Ribeiro, 2018), rhandsontable (Owen, 2018), gtools (Warnes et al., 2020) and rclipboard (Bihorel, 2021).

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Installation instructions

You can install idiogramFISH from CRAN with:

install.packages("idiogramFISH")

Windows users: To avoid installation of packages in OneDrive

.libPaths("D:R/lib") # for example
.libPaths()          # set or read libraries

To do that permanently: Search (magnifier) “environment variables” and set R_LIBS_USER to D:\R\lib (example)

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Releases

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Need help?

Manual in Bookdown style

Documentation in Pkgdown style

Vignettes

Online:

Launch vignettes from R for the installed version:

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

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Citation

To cite idiogramFISH in publications, please use:

Roa F, Telles MPC (2022) idiogramFISH: Shiny app. Idiograms with Marks and Karyotype Indices, Universidade Federal de Goiás. Brazil. R-package. version 2.0.9 https://ferroao.gitlab.io/manualidiogramfish/. doi:10.5281/zenodo.3579417

To write citation to file:

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

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Authors

Fernando Roa

Mariana PC Telles

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1 Working online

For Shiny App in the cloud availability, please check this chapter in the online version
https://ferroao.gitlab.io/idiogramfishhelppages

Each chapter has a jupyter version. A jupyter notebook seems an interactive vignette.

They are hosted in github

They can be accessed with google colab to work online.

	Github
3 Minimal examples	`link`	`Raw`
4 Plotting chromosomes	`link`	`Raw`
5 Multiple OTUs	`link`	`Raw`
6 Changing units	`link`	`Raw`
7 GISH	`link`	`Raw`
8 Groups	`link`	`Raw`
9 Circular Plots	`link`	`Raw`
10 Plotting alongside phylogeny	`link`	`Raw`
11 Citrus	`link`	`Raw`
12 Human Karyotype	`link`	`Raw`

Chapters can be accessed locally in your jupyter-lab or jupyter notebook

After installing jupyter, you can install the R kernel with:

install.packages("IRkernel")
IRkernel::installspec()

2 Shiny App

Attention Windows users, might require the last R version to plot correctly.

library(idiogramFISH)
runBoard()

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13 Functions

https://ferroao.gitlab.io/idiogramfishhelppages

14 Datasets

https://ferroao.gitlab.io/idiogramfishhelppages

News

https://ferroao.gitlab.io/idiogramfishhelppages

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

Romero-Zarco C. 1986. A new method for estimating karyotype asymmetry Taxon, 35(3): 526–530. https://doi.org/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

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://doi.org/10.1111/j.2041-210X.2011.00169.x

Roa F, PC Telles M. 2021. idiogramFISH: Shiny app. Idiograms with marks and karyotype indices Universidade Federal de Goiás, UFG, Goiânia. R-package. version 2.0.0. 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. 2019. 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

Winter DJ. 2017. rentrez: An r package for the NCBI eUtils API The R Journal, 9: 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: 3041–3043. https://doi.org/10.1093/molbev/msy194. https://doi.org/10.1093/molbev/msy194

Shiny App

Bihorel S. 2021. Rclipboard: Shiny/r wrapper for clipboard.js. R package version 0.1.3. https://github.com/sbihorel/rclipboard/

Chang W, Borges Ribeiro B. 2018. Shinydashboard: Create dashboards with shiny. R package version 0.7.1. http://rstudio.github.io/shinydashboard/

Chang W, Cheng J, Allaire J, Sievert C, Schloerke B, Xie Y, Allen J, McPherson J, Dipert A, Borges B. 2021. Shiny: Web application framework for r. R package version 1.6.0. https://shiny.rstudio.com/

Owen J. 2018. Rhandsontable: Interface to the handsontable.js library. R package version 0.3.7. http://jrowen.github.io/rhandsontable/

Warnes GR, Bolker B, Lumley T. 2020. Gtools: Various r programming tools. R package version 3.8.2. https://github.com/r-gregmisc/gtools

Documentation

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

Temple Lang D, CRAN team the. 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. 2019b. Badger: Badge for r package. R package version 0.0.6. https://CRAN.R-project.org/package=badger

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

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