1 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.

3 What’s new in gitlab?

ver. > 1.0.0

Releases:

Gitlab releases

4 Need help?

Manual

online Manual

Documentation

pkgdown style

5 Basic examples

Let’s explore the data.frames for monocentrics:

  chrName shortArmSize longArmSize
1       1            3           4
2       2            4           5
3       3            2           3
4       X            1           2
  markName markColor  style
1       5S       red   dots
2      45S     green square
3     DAPI      blue square
4      CMA    yellow 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       1       5S         p        1         0.5
2       1      45S         q        1         0.5
3       X      45S         p       NA          NA
4       3     DAPI         q        1         1.0
5       1     DAPI       cen       NA          NA
6       X      CMA       cen       NA          NA

Let’s explore the data.frames for holocentrics:

  chrName chrSize
1       1       3
2       2       4
3       3       2
4       4       5
  markName markColor  style
1       5S       red   dots
2      45S     green square
3     DAPI      blue square
4      CMA    yellow square
  chrName markName markPos markSize
1       3       5S     1.0      0.5
2       3     DAPI     2.0      0.5
3       1      45S     2.0      0.5
4       2     DAPI     2.0      0.5
5       4      CMA     2.0      0.5
6       4       5S     0.5      0.5

Plotting both mono. and holo.

Available only for ver. > 1.5.1

Merge data.frames with plyr (Wickham, 2011)

5.1 Let’s explore the data.frames for GISH:

parentalAndHybChrSize
           OTU chrName shortArmSize longArmSize
    Parental 1       1          3.2           4
    Parental 1       4          1.5           2
    Parental 1       5          4.8           6
    Parental 1       6          6.1           7
    Parental 2       1          3.2           4
    Parental 2       2          4.5           5
    Parental 2       3          2.0           3
 Allopolyploid       1          3.2           4
 Allopolyploid       2          4.5           5
 Allopolyploid       3          2.0           3
 Allopolyploid       4          1.5           2
 Allopolyploid       5          4.8           6
 Allopolyploid       6          6.1           7

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

dfAlloParentMarks
           OTU chrName   markName chrRegion
 Allopolyploid       1 Parental 1         p
 Allopolyploid       1 Parental 2         q
 Allopolyploid       1 Parental 2       cen
 Allopolyploid       2 Parental 2         w
 Allopolyploid       3 Parental 2         w
 Allopolyploid       4 Parental 1         w
 Allopolyploid       5 Parental 1         w
 Allopolyploid       6 Parental 1         w
    Parental 1       6 Parental 1         w
    Parental 1       5 Parental 1         w
    Parental 1       1 Parental 1         w
    Parental 1       4 Parental 1         w
    Parental 2       2 Parental 2         w
    Parental 2       1 Parental 2         w
    Parental 2       3 Parental 2         w

6 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:

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