1 idiogramFISH

The goal of idiogramFISH is to plot idiograms of several karyotypes having a set of dataframes for chromosome data and optionally marks’ data. Includes also a function to plot holocentrics and its marks getting sizes in micrometers or Mb (plotIdiogramsHolo) (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)

3 What’s new in gitlab?

ver. > 1.0.0

Releases:

Gitlab releases

4 Need help?

Manual

online Manual

Documentation

pkgdown style

5 Minimal examples

Let’s explore the dataframes 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
  chrName markName markArm markSize markDistCen
1       1       5S       p        1         0.5
2       1      45S       q        1         0.5
3       X      45S       p        1         1.0
4       3     DAPI       q        1         1.0
  chrName markName
1       1     DAPI
2       X      CMA

Let’s explore the dataframes 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

6 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/

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, 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://CRAN.R-project.org/package=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