Idiograms with Marks and Karyotype Indices



 ’’ ’’  ’’
donatedonate

The goal of idiogramFISH is to plot idiograms of several karyotypes having a set of dataframes for chromosome data and optionally marks’ data (plotIdiograms) (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, pkgdown and Rmarkdown (Allaire et al., 2019; Wickham and Hesselberth, 2019; Xie, 2019a, 2019b)

Need help?

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") 

Basic examples

Let’s explore the dataframes for monocentrics:

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

Let’s explore the dataframes for holocentrics:

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

Let’s explore the dataframes for GISH:

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.

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

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*.
Csárdi G. 2017. *Crayon: Colored terminal output*.
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.
R Core Team. 2019. *R: A language and environment for statistical computing* R Foundation for Statistical Computing: Vienna, Austria.
Roa F, Telles MP. 2019. *idiogramFISH: Idiograms with marks and karyotype indices* Universidade Federal de Goiás: UFG, Goiânia.
Romero-Zarco C. 1986. A new method for estimating karyotype asymmetry *Taxon*, 35(3): 526–530.
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.
Wickham H. 2016. *Plyr: Tools for splitting, applying and combining data*.
Wickham H, François R, Henry L, Müller K. 2019a. *Dplyr: A grammar of data manipulation*.
Wickham H, Hesselberth J. 2019. *Pkgdown: Make static html documentation for a package*.
Wickham H, Hester J, Chang W. 2019b. *Devtools: Tools to make developing r packages easier*.
Xie Y. 2019a. *Bookdown: Authoring books and technical documents with r markdown*.
Xie Y. 2019b. *Knitr: A general-purpose package for dynamic report generation in r*.