Presentation

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). Documentation was written with R-packages bookdown, knitr, pkgdown and Rmarkdown (Allaire et al., 2019; Wickham and Hesselberth, 2019; Xie, 2019a, 2019b)

Minimal examples

Let’s explore the dataframes for monocentrics:

If only one species, column OTU is optional

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:

  • chromosome data, if only 1 species, column OTU is optional
chrName chrSize
1 3
2 4
3 2
4 5
  • mark general data
markName markColor style
5S red dots
45S green square
DAPI blue square
CMA yellow square
  • mark position data, if only 1 species, column OTU is optional (mandatory if in d.f of Chr. Size)
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

Plotting both mono. and holo.

Available only for ver. > 1.5.1

Merge data.frames with plyr (Wickham, 2016)

Let’s explore the dataframes 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

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/