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Go to holocentrics Vignette
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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)
2 Installation
Or the dev version
From gitlab with devtools (Wickham et al., 2019) :
Attention windows users, please install Rtools
# This installs package devtools, necessary for installing the dev version
install.packages("devtools")
url <- "https://gitlab.com/ferroao/idiogramFISH"
# Linux with vignettes
devtools::install_git(url = url,build_vignettes = TRUE, force=T)
# Windows with vignettes
devtools::install_git(url = url, build_opts=c("--no-resave-data","--no-manual") )4 Need help?
Manual
Documentation
vignettes:
Online:
Monocentrics
Holocentrics
Groups of chromosomes
Human karyotype
Launch vignettes from R:
5 Minimal examples
How to plot a karyotype:
# fig.width=10, fig.height=6
library(idiogramFISH)
# load some package dataframes
data(dfOfChrSize) # chromsome data
data(dfMarkColor) # mark general data
data(dfOfMarks)   # mark position data (not cen.)
data(dfOfCenMarks)# centromeric mark data
plotIdiograms(dfChrSize=dfOfChrSize,    # data.frame of chr. size
              dfMarkColor=dfMarkColor,  # d.f of mark style
              dfMarkPos=dfOfMarks,      # df of mark positions (not centromeric)
              dfCenMarks=dfOfCenMarks,  # df of centromeric marks
              dotRoundCorr=2,           # correction of dots when non-circular
              
              chrWidth=2.5,             # width of chromosome
              chrSpacing = 2.5,         # horizontal space among chromosomes
              karSpacing=1.6,           # vertical size of karyotype including space
              
              indexIdTextSize=1,        # font size of chr names and indices
              markLabelSize=1,          # font size of legends
              
              rulerPos=-1.9,            # position of rulers
              ruler.tck=-0.02,          # size and orientation of ruler ticks
              rulerNumberPos=.5,        # position of numbers of rulers
              rulerNumberSize=1         # font size of rulers
)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      CMAHow to plot a karyotype of holocentrics:
library(idiogramFISH)
# load some saved dataframes
data(dfChrSizeHolo, dfMarkColor, dfMarkPosHolo)
plotIdiogramsHolo(dfChrSize=dfChrSizeHolo, # data.frame of chr. size
                  dfMarkColor=dfMarkColor, # df of mark style
                  dfMarkPos=dfMarkPosHolo, # df of mark positions
                  addOTUName=FALSE,        # do not add OTU names
                  
                  dotRoundCorr=2.5,        # correction of roundness of dots (marks)  
                  chrWidth=2.5,            # chr. width
                  indexIdTextSize=1,       # font size of chr. name and indices
                  legend="aside" ,         # legend of marks to the right of plot
                  markLabelSize=1,         # font size of mark labels (legend)
                  
                  rulerNumberSize=1,       # font size of ruler
                  rulerPos=-.7,            # position of ruler
                  ruler.tck=-0.04,         # size and orientation of ruler ticks
                  rulerNumberPos=.9,       # position of numbers of rulers
                  
                  xlimLeftMod=1,           # modify xlim left argument of plot
                  xlimRightMod=10,         # modify xlim right argument of plot
                  ylimBotMod=.2)           # modify ylim bottom argument of plotLet’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      0.56 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