idiogramFISH: Idiograms with Marks and Karyotype Indices
Introduction
The goal of idiogramFISH is to plot idiograms of karyotypes, plasmids and circular chr. having a set of data.frames for chromosome data and optionally marks’ data (plotIdiograms
function) (Roa and PC Telles, 2020). Idiograms can also be plotted in concentric circles. Separated chromatids can be visible when not in a circular plot.
Six styles of marks are available: square (squareLeft), dots, cM (cMLeft), cenStyle, upArrow, downArrow; 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 chromosome morphology in the categories of Levan (1964), and Guerra (1986).
IdiogramFISH was written in R (R Core Team, 2019) and also uses crayon (Csárdi, 2017), tidyr (Wickham and Henry, 2020) 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), rmdformats (Barnier, 2020) and RCurl (Temple Lang and CRAN team, 2019). For some vignette figures, packages rentrez (Winter, 2017), plyr (Wickham, 2011), phytools (Revell, 2012), ggtree (Yu et al., 2018), ggplot2 (Wickham, 2016) and ggpubr (Kassambara, 2019) were used.
Installation instructions
You can install idiogramFISH from CRAN with:
Or the devel. version
Install Gitlab dev. ver. with devtools (Wickham et al., 2019b):
Attention windows users, please install Rtools and git
Vignettes use a lua filter, so you would need pandoc ver. > 2. rmarkdown::pandoc_version()
# This installs package devtools, necessary for installing the dev version
install.packages("devtools")
url <- "https://gitlab.com/ferroao/idiogramFISH"
# Necessary packages for vignettes:
list.of.packages <- c(
"plyr",
"knitr",
"kableExtra",
"rmdformats",
"rmarkdown",
"RCurl",
"rvcheck",
"badger",
"rentrez"
)
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)
# Linux with vignettes and Windows
devtools::install_git(url = url,build_vignettes = TRUE, force=TRUE)
# Mac with vignettes
devtools::install_git(url = url, build_opts=c("--no-resave-data","--no-manual") )
Or install it in terminal:
Need help?
Vignettes:
Online:
Launch vignettes from R for the installed version:
Minimal examples
Monocentrics:
Define your plotting window size with something like par(pin=c(10,6))
, or with svg()
, png()
, etc. Add chromosome morphology according to Guerra (1986) or (Levan et al., 1964)
library(idiogramFISH)
data(dfOfChrSize) # chromsome data
data(dfMarkColor) # mark general data
data(dfOfMarks2) # mark position data (inc. cen.)
# column Mbp not for plotting purposes
dfOfChrSize$Mbp<-(dfOfChrSize$shortArmSize+dfOfChrSize$longArmSize)*100
svg("dfOfChrSize.svg",width=10,height=6 )
# png("dfOfChrSize.png", width=500, height=400)
plotIdiograms(dfChrSize =dfOfChrSize, # data.frame of chr. size
dfMarkColor=dfMarkColor, # d.f of mark style <- Optional
dfMarkPos=dfOfMarks2, # df of mark positions (includes cen. marks)
karHeight=5, # kar. height
chrWidth = 1.2, # chr. width
chrSpacing = 1, # space among chr.
morpho="Guerra", # chr. morpho. classif. (Guerra, Levan, both, "" ) ver. >= 1.12 only
chrIndex="CI", # cen. pos. (CI, AR, both, "" ) ver. >= 1.12 only
chrSize = TRUE, # add chr. sizes under chr.
chrSizeMbp = TRUE, # add Mbp sizes under chr. (see above)
rulerPos= 0, # position of ruler
ruler.tck=-0.01, # size and orientation of ruler ticks
rulerNumberSize=.8 # font size of rulers
,xPosRulerTitle = 3 # pos of ruler title
,legendWidth=1 # width of legend items
,fixCenBorder = TRUE # use chrColor as border color of cen. or cen. marks
,distTextChr = 1.2 # chr. text separation
,xlimLeftMod = 2 # xlim left param.
,ylimBotMod = 0 # modify ylim bottom argument
,ylimTopMod = 0 # modify ylim top argument
)
dev.off() # close svg()
Let’s explore the data.frames for monocentrics:
If only one species, column OTU is optional
chrName | shortArmSize | longArmSize | Mbp |
---|---|---|---|
1 | 3 | 4 | 700 |
2 | 4 | 5 | 900 |
3 | 2 | 3 | 500 |
X | 1 | 2 | 300 |
markName | markColor | style |
---|---|---|
5S | red | dots |
45S | chartreuse3 | square |
DAPI | blue | square |
CMA | darkgoldenrod1 | 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 |
Holocentrics:
library(idiogramFISH)
# load some package data.frames - optional
data(dfChrSizeHolo, dfMarkColor, dfMarkPosHolo)
# column Mbp not for plotting purposes
dfChrSizeHolo$Mbp<-dfChrSizeHolo$chrSize*100
# svg("testing.svg",width=14,height=8 )
par(mar = c(0, 0, 0, 0), omi=rep(0,4) )
plotIdiograms(dfChrSize =dfChrSizeHolo, # data.frame of chr. size
dfMarkColor=dfMarkColor, # df of mark style
dfMarkPos =dfMarkPosHolo, # df of mark positions
addOTUName=FALSE, # do not add OTU names
distTextChr = 1, # chr. name distance to chr.
chrSize = TRUE, # show chr. size under chr.
chrSizeMbp = TRUE, # show chr. size in Mbp under chr. requires Mbp column
rulerPos=-0.1, # position of ruler
rulerNumberPos=.9 # position of numbers of rulers
,xPosRulerTitle = 3 # pos. of ruler title (units)
,xlimLeftMod=2 # modify xlim left argument of plot
,ylimBotMod=.2 # modify ylim bottom argument of plot
,legendHeight=.5 # height of legend labels
,legendWidth = 1.2 # width of legend labels
,xModifier = .025 # separ. among chromatids
); #dev.off() # close svg()
Let’s explore the data.frames for holocentrics:
- chromosome data, if only 1 species, column OTU is optional
chrName | chrSize | Mbp |
---|---|---|
1 | 3 | 300 |
2 | 4 | 400 |
3 | 2 | 200 |
4 | 5 | 500 |
- mark general data
markName | markColor | style |
---|---|---|
5S | red | dots |
45S | chartreuse3 | square |
DAPI | blue | square |
CMA | darkgoldenrod1 | square |
- mark position data, if only 1 species, column OTU is optional (mandatory if in d.f of Chr. Size)
chrName | markName | markPos | markSize |
---|---|---|---|
3 | 5S | 1.0 | 0.5 |
3 | DAPI | 1.5 | 0.5 |
1 | 45S | 2.0 | 0.5 |
2 | DAPI | 2.0 | 0.5 |
4 | CMA | 2.0 | 0.5 |
4 | 5S | 0.5 | 0.5 |
Plotting both mono. and holo.
Merge data.frames with plyr
(Wickham, 2011)
# chromosome data, if only 1 species, column OTU is optional
require(plyr)
dfOfChrSize$OTU <- "Species mono"
dfChrSizeHolo$OTU <- "Species holo"
monoholoCS <- plyr::rbind.fill(dfOfChrSize,dfChrSizeHolo)
dfOfMarks2$OTU <-"Species mono"
dfOfMarks2[which(dfOfMarks2$markName=="5S"),]$markSize<-.7
dfMarkPosHolo$OTU <-"Species holo"
monoholoMarks <- plyr::rbind.fill(dfOfMarks2,dfMarkPosHolo)
Plot
library(idiogramFISH)
#svg("testing.svg",width=14,height=10 )
png("monoholoCS.png", width=700, height=600)
par(mar=rep(0,4))
plotIdiograms(dfChrSize = monoholoCS, # data.frame of chr. size
dfMarkColor= dfMarkColor, # df of mark style
dfMarkPos = monoholoMarks,# df of mark positions, includes cen. marks
chrSize = TRUE, # show chr. size under chr.
squareness = 4, # vertices squareness
roundedCen = FALSE, # triangular cen.
addOTUName = TRUE, # add OTU names
OTUTextSize = .7, # font size of OTU
distTextChr = .5, # separ. among chr. and text and among chr. name and indices
karHeiSpace = 4, # karyotype height inc. spacing
karIndexPos = .2, # move karyotype index
legendHeight= 1, # height of legend labels
legendWidth = 1, # width of legend labels
fixCenBorder = TRUE, # use chrColor as border color of cen. or cen. marks
rulerPos= 0, # position of ruler
ruler.tck=-0.02, # size and orientation of ruler ticks
rulerNumberPos=.9, # position of numbers of rulers
xPosRulerTitle = 3.5, # ruler title (units) position
xlimLeftMod=1, # modify xlim left argument of plot
xlimRightMod=3, # modify xlim right argument of plot
ylimBotMod= .2 # modify ylim bottom argument of plot
,chromatids=FALSE # do not show separ. chromatids
# for Circular Plot, add:
# ,circularPlot = TRUE # circularPlot
# ,shrinkFactor = .9 # percentage 1 = 100% of circle with chr.
# ,circleCenter = 3 # X coordinate of circleCenter (affects legend pos.)
# ,chrLabelSpacing = .9 # chr. names spacing
# ,OTUsrt = 0 # angle for OTU name (or number)
# ,OTUplacing = "number" # Use number and legend instead of name
# ,OTULabelSpacerx = -1.5 # modify position of OTU label, when OTUplacing="number" or "simple"
# ,OTUlegendHeight = 1.5 # space among OTU names when in legend - OTUplacing
)
dev.off() # close png
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 1.16.7 https://ferroao.gitlab.io/manualidiogramfish/. doi:10.5281/zenodo.3579417
To write citation to file:
1 Plotting chromosomes
2 Several OTUs
3 Changing Units
5 Using groups
6 Circular plots
7 Plotting alongside phylogeny
9 Human karyotype
10 Functions
11 Datasets
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. https://link.springer.com/article/10.1007/PL00013869
R-packages
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. https://www.jstatsoft.org/article/view/v040i01
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, Henry L. 2020. Tidyr: Tidy messy data. R package version 1.0.2. https://CRAN.R-project.org/package=tidyr
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
Winter DJ. 2017. rentrez: An r package for the ncbi eUtils api The R Journal, 9(2): 520–526
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
Barnier J. 2020. Rmdformats: HTML output formats and templates for ’rmarkdown’ documents. R package version 0.3.7. https://CRAN.R-project.org/package=rmdformats
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. https://yihui.org/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 JJ, 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