idiogramFISH
Idiograms with Marks and Karyotype Indices
The goal of idiogramFISH is to plot idiograms of karyotypes, plasmids
and circ. 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. Seven styles of marks are available: square, 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), prettydoc (Qiu, 2019) 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
You can install idiogramFISH from CRAN with:
install.packages("idiogramFISH")
Or the devel version of idiogramFISH
From gitlab with devtools (Wickham et al., 2019b)
Attention windows users, please install Rtools and git.
Vignettes use a lua filter, so you 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",
"prettydoc",
"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:
# clone repository:
git clone "https://gitlab.com/ferroao/idiogramFISH"
R CMD build idiogramFISH
# install
R CMD INSTALL idiogramFISH_*.tar.gz
Releases
Need help?
Manual in Bookdown style
Documentation in Pkgdown style
Vignettes:
Online:
Launch vignettes from R for the installed version:
packageVersion("idiogramFISH")
browseVignettes("idiogramFISH")
Basic examples
1 How to plot a karyotype:
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.)
dfOfMarks2[which(dfOfMarks2$markName=="5S"),]$markSize<-0.8 # modif. of mark size
# svg("testing.svg",width=11,height=4.5 )
opar <- par(no.readonly = TRUE) # make a copy of current settings if you want to restore them later
#par(opar) # recover par
par(mar=rep(0,4))
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
rulerPos= 0, # position of ruler
ruler.tck=-0.01, # size and orientation of ruler ticks
rulerNumberSize=.8 # font size of rulers
,ylabline= -6 # ruler units (title) pos.
,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 = -1 # modify ylim bottom argument
,ylimTopMod = 0 # modify ylim top argument
# ,asp=1 # y/x aspect, see ?plot
)
# dev.off() # close svg()
Let’s explore the data.frames for monocentrics:
dfOfChrSize
chrName
shortArmSize
longArmSize
1
3
4
2
4
5
3
2
3
X
1
2
dfMarkColor
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
.
dfOfMarks2
chrName
markName
chrRegion
markSize
markDistCen
1
5S
p
0.8
0.5
1
45S
q
1.0
0.5
X
45S
p
NA
NA
3
DAPI
q
1.0
1.0
1
DAPI
cen
NA
NA
X
CMA
cen
NA
NA
2 How to plot a karyotype of holocentrics:
function plotIdiogramsHolo
deprecated after ver. > 1.5.1
library(idiogramFISH)
# load some package data.frames - optional
data(dfChrSizeHolo, dfMarkColor, dfMarkPosHolo)
# svg("testing.svg",width=14,height=8 )
par(mar = c(0, 0, 0, 0), omi=rep(0,4), oma=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 = .5, # chr. name distance to chr.
rulerPos=-.4, # position of ruler
rulerNumberPos=.9, # position of numbers of rulers
ylabline=-3, # ruler units (title) pos.
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:
dfChrSizeHolo
chrName
chrSize
1
3
2
4
3
2
4
5
dfMarkColor
markName
markColor
style
5S
red
dots
45S
green
square
DAPI
blue
square
CMA
yellow
square
dfMarkPosHolo
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
3. Plotting both mono. and holo.
See vignettes for a circular version.
Merge data.frames with plyr (Wickham, 2011)
# chromsome 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)
library(idiogramFISH)
# svg("testing.svg",width=14,height=10 )
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
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 = 3, # 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
ylabline=-6, # ruler units (title) pos.
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 svg()
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 1.15.1 https://ferroao.gitlab.io/manualidiogramfish/. doi:10.5281/zenodo.3579417
To write citation to file:
sink("idiogramFISH.bib")
toBibtex(citation("idiogramFISH"))
sink()
Authors
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. http://link.springer.com/article/10.1007/PL00013869
R-packages references
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 references
Qiu Y. 2019. Prettydoc: Creating pretty documents from r markdown. R package version 0.3.0. https://CRAN.R-project.org/package=prettydoc
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. http://yihui.name/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
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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
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