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, 2021). 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.

In addition, the shiny app runBoard() uses shiny (Chang et al., 2021), shinydashboard (Chang and Borges Ribeiro, 2018), rhandsontable (Owen, 2018), gtools (Warnes et al., 2020), rclipboard (Bihorel, 2021).

Installation instructions

CRAN repo 10.5281/zenodo.3579417

You can install idiogramFISH from CRAN with:

install.packages("idiogramFISH")

Windows users: To avoid installation of packages in OneDrive

.libPaths("D:R/lib") # for example
.libPaths()          # set or read libraries

To do that permanently: Search (magnifier) “environment variables” and set R_LIBS_USER to D:\R\lib (example)

Other option: something in the line of this

Devel. version

gitlab repo

Install Gitlab dev. ver. with devtools (Wickham et al., 2019b):

Attention windows users, please install Rtools and git (compilation tools).

Vignettes (optional) use a lua filter, so you would need pandoc ver. > 2. and pandoc-citeproc or citeproc. RStudio comes with pandoc. rmarkdown::pandoc_version()

# This installs package devtools, necessary for installing the dev version
install.packages("devtools")

url <- "https://gitlab.com/ferroao/idiogramFISH"

# Packages for vignettes: (optional)
list.of.packages <- c(
    "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") )

Installing in system terminal

# clone repository:
git clone "https://gitlab.com/ferroao/idiogramFISH"

R CMD build idiogramFISH
# install
R CMD INSTALL idiogramFISH_*.tar.gz

Releases

NEWS

archive

downloads

Need help?

Manual in Bookdown style

https://ferroao.gitlab.io/manualidiogramfish

Documentation in Pkgdown style

https://ferroao.gitlab.io/idiogramFISH

Vignettes:

Online:

https://ferroao.gitlab.io/idiogramfishhelppages

Launch vignettes from R for the installed version:

library(idiogramFISH)
packageVersion("idiogramFISH")
browseVignettes("idiogramFISH")

Citation

To cite idiogramFISH in publications, please use:

Roa F, Telles MPC (2021) idiogramFISH: Shiny app. Idiograms with Marks and Karyotype Indices, Universidade Federal de Goiás. Brazil. R-package. version 2.0.5 https://ferroao.gitlab.io/manualidiogramfish/. doi:10.5281/zenodo.3579417

To write citation to file:

sink("idiogramFISH.bib")
toBibtex(citation("idiogramFISH"))
sink()