Introduction

The goal of idiogramFISH functions or shiny-app is to plot karyotypes, plasmids and circular chr. having a set of data.frames for chromosome data and optionally marks’ data (Roa and PC Telles, 2021). Karyotypes can also be plotted in concentric circles.

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).

Six styles of marks are available: square (squareLeft), dots, cM (cMLeft), cenStyle, upArrow (downArrow), exProtein (inProtein) (column style in dfMarkColor data.frame); its legend (label) (parameter legend) can be drawn inline or to the right of karyotypes. Three styles of centromere are available: rounded, triangle and inProtein (cenFormat parameter). Chromosome regions (column chrRegion in dfMarkPos data.frame) for monocentrics are p, q, cen, pcen, qcen. The last three cannot accommodate most mark styles, but can be colored. The region w can be used both in monocentrics and holocentrics.

IdiogramFISH was written in R (R Core Team, 2019) and also uses crayon (Csárdi, 2017), tidyr (Wickham and Henry, 2020), plyr (Wickham, 2011) 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), 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) and rclipboard (Bihorel, 2021).

install.packages("idiogramFISH")

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

# 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") )

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

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

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

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

News

https://ferroao.gitlab.io/idiogramfishhelppages

References