Introduction

The goal of idiogramFISH functions or the shiny-app is to plot karyotypes, plasmids and circular chr. having a set of data.frames for chromosome data and optionally marks’ data [@Roa2021]. Karyotypes can also be plotted in concentric circles.

It is possible to calculate also chromosome and karyotype indexes [@Watanabe1999;@Zarco1986new] and classify chromosome morphology in the categories of Levan [-@Levan1964], and Guerra [-@Guerra1986d].

Six styles of marks are available: square (and squareLeft), dots, cM (cMLeft), cenStyle, upArrow (downArrow), exProtein (inProtein) (in column style in dfMarkColor data.frame); its legend (label) (parameter legend) can be drawn inline or to the right (aside) 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 (short), q (long), cen, pcen, qcen. The last three cannot accommodate most mark styles, but can be colored. The region w (whole) can be used both in monocentrics and holocentrics.

IdiogramFISH was written in R [@R-base] and also uses crayon [@R-crayon], tidyr [@R-tidyr], plyr [@plyr2011] and dplyr packages [@R-dplyr]. Documentation was written with R-packages roxygen2 [@R-roxygen2], usethis [@R-usethis], bookdown [@bookdown2016], knitr [@Xie2015], pkgdown [@R-pkgdown], Rmarkdown [@rmarkdown2018], rvcheck [@R-rvcheck], badger [@R-badger], kableExtra [@R-kableExtra], rmdformats [@R-rmdformats] and RCurl [@R-RCurl]. For some vignette figures, packages rentrez [@rentrez2017], phytools [@phytools2012], ggtree [@ggtree2018], ggplot2 [@ggplot22016] and ggpubr [@R-ggpubr] were used.

In addition, the shiny app runBoard() uses shiny [@R-shiny], shinydashboard [@R-shinydashboard], rhandsontable [@R-rhandsontable], gtools [@R-gtools] and rclipboard [@R-rclipboard].

docker pull fercyto/idiogramfish

# Run the image
docker run -d -p 8080:8080 fercyto/idiogramfish

# Stop the container
docker ps
docker stop {container id}

install.packages("idiogramFISH")

.libPaths()          # read library location
.libPaths("D:R/lib") # set

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

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

News

https://ferroao.gitlab.io/idiogramfishhelppages

References