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 (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 (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 Core Team, 2019) and also uses crayon (Csárdi, 2017), tidyr (Wickham and Henry, 2020), plyr (Wickham, 2011) and dplyr packages (Wickham et al., 2019). 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).
Run the Shiny app with docker
- No need to install R
- Install docker on your system
- Make sure you can run a docker example image, i.e. ubuntu, in the console (system terminal)
docker pull fercyto/idiogramfish
# Run the image
docker run -d -p 8080:8080 fercyto/idiogramfishIn your internet browser go to http://localhost:8080
# Stop the container
docker ps
docker stop {container id}Installation instructions
You can install idiogramFISH from CRAN with:
install.packages("idiogramFISH")Windows users: To avoid installation of R-packages in OneDrive
.libPaths() # read library location
.libPaths("D:R/lib") # setTo 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 link
Need help?
Vignettes
Online:
Launch vignettes from R for the installed version:
library(idiogramFISH)
packageVersion("idiogramFISH")
browseVignettes("idiogramFISH")