A lightweight interactive HTML widget in R for rendering an interactive ideogram diagram displaying shared identity-by-descent (IBD) regions between individuals detected from IBIS or TRUFFLE using Ideogram.js (https://github.com/eweitz/ideogram). The annotation bands on the chromosomes of the created ideogram register click events and display tooltips. This interactive ideogram widget can be embedded in Shiny applications or R-markdown documents (Rmd).

Screenshot from 2022年08月26日 20-35-13

• R (>4.2.1)
• htmlwidgets (>=1.5.4 )
• pals (>=1.7)
• DescTools (>=0.99.45)

To install all the widget's dependencies, type the following in R:

install.packages(c("htmlwidgets", "pals", "DescTools"))

To download the latest release of the Ideogram htmlwidget library click here. To install the ideogram R library, download the tar file (.tar.gz) and run the following command in R using the downloaded ideogram tar file path:

install.packages("ideogram-0.1.0-alpha.tar.gz", type="source", repos=NULL)

The input IBD segment file containing IBD segment to be displayed on the ideogram widget can be either an IBIS IBD segment file (.seg) or a TRUFFLE segments file (.segment).

An example IBIS segment file (default file is usually headerless)

Screenshot from 2022年09月16日 14-33-30

If a header is provided, the header must be specified as follows:

Screenshot from 2022年09月16日 14-35-17

An example Truffle segments file (taken from an example provided on the TRUFFLE website at https://adimitromanolakis.github.io/truffle-website/documentation/doc.html) image

To start using the ideogram library in the R environment, type the following in R:

library(ideogram)

After installation of the ideogram library in R, create the htmlwidget in R by calling the ideogram function with an IBD segment file (.seg/.segment from IBIS/TRUFFLE):

ideogram("ibd_segment.txt")

The ideogram library has two Shiny binding functions:

1. ideogramOutput - Shiny front-end function (with a widget id)

2. renderIdeogram - Shiny back-end (server) function to render the ideogram

To embed the widget in a Shiny App, use the ideogramOutput in the Shiny front-end function with a custom ID and invoke the ideogram function in a renderIdeogram function in the back-end (server), as demonstrated in a basic Shiny app below:

install.packages(shiny) # if not installed
library(shiny)
# render Shiny UI
ui <- fluidPage(
 ideogramOutput("ideogram_id")
)
# server logic code
serve <- function(input, output){
 output$ideogram_id <- renderIdeogram({
 ideogram("ibd_segment_file_path.seg")
 })
}
shinyApp(ui, output)

For any questions, feature requests, bug reports or issues regarding the latest version of Ideogram, please click on the "issues" tab present at the top-left of the GitHub repository page.