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Ideogram

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 2022-08-26 20-35-13

System Requirements

  • 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"))

Download and Installation

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)

IBD Segment File

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 2022-09-16 14-33-30

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

Screenshot from 2022-09-16 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

Usage

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")

Embedding the ideogram widget in a Shiny Application

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)

Questions, Feature Requests, Bug Reports and Issues

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.