Interactive Visualization of Relatedness from KING

This repository is for the interactive visualization of relatedness from KING. We use HapMap (https://www.dropbox.com/s/3dgjlmdc9b1tigq/HapMap.zip?dl=0) as the example dataset.

Use curl to download the example dataset.

curl https://www.dropbox.com/s/3dgjlmdc9b1tigq/HapMap.zip?dl=0 -O -J -L

Then use unzip to unzip the zipped file.

unzip HapMap.zip 

Or we can click the Dropbox link, and then click the download button at the top right corner to download files. And then use unzip to unzip the zipped file.

unzip HapMap.zip 

Related KING output files are saved at HapMap folder.

Required R packages for these shiny apps.

Name	Required R packages
viewROH	'shiny', 'ggplot2'
viewIBD	'shiny', 'ggplot2' and 'data.table', 'R.utils'
viewFamily	'shiny', 'ggplot2', 'data.table', 'kinship2' and 'igraph', 'R.utils'

Interactive plots for ROH

Run KING to get required files. They are *.roh, *.rohseg.gz and *allsegs.txt

king -b hapmap.bed --roh --prefix hapmap

Run the following R code in R to get interactive plots. Package 'shiny' and 'ggplot2' are required. Related R files are saved at viewROH folder.

library(shiny)
runGitHub("InteractiveRelatednessPlots", "chenlab-uva", ref = "main", subdir = "viewROH")

Example output

After selecting the *.roh file from KING, we will see each sample's F_ROH and F_ROH on X chromosome.

We can explore each sample's detailed ROH information by clicking a dot on the interactive display plot.

Also, we can type a family ID that we are interested in, and then select a sample within that family to look into the details.

Interactive plots for IBD Segments

Run KING to get the required three files. They are *.seg, *.segments.gz and *allsegs.txt

king -b hapmap.bed --ibdseg --prefix hapmap

Run the following R code in R to get interactive plots. Package 'shiny', 'data.table' and 'ggplot2' are required. Related R files are saved at viewIBD folder.

library(shiny)
runGitHub("InteractiveRelatednessPlots", "chenlab-uva", ref = "main", subdir = "viewIBD")

Example output

After selecting the *.seg file from KING, we will see the shared IBD information, ploting length proportion of IBD2 segments against length proportion of IBD1 Segments.

We can see the detailed IBD sharing by clicking a dot from the interactive display of IBD relatedness plot.

Also, we can type a family ID that we are interested in, and then select a pair within that family to look into the details.

Visualization of Families

Run KING to get the required four files. They are *.seg, *.segments.gz, *allsegs.txt and *splitped.txt. Related R files are saved at viewFamily folder.

king -b hapmap.bed --ibdseg --prefix hapmap

Package 'shiny', 'kinship2', 'igraph', 'data.table' and 'ggplot2' are required.

library(shiny)
runGitHub("InteractiveRelatednessPlots", "chenlab-uva", ref = "main", subdir = "viewFamily")

Example output

First, select the *.seg file from KING, and then type a family ID to be visualized. We will see two plots with reported pedigree information and the inferred relatedness.

We can explore the detailed IBD sharing by clicking the lines on the interactive display of relatedness plot.

Also, we can explore the family relatedness under a particular family size. And then choose a family of that family size. Detailed IBD sharing will be displayed under these two plots by clicking the lines on the interactive inferred relatedness plot.