This repository is for the interactive plots 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.
| 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' |
Run KING to get the required three 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("InteractivePlots", "chenlab-uva", ref = "main", subdir = "viewROH")
Example output
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("InteractivePlots", "chenlab-uva", ref = "main", subdir = "viewIBD")
Example output
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("InteractivePlots", "chenlab-uva", ref = "main", subdir = "viewFamily")
