Multiple Phenotype Interactive Locus Zoom R Shiny App

• Author(s) - Frank Grenn
• Date Started - December 2020
• Tools - LocusZoom.js, RShiny
• Quick Description: A simple R Shiny application that incorporates code from LocusZoom.js to create a multiple phenotype interactive locus zoom plot.

Setup

1. Format Summary Statistics into JSON Format

Follow code in locus_zoom_data.ipynb or locus_zoom_data.R to do the conversion explained below.

We want to get the chromosome, basepair, pvalue, reference allele, and variant id (can be chr:bp, rsid, etc) from the summary statistics and save in a json format that the interactive locus zoom tool can read. For example, we want to convert something like:

CHR	BP	SNP	A1	A2	N	P	OR
1	11154	chr1:11154	C	A	4	0.7911	0.9818
1	11565	chr1:11565	G	T	5	0.8735	0.9924
1	11710	chr1:11710	T	G	4	0.7793	0.9806

To a json format like this:

{
   "data":
   {
      "chromosome":["1","1","1"],
      "log_pvalue":[0.102,0.059,0.108],
      "position":[11154,11565,11710],
      "ref_allele":["C","G","T"],
      "variant":["chr1:11154","chr1:11565","chr1:11710"]
   }

}

2. Place the Formatted JSON Files in the Shiny App /jsons Folder

3. Change Arguments in call_locus_zoom.js

a. Display Range

Change the values of the default_range variable to select the region to plot.

var default_range = {
  chr:"14",
  start:87523488,
  end:89523488
}

b. Plot Dimensions

Set the width of the plot. Height is determined by gene panel.

var default_width = 1200;

c. Phenotypes to Include

Add each phenotype to the phenos array (you can have more than two).

var phenos = [

    { namespace:"MS", title:"MS", filename:"ms_sumstats_chr14_87523488_89523488.json", color: "rgb(255,0,0)"},
    { namespace:"PD", title:"PD", filename:"pd_sumstats_chr14_87523488_89523488.json", color: "rgb(0,0,255)"}
];

4. Run the Shiny App

5. Display All Genes and Download PNG

Don't forget to click the "Resize" button to display all genes in the region!

6. Alter Plot

Shift + scroll to zoom in and out on plot.

Click and drag to move up/down chromosome.

Click "Data Layers" to alter the display of the variants.