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Interactive Plot

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Boxiang Liu edited this page Sep 11, 2018 · 3 revisions

Overview

The interactive plot page shows 3 plots:

  1. A LocusCompare plot.
  2. A Manhattan plot (aka LocusZoom plot) for the GWAS dataset.
  3. A Manhattan plot for the eQTL dataset.

The LocusCompare plot is a scatter plot where the data points are colored according to the LD to the selected variant. The purpose of LocusCompare is to detect colocalization, i.e. whether a single causal variant influences both the eQTL and GWAS trait.

In addition to the 3 plots, the webpage also displays the following information:

  1. Information for the selected SNP, such as chromosome, position, and allele frequencies.
  2. SNPs in LD with the selected SNP.
  3. A download button to save the plots and information on display.

Usage

The interactive plot will accept the following types of interactions:

  1. Selecting on a data point anywhere on the plotting area will update the LD coloring with respect to the selected variant.

  2. Dragging horizontally on the Manhattan plots and then double-clicking will zoom in.

  3. Double-clicking on the Manhattan plots will zoom out.

  4. If there is a SNP of interest, you can select it from using the drop-down menu on top of the LocusCompare plot.

  5. Choose the population upon which the LD calculation is based.

  6. Downloading the plot and information using the Download button at the bottom.

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