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Locuszoom genome wide association viewer plots

Project Description

LocusZoom Association Viewer

Summary

The LocusZoom Association Viewer allows the user to easily view the results of their own genome wide association tests, including PLINK, RAREMETALWORKER, and EPACTS. Upon runnning this program, the user browses to localhost (127.0.0.1) on their browser, at the port they specified. Three different types of graphs are available:

  • Manhattan Plot
  • LocusZoom Plot
  • QQ Plot
    • Currently, only available for EPACTS files

Manhattan Plot

The manhattan plot is a scatterplot of all points. Points have tooltips and are clickable if they are deemed statistically significant ( > 1e-4). However, if the point is deemed as statistically insignificant, it is binned, and therefore will not include tooltips and will not be clickable. Upon click, the user is taken to a LocusZoom Plot with a region that is centered around the point clicked.

QQ Plot

The QQ plot generates multiple scatter plots on the same chart based on differing MAF ranges if the input file is EPACTS; Otherwise, a normal QQ plot is generated.

LocusZoom Plot

The LocusZoom Plot is a scatterplot of a specific region of a chromosome. Points have tooltips that show additional information.

Command Line Options

The only required command line argument is the filename, which should be directly after the program name. The program is ran with multiple options including:

--help list off all of the command line options
--port you can specify a port at which to view the results
--range

specify a specific range of format [CHROMOSOME]:[START POSITION]-[END POSITION] to view.

  • if range is specified, the default homepage is the LocusZoom Plot with specified range.
  • if range is not specified, the default homepage is the Manhattan Plot

Sample use of command line options:

lz_assoc_viewer my_results.gz 11:113580000-114150000 –port 5541

Release History

Release History

This version
History Node

1.0.2

History Node

1.0.1

History Node

1.0.0

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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
lz_assoc_viewer-1.0.2.tar.gz (51.9 kB) Copy SHA256 Checksum SHA256 Source Aug 23, 2016

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