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hudson: A User-Friendly R Package to Extend Manhattan Plots

Anastasia Lucas, Anurag Verma, Marylyn D. Ritchie
doi: https://doi.org/10.1101/2022.01.25.474274
Anastasia Lucas
1Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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Anurag Verma
1Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
2Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
3Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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Marylyn D. Ritchie
1Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
3Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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  • For correspondence: marylyn@pennmedicine.upenn.edu
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Abstract

The Manhattan plot is one of the most widely used visualization techniques when plotting summary statistics from genome-wide or phenome-wide association studies. While there are a number of existing tools to create these plots, there is room for extending their utility to satisfy increasingly complex and comprehensive analyses as well as the need for comparisons between different sets of results or between discovery and replication datasets. The R package presented here, hudson, provides user-friendly plotting functions intended for use with genome, phenome, and exposome-wide association studies, but its flexible framework can be utilized for a wide variety genome-wide analyses. Further, we have extended these figures to allow for interactive elements to facilitate results exploration for the ever-increasing large-scale dimensionality of these data. hudson can be obtained from https://github.com/RitchieLab/hudson.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/RitchieLab/hudson/tree/master/data

  • http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST006001-GCST007000/GCST006259/

  • http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST006001-GCST007000/GCST006258/

  • http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST004001-GCST005000/GCST004232/

  • http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST004001-GCST005000/GCST004233/

  • http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST004001-GCST005000/GCST004235/

  • http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST004001-GCST005000/GCST004237/

  • https://github.com/RitchieLab/utility/tree/master/personal/ana/hudson-paper

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted January 27, 2022.
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hudson: A User-Friendly R Package to Extend Manhattan Plots
Anastasia Lucas, Anurag Verma, Marylyn D. Ritchie
bioRxiv 2022.01.25.474274; doi: https://doi.org/10.1101/2022.01.25.474274
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hudson: A User-Friendly R Package to Extend Manhattan Plots
Anastasia Lucas, Anurag Verma, Marylyn D. Ritchie
bioRxiv 2022.01.25.474274; doi: https://doi.org/10.1101/2022.01.25.474274

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