JSM 2015 Preliminary Program

Online Program Home
My Program

Abstract Details

Activity Number: 166
Type: Topic Contributed
Date/Time: Monday, August 10, 2015 : 10:30 AM to 12:20 PM
Sponsor: Section on Statistical Computing
Abstract #316111 View Presentation
Title: Espaliers: A Visualization Method for Big Data
Author(s): Robert Robinson* and Gustavo Glusman and Joseph G. Vockley and John E. Niederhuber and Greg Eley
Companies: Institute for Systems Biology and Institute for Systems Biology and Inova Translational Medicine Institute and Inova Translational Medicine Institute and Scimentis, LLC
Keywords: genomics ; population genetics ; visualization ; big data ; hypergraph

As thousands of human genomes become available, there is pressing need for efficient and intuitive analysis and visualization methods. The genotypes observed in a set of genomes can be represented as a [genome x variant] matrix. Standard PCA-based visualizations of genotype matrices can reveal population structure, but give little insight into genetic admixture in individuals or the history of individual variants.

We present Espaliers, a novel visualization of non-negative matrices, including genotype matrices. Given an ordering of the genomes (columns), we compute a position for each variant (row) that reflects the information in the genotype matrix. An Espalier plots each variant by this position and its population frequency (row sum), which is related to the variant's age. The resulting Espalier plot resembles a parsimonious evolutionary tree connecting the genomes, that is consistent with the input ordering of the genomes.

We compare Espaliers with PCA, provide examples of Espaliers for Big Data sets from genomics and transcriptomics, and discuss potential future directions.

Authors who are presenting talks have a * after their name.

Back to the full JSM 2015 program

For program information, contact the JSM Registration Department or phone (888) 231-3473.

For Professional Development information, contact the Education Department.

The views expressed here are those of the individual authors and not necessarily those of the JSM sponsors, their officers, or their staff.

2015 JSM Online Program Home