Format

Send to

Choose Destination
See comment in PubMed Commons below
BMC Bioinformatics. 2016 Apr 18;17:169. doi: 10.1186/s12859-016-1051-4.

gtrellis: an R/Bioconductor package for making genome-level Trellis graphics.

Gu Z1,2, Eils R1,2,3, Schlesner M4.

Author information

  • 1Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
  • 2Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
  • 3Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant Center, Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.
  • 4Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany. m.schlesner@dkfz.de.

Abstract

BACKGROUND:

Trellis graphics are a visualization method that splits data by one or more categorical variables and displays subsets of the data in a grid of panels. Trellis graphics are broadly used in genomic data analysis to compare statistics over different categories in parallel and reveal multivariate relationships. However, current software packages to produce Trellis graphics have not been designed with genomic data in mind and lack some functionality that is required for effective visualization of genomic data.

RESULTS:

Here we introduce the gtrellis package which provides an efficient and extensible way to visualize genomic data in a Trellis layout. gtrellis provides highly flexible Trellis layouts which allow efficient arrangement of genomic categories on the plot. It supports multiple-track visualization, which makes it straightforward to visualize several properties of genomic data in parallel to explain complex relationships. In addition, gtrellis provides an extensible framework that allows adding user-defined graphics.

CONCLUSIONS:

The gtrellis package provides an easy and effective way to visualize genomic data and reveal high dimensional relationships on a genome-wide scale. gtrellis can be flexibly extended and thus can also serve as a base package for highly specific purposes. gtrellis makes it easy to produce novel visualizations, which can lead to the discovery of previously unrecognized patterns in genomic data.

KEYWORDS:

Genomic data visualization; Software; Trellis graphics

PMID:
27089965
PMCID:
PMC4835841
DOI:
10.1186/s12859-016-1051-4
[PubMed - indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for BioMed Central Icon for PubMed Central
    Loading ...
    Support Center