How can we visualize a 3,000,000 x 3,000,000 cell matrix and allow analysts to explore features across a wide range of different scales? We built HiGlass, a web-based visualization tool for analysis of Hi-C and other genome-wide chromosome interaction data that enables comparison of multiple contact matrices and integration of other data types. To complement this functionality, we also created HiPiler, which enables investigators to view and explore thousands of features such as loops or TADs and correlate their appearance with their genomic locations and experimental conditions. In my talk, I will discuss the design of HiGlass and HiPiler and present a range of use cases for these applications.
(Thanks to Fritz Lekschas for providing many of the slides.)
HiGlass + HiPiler: Making Sense of Chromosome Interaction Data with Multi-Scale Data Visualization Tools
HiGlass + HiPiler
Making Sense of Chromosome
Interaction Data with Multi-Scale
Data Visualization Tools
Nils Gehlenborg / Harvard Medical School
Web: http://gehlenborglab.org / Twitter: @ngehlenborg
With Peter Kerpedjiev, Fritz Lekschas, Nezar Abdennur,
Hanspeter Pﬁster, Leonid Mirny, Peter J Park, and more!
• How do speciﬁc pattern or
average pattern look?
• How variable and noisy are
• Are there subgroups among
• How are patterns related to
other data attributes?
• What does the patterns
neighborhood look like?
• Pan & Zoom
Kerpedjiev et al.: HiGlass
• Lenses / Multifocus
Rao and Card: Table Lens
Elmquist et al.: Melange
• Abstraction / Aggregation
Dunne et al.: Motif Simpliﬁcation
Elmquist et al.: ZAME
• Small Multiples
Bach et al.: Multipiles
Pile Inspection Attribute correlations
Multidimensional Clustering Dataset Comparison
More at http://hipiler.higlass.io
User study with 5 domain experts: Evaluating usability and
Snippet approach is useful: Average / variance assessment
and parameter estimation
Context matters: Coordination between the snippets and
matrix is highly appreciated
HiPiler is easy-to-use and useful: Domain experts ask for
Limitations: Fixed matrix ordering and ﬁxed aspect ratio of
HiGlass + HiPiler
I am hiring!
Chromatin Interaction + Epigenomics