A Fresh Look at Genomics Data: Grammar-Based Visualization

Visualization of genomics data for exploration and communication has a long history in molecular biology. Over the years, dozens of techniques and hundreds of tools to view and explore genomics data have been developed. This rich set of tools and techniques demonstrates the importance of data visualization in genomics. However, it also poses significant challenges for data analysts, who often need to convert between different data formats and use multiple tools for their analysis tasks. To address these challenges, we designed the Gosling visualization grammar (http://gosling-lang.org) that can be used to generate virtually any previously described interactive visualization technique for genome-mapped data. I will explain how we developed Gosling and introduce the tool ecosystem that we built to support Gosling-based visualizations. Finally, I will propose opportunities for future research in genomics data visualization.

Keynote from IBMI Tuebingen Kick Off Event June 2022: https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/interfakultaere-einrichtungen/ibmi/veranstaltungen/kick-off-meeting/

Transcript

1. A Fresh Look at Genomics Data:
   Grammar-Based Visualization
   @ngehlenborg ∙ http://gehlenborglab.org ∙ nils@hms.harvard.edu
   Nils Gehlenborg
   Biomedical Informatics
   Harvard Medical School
   

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2. http://gehlenborglab.org
   

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3. http://gehlenborglab.org
   

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4. http://gehlenborglab.org
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10. HiGlass HiPiler Cistrome Explorer Gosling Gos
    

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11. Vitessce
    

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12. Vitessce Avivator Vizarr
    

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13. Halyos Discovery Discovery Mobile Visual Consent Periphery Plots
    

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14. StratomeX OncoThreads ThreadStates UpSet Plots
    

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15. StratomeX OncoThreads ThreadStates UpSet Plots 4CE Explorer
    

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19. Tool Catalogs
    http://genocat.tools
    https://cmdcolin.github.io/awesome-genome-visualization
    475 Tools 100 Tools
    Awesome Genome Visualization GenoCAT
    

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20. Why are there so
    many genomics
    visualization tools?
    

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21. Challenges in Genomics Data Visualization
    - Everything is connected
    - Need to integrate different data types: sequence, expression levels,
    metabolites, phenotype information, etc.
    - Need to load many different types of data into a single software
    - Large space with sparse distribution of patterns across multiple scales
    - Many types of patterns along the genome: SNPs, epigenomic peaks, genomic
    rearrangements, etc.
    Nusrat, Harbig & Gehlenborg, 2019
    

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22. Can we design a tool to
    build effective genomics
    visualizations efficiently?
    

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23. Yes we can!
    

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24. Yes we can!
    Map the design space of
    genomics visualizations
    Define a language to describe
    interactive genomics visualizations
    Implement a framework for
    visualization of real world data
    1
    2
    3
    

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25. 1
    Map the design space of
    genomics visualizations
    

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26. Taxonomies for Genomics Data Visualization
    - Only considered data that is visualized in the sequence context, i.e., genomic location is
    represented in the visualization
    - Treat genome/sequence as a coordinate system
    - Address concerns separately:
    - Data Taxonomy
    What data types can be mapped to the genome?
    - Visualization Taxonomy
    How can the coordinate system be laid out? How can the mapped data be encoded?
    - Task Taxonomy
    What kind of tasks are users trying to address with genomic data?
    Nusrat, Harbig & Gehlenborg, 2019
    

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27. Lt Locate
    Layout Partition Abstraction Arrangement
    Tracks
    Encoding
    View Configurations
    Views Scales Foci
    Feature Sets
    Type
    Sparse
    Contiguous
    Interconnection
    None
    Within
    Between
    Data Taxonomy Visualization Taxonomy
    Coordinate System
    One
    Many
    Alignment
    Task Taxonomy
    Positions
    Feature Sets
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    Lp I
    B S
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    B Browse
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    Lp Lookup I Identify
    E Explore
    Tasks
    Query
    Search
    Mapping
    Nusrat, Harbig & Gehlenborg, 2019
    Taxonomies for Genomics Data Visualization
    

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28. Lt Locate
    Layout Partition Abstraction Arrangement
    Tracks
    Encoding
    View Configurations
    Views Scales Foci
    Feature Sets
    Type
    Sparse
    Contiguous
    Interconnection
    None
    Within
    Between
    Data Taxonomy Visualization Taxonomy
    Coordinate System
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    Many
    Alignment
    Task Taxonomy
    Positions
    Feature Sets
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    E Explore
    Tasks
    Query
    Search
    Mapping
    Nusrat, Harbig & Gehlenborg, 2019
    Taxonomies for Genomics Data Visualization
    

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29. Coordinate System
    Mapping of genomic coordinates into the visualization space
    Track
    Dataset and mapping of features to visual properties
    View
    Genomic region and one or more tracks
    View Configurations
    Relationship of two or more views to each other
    Nusrat, Harbig & Gehlenborg, 2019
    Taxonomies for Genomics Data Visualization
    

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30. Lt Locate
    Layout Partition Abstraction Arrangement
    Tracks
    Encoding
    View Configurations
    Views Scales Foci
    Feature Sets
    Type
    Sparse
    Contiguous
    Interconnection
    None
    Within
    Between
    Data Taxonomy Visualization Taxonomy
    Coordinate System
    One
    Many
    Alignment
    Task Taxonomy
    Positions
    Feature Sets
    S
    Lt
    E
    C
    Lp I
    B S
    S E
    B Browse
    C Compare
    S Summarize
    Lp Lookup I Identify
    E Explore
    Tasks
    Query
    Search
    Mapping
    Nusrat, Harbig & Gehlenborg, 2019
    Taxonomies for Genomics Data Visualization
    

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31. Layout
    EpiViz
    

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32. Layout
    EpiViz: Linear
    

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33. Layout
    MizBee
    

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34. Layout
    MizBee: Circular
    

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35. Layout
    Hilbert Curve
    

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36. Layout
    Hilbert Curve: Space-filling
    

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37. Layout
    HiC3D Viewer
    

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38. Layout
    HiC3D Viewer: Spatial
    

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39. Lt Locate
    Layout Partition Abstraction Arrangement
    Tracks
    Encoding
    View Configurations
    Views Scales Foci
    Feature Sets
    Type
    Sparse
    Contiguous
    Interconnection
    None
    Within
    Between
    Data Taxonomy Visualization Taxonomy
    Coordinate System
    One
    Many
    Alignment
    Task Taxonomy
    Positions
    Feature Sets
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    Lp I
    B S
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    B Browse
    C Compare
    S Summarize
    Lp Lookup I Identify
    E Explore
    Tasks
    Query
    Search
    Mapping
    Nusrat, Harbig & Gehlenborg, 2019
    Taxonomies for Genomics Data Visualization
    

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40. Lt Locate
    Layout Partition Abstraction Arrangement
    Tracks
    Encoding
    View Configurations
    Views Scales Foci
    Feature Sets
    Type
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    Interconnection
    None
    Within
    Between
    Data Taxonomy Visualization Taxonomy
    Coordinate System
    One
    Many
    Alignment
    Task Taxonomy
    Positions
    Feature Sets
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    S E
    B Browse
    C Compare
    S Summarize
    Lp Lookup I Identify
    E Explore
    Tasks
    Query
    Search
    Mapping
    Nusrat, Harbig & Gehlenborg, 2019
    Taxonomies for Genomics Data Visualization
    

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41. Arrangement
    Cinteny
    

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42. Arrangement
    Cinteny: Parallel
    

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43. Arrangement
    Synteny Explorer
    

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44. Arrangement
    Synteny Explorer: Serial
    

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45. Arrangement
    HiGlass
    

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46. Arrangement
    HiGlass: Orthogonal
    

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    Layout Partition Abstraction Arrangement
    Tracks
    Encoding
    View Configurations
    Views Scales Foci
    Feature Sets
    Type
    Sparse
    Contiguous
    Interconnection
    None
    Within
    Between
    Data Taxonomy Visualization Taxonomy
    Coordinate System
    One
    Many
    Alignment
    Task Taxonomy
    Positions
    Feature Sets
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    B S
    S E
    B Browse
    C Compare
    S Summarize
    Lp Lookup I Identify
    E Explore
    Tasks
    Query
    Search
    Mapping
    Nusrat, Harbig & Gehlenborg, 2019
    Taxonomies for Genomics Data Visualization
    

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48. Lt Locate
    Layout Partition Abstraction Arrangement
    Tracks
    Encoding
    View Configurations
    Views Scales Foci
    Feature Sets
    Type
    Sparse
    Contiguous
    Interconnection
    None
    Within
    Between
    Data Taxonomy Visualization Taxonomy
    Coordinate System
    One
    Many
    Alignment
    Task Taxonomy
    Positions
    Feature Sets
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    Lt
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    B S
    S E
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    C Compare
    S Summarize
    Lp Lookup I Identify
    E Explore
    Tasks
    Query
    Search
    Mapping
    Nusrat, Harbig & Gehlenborg, 2019
    Taxonomies for Genomics Data Visualization
    

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49. Alignment
    EpiViz
    

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50. Alignment
    EpiViz: Parallel
    

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51. Alignment
    EpiViz
    

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52. Alignment
    EpiViz: Overlaid
    

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53. Lt Locate
    Layout Partition Abstraction Arrangement
    Tracks
    Encoding
    View Configurations
    Views Scales Foci
    Feature Sets
    Type
    Sparse
    Contiguous
    Interconnection
    None
    Within
    Between
    Data Taxonomy Visualization Taxonomy
    Coordinate System
    One
    Many
    Alignment
    Task Taxonomy
    Positions
    Feature Sets
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    C Compare
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    Lp Lookup I Identify
    E Explore
    Tasks
    Query
    Search
    Mapping
    Nusrat, Harbig & Gehlenborg, 2019
    Taxonomies for Genomics Data Visualization
    

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54. Lt Locate
    Layout Partition Abstraction Arrangement
    Tracks
    Encoding
    View Configurations
    Views Scales Foci
    Feature Sets
    Type
    Sparse
    Contiguous
    Interconnection
    None
    Within
    Between
    Data Taxonomy Visualization Taxonomy
    Coordinate System
    One
    Many
    Alignment
    Task Taxonomy
    Positions
    Feature Sets
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    Lt
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    C Compare
    S Summarize
    Lp Lookup I Identify
    E Explore
    Tasks
    Query
    Search
    Mapping
    Nusrat, Harbig & Gehlenborg, 2019
    Taxonomies for Genomics Data Visualization
    

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55. View Configuration
    Synteny Explorer: Multi-View + Single-Scale + Single-Focus
    

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56. View Configuration
    MizBee: Multi-View + Multi-Scale + Single-Focus
    

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57. View Configuration
    IGV Multi-View + Single-Scale + Multi-Focus
    

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58. Lt Locate
    Layout Partition Abstraction Arrangement
    Tracks
    Encoding
    View Configurations
    Views Scales Foci
    Feature Sets
    Type
    Sparse
    Contiguous
    Interconnection
    None
    Within
    Between
    Data Taxonomy Visualization Taxonomy
    Coordinate System
    One
    Many
    Alignment
    Task Taxonomy
    Positions
    Feature Sets
    S
    Lt
    E
    C
    Lp I
    B S
    S E
    B Browse
    C Compare
    S Summarize
    Lp Lookup I Identify
    E Explore
    Tasks
    Query
    Search
    Mapping
    Nusrat, Harbig & Gehlenborg, 2019
    Taxonomies for Genomics Data Visualization
    

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59. Lt Locate
    Layout Partition Abstraction Arrangement
    Tracks
    Encoding
    View Configurations
    Views Scales Foci
    Feature Sets
    Type
    Sparse
    Contiguous
    Interconnection
    None
    Within
    Between
    Data Taxonomy Visualization Taxonomy
    Coordinate System
    One
    Many
    Alignment
    Task Taxonomy
    Positions
    Feature Sets
    S
    Lt
    E
    C
    Lp I
    B S
    S E
    B Browse
    C Compare
    S Summarize
    Lp Lookup I Identify
    E Explore
    Tasks
    Query
    Search
    Mapping
    Nusrat, Harbig & Gehlenborg, 2019
    Taxonomies for Genomics Data Visualization
    

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60. Yes we can!
    Map the design space of
    genomics visualizations
    Define a language to describe
    interactive genomics visualizations
    Implement a framework for
    visualization of real world data
    1
    2
    3
    

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61. Define a language to describe
    interactive genomics visualizations
    2
    

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62. Gosling
    Grammar Of Scalable, Linked, Interactive Nucleotide Graphics
    L’Yi, Wang, Lekschas & Gehlenborg, 2021
    

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63. Gosling Grammar
    Encoding
    

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64. Gosling Grammar
    Encoding
    

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65. Gosling Grammar
    Encoding
    

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66. Gosling Grammar
    Encoding
    

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67. Gosling Grammar
    Encoding
    

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68. Gosling Grammar
    Encoding
    Overlay
    

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69. Gosling Grammar
    Overlay
    

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70. Gosling
    Tracks and Views
    L’Yi, Wang, Lekschas & Gehlenborg, 2021
    

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71. Gosling
    Track Alignment: Overlay
    L’Yi, Wang, Lekschas & Gehlenborg, 2021
    

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72. Gosling Grammar
    Overlay
    

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73. Gosling
    Layout and Arrangement
    L’Yi, Wang, Lekschas & Gehlenborg, 2021
    

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74. Gosling
    Expressiveness
    L’Yi, Wang, Lekschas & Gehlenborg, 2021
    

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81. Gosling
    Semantic Zooming
    L’Yi, Wang, Lekschas & Gehlenborg, 2021 | https://gosling.js.org
    - Visualizations often
    best represent
    information at a
    particular scale
    - Semantic zoom
    allows switching of
    visual encodings at
    different scales
    

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82. Gosling
    Semantic Zooming
    L’Yi, Wang, Lekschas & Gehlenborg, 2021 | https://gosling.js.org
    

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83. Gosling
    Semantic Zooming
    L’Yi, Wang, Lekschas & Gehlenborg, 2021 | https://gosling.js.org
    

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84. Interaction Techniques
    Multiple Linked Views
    L’Yi, Wang, Lekschas & Gehlenborg, 2021 | https://gosling.js.org
    

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85. Gosling
    Responsive Visualization Design
    L’Yi and Gehlenborg, 2022 | https://osf.io/pd7vq/
    

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86. Yes we can!
    Map the design space of
    genomics visualizations
    Define a language to describe
    interactive genomics visualizations
    Implement a framework for
    visualization of real world data
    1
    2
    3
    

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87. 3
    Implement a framework for
    visualization of real world data
    

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88. Gosling.js Implementation
    Gosling JSON Specification + HiGlass Rendering and Data Access
    L’Yi, Wang, Lekschas & Gehlenborg, 2021 | https://gosling.js.org
    

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89. Gosling.js Implementation
    Integration into Exploratory Tools
    L’Yi, Wang, Lekschas & Gehlenborg, 2021 | https://gosling.js.org
    

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90. Gosling.js Implementation
    Integration into Exploratory Tools: Structural Variant Exploration
    L’Yi and Gehlenborg, Work in Progress
    

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91. Can we apply this to genomic
    data visualization in Python?
    

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92. Gos
    A declarative genomics visualization library for Python
    • Author Gosling visualizations in with Python scripts github.com/gosling-lang/gos
    
    • Concise syntax with shorthand for common Gosling patterns
    
    • Integrates in Jupyter Notebooks for analysis and visualization of large
    datasets
    Manz, L’Yi, and Gehlenborg, https://osf.io/yn3ce/
    

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93. Gos
    A declarative genomics visualization library for Python
    Gos
    Manz, L’Yi, and Gehlenborg, https://osf.io/yn3ce/
    

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94. Gos
    Example Composition
    

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95. Gos
    Local and in-memory datasets
    • Data sources for Gosling must be accessible via HTTP
    
    • This requirement allows Gosling visualizations to be easily shared, but it can
    be challenging to load local datasets
    
    • Gos transparently handles local and remote datasets
    
    • Gos supports DataFrames and other in-memory objects as data sources
    Manz, L’Yi, and Gehlenborg, https://osf.io/yn3ce/
    

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96. Where do we go from here?
    

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97. Future Directions
    Recommendation System: GenoREC
    Pandey, L’Yi, Wang, Borkin & Gehlenborg, 2022 | https://osf.io/rscb4/
    Output Compiler
    A Input
    Data
    Task
    Identify
    Contiguous
    Point
    B Knowledge-based Recommendation
    C
    D Alternate Visualizations
    GenoREC’s Recommendation
    GenoREC UI GenoREC Backend GenoREC UI
    Input Compiler GenoREC Model
    Algorithm
    rect+interval
    hue
    rect+interval
    saturation
    rect+interval
    length
    overlayed
    segregated
    parallel
    adjacent
    orthogonal
    parallel
    adjacent
    coordinated
    interaction
    focus
    +
    context
    Encoding Alignment Layout Partition Arrangement Interactivity
    rect
    length
    rect
    saturation
    line
    position
    point
    position
    rect
    hue
    ABC XYZ
    text
    linear
    circular
    space
    filling
    stacked
    contiguous
    ABCXYZ
    

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98. Future Directions
    - Recommendation systems
    - Moving away from custom tools towards a platform for visualization
    - GUI-based construction of visualizations
    - Collaborative visual exploration of genome-mapped data
    

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99. Team
    Trevor Manz
    Peter Kerpedjiev
    Nezar Abdennur
    Fritz Lekschas
    Aditeya Pandey
    Qianwen Wang
    Sehi L’Yi
    Sabrina Nusrat
    Theresa Harbig
    

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100. ?
     Team
     Trevor Manz
     Peter Kerpedjiev
     Nezar Abdennur
     Fritz Lekschas
     Aditeya Pandey
     Qianwen Wang
     Sehi L’Yi
     Sabrina Nusrat
     Theresa Harbig You?
     Postdoctoral Fellow
     Senior) UI/UX Developer
     (Senior) Software Developer
     Join us as a
     Email nils@hms.harvard.edu if interested!
     

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101. Project Website
     http://gosling-lang.org
     Online Editor
     https://gosling.js.org
     Postdoctoral Fellow
     Senior) UI/UX Developer
     (Senior) Software Developer
     Join us as a
     Email nils@hms.harvard.edu if interested!
     

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102. A Fresh Look at Genomics Data:
     Grammar-Based Visualization
     @ngehlenborg ∙ http://gehlenborglab.org ∙ nils@hms.harvard.edu
     Nils Gehlenborg
     Biomedical Informatics
     Harvard Medical School
     

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