GenomeSpy

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  Abstract example: Using rect and text marks to specify a labeled bar chart.
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  Abstract example: Using rect and text marks to make a labeled heatmap. The labels are automatically scaled to fit the cells. Try to zoom in and out!
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  A scatter plot with one and a half million points decorated with some annotations visualizes a miserably failed t-SNE attempt.
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  A Manhattan plot for Genome-Wide Association Study (GWAS).
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  A multiple sequence alignment that loads data from a FASTA file and displays it as a scrollable heatmap and sequence logo.
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  A structural variation visualization that uses the link mark to show arcs connecting the breakpoints. It also includes segmented copy-number data.
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  GC content of the human genome: One dataset, two visual representations. The data are loaded lazily from a BigWig file and the scale domains are autoscaled to accommodate the region.
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  Using lazy data loading, data transformations, and multiple layers to visualize the GENCODE gene annotation stored in a hierarchical GFF3 file.
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  An Observable notebook that describes how to replicate ASCAT's copy-number segmentation visualization. The visualization is interactive and thoroughly commented.
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  Exploring a sample collection with the GenomeSpy App. The visualization shows several cell-line samples with segmented copy numbers, loss of heterozygosity, and SNPs and indels.
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  GenomeSpy App visualizes ovarian high-grade serous carcinoma copy number data in the DECIDER cohort. A companion visualization for Lavikka, K., Oikkonen, J., et al. (2024) Deciphering Cancer Genomes with GenomeSpy: A Grammar-Based Visualization Toolkit. GigaScience, 13(8), giad040.
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  SegmentModel Spy. Visualizes GATK's copy-number segment models together with read and allelic counts. This is an example of using GenomeSpy as a visualization library in a special-purpose web application.

GenomeSpy App

GenomeSpy App is a visual analytics application for interactive exploration of multi-sample cancer genomics data. It supports overview-to-detail analysis of large sample collections, allowing users to identify cohort-wide patterns and then inspect individual samples, genomic regions, and outliers in detail.

It builds on the GenomeSpy Core package, enabling extensive customization for different data modalities, including copy-number variation, structural variants, mutations, methylation, continuous genomic signals such as coverage and accessibility, and sample metadata.

The App provides incremental, provenance-aware actions for filtering, grouping, and reorganizing samples, as well as for deriving new attributes from genome-aligned point and segment features. Users can bookmark and share action-defined views as URLs.