Nr4a3-Tocky Interactive 3D Visualisations

This repository hosts browser-viewable HTML models showing thymocytes in CD4 differentiation score × CD8 differentiation score × Tocky Time space. The models were generated from the Nr4a3-Tocky thymocyte analysis and are intended to provide an intuitive view of the shared developmental-temporal geometry reconstructed by mCanonicalTockySeq.

What the models show

These models display thymocytes in a three-dimensional space defined by:

• CD4 differentiation score
• CD8 differentiation score
• Tocky Time

This geometry was reconstructed from the Nr4a3-Tocky single-cell transcriptomic analysis using mCanonicalTockySeq, mGradientTockySeq, mGetFateScores, and trajectory-tube analysis.

Tocky Time model

The base model shows the continuous Tocky temporal coordinate across the inferred developmental-temporal manifold.

Gene-associated tube identity model

The lineage-coloured model shows overlapping gene-associated developmental corridors inferred from trajectory-tube analysis, allowing non-mutually exclusive developmental identities to be visualised directly.

How to use

Interactive controls:

• Click and drag to rotate
• Scroll to zoom
• Hover to inspect values
• Open fullscreen for easier exploration

Biological context

The Nr4a3-Tocky system uses a Fluorescent Timer reporter to provide an experimentally anchored readout of strong T-cell receptor signalling history. In the thymus, this allows temporal progression associated with TCR signalling to be analysed jointly with developmental progression toward CD4 and CD8 single-positive states.

These interactive 3D models are intended as visual summaries of that shared developmental-temporal structure.

Citation

If you use or refer to these models, please cite the mCanonicalTockySeq package and paper.

bioRxiv preprint

For a detailed description of the biological applications and the underlying methodology of mCanonicalTockySeq, please refer to our preprint:

@article{Ono2026mCanonicalTocky,
  author = {Ono, Masahiro and others},
  title = {Canonical Analysis of Fluorescent Timer-Anchored Transcriptomes Resolves Joint Temporal and Developmental Progression},
  elocation-id = {},
  year = {2026},
  doi = {},
  publisher = {Cold Spring Harbor Laboratory},
  journal = {bioRxiv},
  url = {https://www.biorxiv.org}
}

R package

@Manual{OnomCanonicalTockySeq,
  title = {mCanonicalTockySeq: Multidimensional Canonical Tocky Analysis of Temporal and Developmental Structure in Single-Cell Transcriptomes},
  author = {Masahiro Ono},
  year = {2026},
  note = {R package version 0.1.0},
  url = {https://github.com/MonoTockyLab/mCanonicalTockySeq},
  doi = {}
}

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