Clarify non-span-normalised pca #3359
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petrelharp
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Jan 5, 2026
petrelharp
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Comments resolved, ready to merge if you tick as "approved", @petrelharp. Thanks! |
petrelharp
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Jan 6, 2026
| between sample :math:`i` and sample :math:`j`, then by default this returns | ||
| the top ``num_components`` eigenvectors of :math:`M`, so that | ||
| Concretely, take :math:`M` as the matrix of non-span-normalised | ||
| branch-based genetic relatedness values, for instance obtained by |
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| branch-based genetic relatedness values, for instance obtained by | |
| genetic relatedness values, for instance obtained by |
petrelharp
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Jan 6, 2026
| Concretely, take :math:`M` as the matrix of non-span-normalised | ||
| branch-based genetic relatedness values, for instance obtained by | ||
| setting :math:`M_{ij}` to be the :meth:`~.TreeSequence.genetic_relatedness` | ||
| between sample :math:`i` and sample :math:`j` with ``mode="branch"``, |
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| between sample :math:`i` and sample :math:`j` with ``mode="branch"``, | |
| between sample :math:`i` and sample :math:`j` with the specified ``mode``, |
petrelharp
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Jan 6, 2026
| thing, except with :math:`M_{ij}` either the relatedness between | ||
| ``samples[i]`` and ``samples[j]`` or the average relatedness between the | ||
| nodes of ``individuals[i]`` and ``individuals[j]``, respectively. | ||
| Factors are normalized to have L2 norm 1, i.e., |
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| Factors are normalized to have L2 norm 1, i.e., | |
| Factors are normalized to have norm 1, i.e., |
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With these comments, I approve.
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Whoops - I don't think you applied the suggested changes. |
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Fixes #3358