diff --git a/python/tskit/trees.py b/python/tskit/trees.py index 8c8e3b37df..cc546b29de 100644 --- a/python/tskit/trees.py +++ b/python/tskit/trees.py @@ -9304,9 +9304,9 @@ def pca( randomized singular value decomposition (rSVD) algorithm. Concretely, take :math:`M` as the matrix of non-span-normalised - branch-based genetic relatedness values, for instance obtained by + 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"``, + between sample :math:`i` and sample :math:`j` with the specified ``mode``, ``proportion=False`` and ``span_normalise=False``. Then by default this returns the top ``num_components`` eigenvectors of :math:`M`, so that ``output.factors[i,k]`` is the position of sample `i` on the `k` th PC. @@ -9314,7 +9314,7 @@ def pca( 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., + Factors are normalized to have norm 1, i.e., ``output.factors[:,k] ** 2).sum() == 1)`` for any ``k``. The parameters ``centre`` and ``mode`` are passed to