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update plot command to auto-detect oddball matrices #2228

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ctb opened this issue Aug 20, 2022 · 0 comments
Open

update plot command to auto-detect oddball matrices #2228

ctb opened this issue Aug 20, 2022 · 0 comments

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@ctb
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ctb commented Aug 20, 2022

with the addition of compare --distance in #2225, it turns out that sourmash plot doesn't like distance matrices 🤔 . In particular, scipy linkage doesn't like it - with #2225,

sourmash compare -o cmp podar-ref/*.fa.sig -k 21 --ani --distance
sourmash plot cmp

I get:

/Users/t/dev/sourmash/src/sourmash/commands.py:297: ClusterWarning: scipy.cluster: The symmetric non-negative hollow observation matrix looks suspiciously like an uncondensed distance matrix
  Y = sch.linkage(D, method='single')

we could/should autodetect/warn in situations where the diagonal isn't 1, and/or where the matrix isn't symmetric. (we already do for matrices with values outside of [0, 1].)

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