Add unsupervised clustering of genomes#17
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This script performs unsupervised clustering of genomes to investigate the separation of light ecotypes using various clustering techniques and visualizations.
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I need to check Evan's remodified workflow to see where this step makes the most sense and is consistent with the rest of the scripts. Feel free to look over the PR to make sure the logic is sound but note that it will be edited as the rest of the workflow is established |
CJohnsonPnnl
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Mar 13, 2026
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@charmvang @epbrenner, does this script need to be renamed before merging to keep with Evan's numbering? |
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- sapply to purrr map function - alpine path - file saves - pkg::function calls in some cases - switched to here::here and readr for consistency - c is for concatenate. d is inbuilt function too. risky to set a variable name to `c`!! check new names nad runs.
jananiravi
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Apr 16, 2026
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@charmvang, check with @epbrenner tomorrow to figure out what's to be done with this:
- if merging, where does this belong (tentative numbering)? any figures to be incorporated (maybe during review period) as suppl. figures? Is this part of the other unsup script but with a
XXbnumber? - if not merging, check fixes locally, and keep on standby as 'draft PR'
- added other minor comments along with the previous commit
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Not included in the current manuscript workflow, but worth considering for future analysis. Changed to draft to reflect that it isn't necessary to merge currently. |
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This script performs unsupervised clustering of genomes to investigate the separation of light ecotypes using various clustering techniques and visualizations.
Related to issue #2