upgrade labels on sourmash plot with --labels-from or some such
#2452
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Good idea. As a workaround, I've been editing the |
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Feb 6, 2024
…tter customization (#2598) Adds `sourmash compare --labels-to` and `sourmash plot --labels-from` to support better label customization. Fixes #2452 Fixes #2915 ## `sourmash compare --labels-to` This command will generate a 'labels-to' file. Running: ``` sourmash compare tests/test-data/demo/*.sig -o compare-demo \ --labels-to compare-demo-labels.csv ``` will produce a file that looks like this: file `compare-demo-labels.csv`: ```csv order,md5,label,name,filename,signature_file 1,60f7e23c24a8d94791cc7a8680c493f9,SRR2060939_1.fastq.gz,,SRR2060939_1.fastq.gz,../tests/test-data/demo/SRR2060939_1.sig 2,4e94e60265e04f0763142e20b52c0da1,SRR2060939_2.fastq.gz,,SRR2060939_2.fastq.gz,../tests/test-data/demo/SRR2060939_2.sig 3,f71e78178af9e45e6f1d87a0c53c465c,SRR2241509_1.fastq.gz,,SRR2241509_1.fastq.gz,../tests/test-data/demo/SRR2241509_1.sig 4,6d6e87e1154e95b279e5e7db414bc37b,SRR2255622_1.fastq.gz,,SRR2255622_1.fastq.gz,../tests/test-data/demo/SRR2255622_1.sig 5,0107d767a345eff67ecdaed2ee5cd7ba,SRR453566_1.fastq.gz,,SRR453566_1.fastq.gz,../tests/test-data/demo/SRR453566_1.sig 6,f0c834bc306651d2b9321fb21d3e8d8f,SRR453569_1.fastq.gz,,SRR453569_1.fastq.gz,../tests/test-data/demo/SRR453569_1.sig 7,b59473c94ff2889eca5d7165936e64b3,SRR453570_1.fastq.gz,,SRR453570_1.fastq.gz,../tests/test-data/demo/SRR453570_1.sig ``` The `label` column in this file can be edited to suit the user's needs; the index column is `order`, and all other columns can be ignored or deleted or updated without consequence. ## `sourmash plot --labels-from` This command will load labels from a file. Running: ``` sourmash plot --labels-from compare-demo-new-labels.csv compare-demo ``` uses the `label` column from the CSV as labels, in the order specified by the `order` column (interpreted as integers and sorted from lowest to highest). All other columns are ignored. ## Example in a Jupyter Notebook Some example code for updating the labels is available here: https://github.com/sourmash-bio/sourmash/blob/compare_labels/doc/plotting-compare.ipynb ## TODO - [x] add test for `args.labeltext and args.labels_from` check - [x] check the notebook update ## Future: - [ ] Consider switching to `LinearIndex` in the signature loading code, as that would let us maintain the location in the code without the current machinations. Also worth thinking about enabling lazy loading, which some future `Index`-code based modification might support. - [ ] consider if and how to validate --labels-from CSV file... --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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sourmash plotare complicated and ugly ;(.Random thought: we could add a
--labels-tooption tosourmash comparethat supports a simple labeling output spreadsheet, and then support a--labels-fromoption withsourmash plot.The text was updated successfully, but these errors were encountered: