Extend usefulness of tip labels #1668
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You can test the above dataset using this PR at https://nextstrain-s-nextstrain-wpreme.herokuapp.com/staging/monkeypox/mpxv/auspice-pr-1668 |
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There's conflicts with files I've edited since this PR was opened. Addressing them with a rebase onto latest |
victorlin
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Any normal `node_attr` in the tree can be used as a tip label, as well as the special-cases of strain-name and "none". Previously we only allowed valid colorings. Normal here means a node_attr value which is an object with a "value" key, thus excluding special-cases such as "div", "hidden", "vaccine" etc - see the JSON schema for more context <https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v2.json>
jameshadfield
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This is a companion commit to changes in Auspice <nextstrain/auspice#1668> which allow any node-attr to be used as the tip label and which displays this tip label in the node hover/click boxes as well as alongside nodes (at suitable zoom levels). This allows us to drop the `set_final_strain_name` script and ensures all node names are unique which improves the behaviour of Auspice This commit only changes the Nextstrain datasets, not the Nextclade ones
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I've rebased this onto master and also simplified the process by allowing any mpox testing datasets available at:
or use this test version of auspice.us @j23414 / @kimandrews if you have any applicable datasets could you test them here? |
Testing <nextstrain/auspice#1668> Following changes made in mpox <nextstrain/mpox@4a268ba>
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Changes make sense to me.
Used nextstrain/zika#72 to produce testing zika dataset for the new Auspice view.
| for (const [attrKey, attrValue] of Object.entries(d.node_attrs || {})) { | ||
| if (typeof attrValue === 'object' && 'value' in attrValue) { | ||
| nodeAttrKeys.add(attrKey) | ||
| } | ||
| } |
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non-blocking, probably more of a change in Augur
I was looking at the augur export schema to figure out which attrs this would be included here. Worth noting that we would not be able to use accession as the tip label because it does not use the value key.
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Yeah, that's a good point. I wish we had made the schema so that every node-attr was the same structure.
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I'm going to refrain from addressing this here, but I do think moving all node_attrs values to objects will reduce complexity in Auspice a lot, see for example all these different getters. We don't have to do this on the augur side (necessitating schema changes and all that), we could probably do it within treeJsonProcessing.js.
| @@ -56,10 +62,7 @@ export function collectAvailableTipLabelOptions(colorings) { | |||
| */ | |||
| {value: 'none', label: "none"}, | |||
| {value: strainSymbol, label: "Sample Name"}, | |||
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One oddity I noticed here is the hardcoding of node.name to "Sample Name" which is a little jarring when we use accessions for node.name.
This generally better reflects the intention of changing the tip label key, which was previously only reflected in text drawn to the RHS of tree nodes at certain zoom levels. The motivating use case is the proliferation of datasets using an accession for `node.name` but who wish to see node names of another piece of metadata. This is possible by adding the desired name as a node_attr and (optionally) setting this as the default tip label. Note that the order of items in the node-clicked modal has been slightly altered and is now more consistent across internal branches, terminal branches & tips
jameshadfield
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The motivating use case is the proliferation of datasets using an accession for
node.namebut who wish to see node names of another piece of metadata. See commit messages for more details.Using our current monkeypox/mpxv dataset with the following differences:
node.nameis the accession (which is the uniq ID used throughout the pipeline). This removes the need for the pipelines to use JSON-modification scripts such asset_final_strain_name.py.node_attrsreflecting the original strain name. (Any name can be used here.)"tip_label": "strain"added as adisplay_defaultsOn hover boxes show both the chosen tip-label and the underlying node name (accession). (On-click modals are similar)
Filtering to duplicate strain names works intuitively
