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Add sampling year coloring #12

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merged 2 commits into from
Aug 22, 2024
Merged

Add sampling year coloring #12

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0162bf4
Add sampling year coloring
jameshadfield Aug 22, 2024
0534d0d
Add date metadata
jameshadfield Aug 22, 2024
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8 changes: 7 additions & 1 deletion phylogenetic/defaults/auspice_config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,11 @@
"title": "Country",
"type": "categorical"
},
{
"key": "year",
"title": "Sampling year",
"type": "continuous"
},
{
"key": "host",
"title": "Host",
Expand Down Expand Up @@ -60,6 +65,7 @@
"author",
"strain",
"division",
"location"
"location",
"date"
]
}
15 changes: 15 additions & 0 deletions phylogenetic/rules/annotate_phylogeny.smk
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Expand Up @@ -51,3 +51,18 @@ rule translate:
--output {output.node_data} \
2>&1 | tee {log}
"""

rule add_year_metadata:
input:
metadata = "data/metadata.tsv",
params:
strain_id = config["strain_id_field"],
output:
node_data = "results/year.json"
run:
from augur.io import read_metadata
import json
m = read_metadata(input.metadata, id_columns=[params.strain_id])
nodes = {name: {'year': date.split('-')[0]} for name,date in zip(m.index, m['date']) if date and not date.startswith('X')}
with open(output.node_data, 'w') as fh:
json.dump({"nodes": nodes}, fh)
3 changes: 2 additions & 1 deletion phylogenetic/rules/export.smk
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Expand Up @@ -13,6 +13,7 @@ rule export:
branch_lengths = "results/branch_lengths.json",
nt_muts = "results/nt_muts.json",
aa_muts = "results/aa_muts.json",
year = "results/year.json",
colors = config["files"]["colors"],
auspice_config = config["files"]["auspice_config"],
description = config["files"]["description"]
Expand All @@ -30,7 +31,7 @@ rule export:
--tree {input.tree} \
--metadata {input.metadata} \
--metadata-id-columns {params.strain_id} \
--node-data {input.branch_lengths} {input.nt_muts} {input.aa_muts} \
--node-data {input.branch_lengths} {input.nt_muts} {input.aa_muts} {input.year} \
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not asking for a change, just curious

Instead of making another node-data JSON, why not just add a year column to the metadata.tsv that can be used directly as a coloring?

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I found the approach here cleaner to implement, although if other rules used the data I'd have probably gone for modifying the TSV. It should also be trivial to copy & paste into other workflows which would benefit from this. Of course, once Auspice has a proper temporal scale this'll all be removed anyways.

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Perhaps analogous to avian-flu where we currently add in a column (H5 LABEL) to the TSV but want to switch away from this to a node-data JSON

--colors {input.colors} \
--auspice-config {input.auspice_config} \
--include-root-sequence-inline \
Expand Down