Merge pull request #177 from nextstrain/set-subclade-colors-for-publi…

…c-builds Add segment-specific Auspice configs for 2y builds
nextstrain · Aug 30, 2024 · 1677cc2 · 1677cc2
2 parents c775b5a + 101f5fe
commit 1677cc2
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diff --git a/config/h1n1pdm/ha/auspice_config.json b/config/h1n1pdm/ha/auspice_config.json
@@ -0,0 +1,243 @@
+{
+  "title": "Real-time tracking of influenza A/H1N1pdm evolution",
+  "maintainers": [
+    {
+      "name": "Jennifer Chang",
+      "url": "https://bedford.io/team/jennifer-chang/"
+    },
+    {
+      "name": "Jover Lee",
+      "url": "https://bedford.io/team/jover-lee/"
+    },
+    {
+      "name": "John Huddleston",
+      "url": "https://bedford.io/team/john-huddleston/"
+    },
+    {
+      "name": "Richard Neher",
+      "url": "https://neherlab.org/richard-neher.html"
+    },
+    {
+      "name": "Trevor Bedford",
+      "url": "https://bedford.io/team/trevor-bedford/"
+    }
+  ],
+  "data_provenance": [
+    {
+      "name": "GISAID"
+    }
+  ],
+  "build_url": "https://github.com/nextstrain/seasonal-flu",
+  "colorings": [
+    {
+      "key": "gt",
+      "title": "Genotype",
+      "type": "categorical"
+    },
+    {
+      "key": "num_date",
+      "title": "Date",
+      "type": "continuous"
+    },
+    {
+      "key": "clade_membership",
+      "title": "Clade",
+      "type": "categorical"
+    },
+    {
+      "key": "subclade",
+      "title": "Subclade",
+      "type": "categorical",
+      "scale": [
+        [
+          "C.1",
+          "#492AB5"
+        ],
+        [
+          "C.1.1",
+          "#3F4CCB"
+        ],
+        [
+          "C.1.2",
+          "#4271CE"
+        ],
+        [
+          "C.1.5",
+          "#4C8FC0"
+        ],
+        [
+          "C.1.7",
+          "#5AA5A8"
+        ],
+        [
+          "C.1.7.1",
+          "#6DB38A"
+        ],
+        [
+          "C.1.7.2",
+          "#85BA6F"
+        ],
+        [
+          "C.1.8",
+          "#A0BE59"
+        ],
+        [
+          "C.1.9",
+          "#BBBC49"
+        ],
+        [
+          "D",
+          "#D2B340"
+        ],
+        [
+          "D.1",
+          "#E19F3A"
+        ],
+        [
+          "D.2",
+          "#E68033"
+        ],
+        [
+          "D.3",
+          "#E2562B"
+        ],
+        [
+          "D.4",
+          "#DB2823"
+        ]
+      ]
+    },
+    {
+      "key": "haplotype",
+      "title": "Derived haplotype",
+      "type": "categorical"
+    },
+    {
+      "key": "cTiter",
+      "title": "Antigenic advance (tree model)",
+      "type": "continuous"
+    },
+    {
+      "key": "cTiterSub",
+      "title": "Antigenic advance (sub model)",
+      "type": "continuous"
+    },
+    {
+      "key": "cTiter_x",
+      "title": "HI antigenic novelty",
+      "type": "continuous"
+    },
+    {
+      "key": "lbi",
+      "title": "Local branching index",
+      "type": "continuous"
+    },
+    {
+      "key": "ep",
+      "title": "Epitope mutations",
+      "type": "continuous"
+    },
+    {
+      "key": "ne",
+      "title": "Non-epitope mutations",
+      "type": "continuous"
+    },
+    {
+      "key": "glyc",
+      "title": "Glycosylation changes",
+      "type": "continuous"
+    },
+    {
+      "key": "region",
+      "title": "Region",
+      "type": "categorical"
+    },
+    {
+      "key": "country",
+      "title": "Country",
+      "type": "categorical"
+    },
+    {
+      "key": "division",
+      "title": "Division",
+      "type": "categorical"
+    },
+    {
+      "key": "accession_ha",
+      "title": "Accession (HA)",
+      "type": "categorical"
+    },
+    {
+      "key": "accession_na",
+      "title": "Accession (NA)",
+      "type": "categorical"
+    },
+    {
+      "key": "submitting_lab",
+      "title": "Submitting lab",
+      "type": "categorical"
+    },
+    {
+      "key": "originating_lab",
+      "title": "Originating lab",
+      "type": "categorical"
+    },
+    {
+      "key": "recency",
+      "title": "Submission date",
+      "type": "ordinal"
+    },
+    {
+      "key": "epiweek",
+      "title": "Epiweek (CDC)",
+      "type": "ordinal"
+    },
+    {
+      "key": "year_month",
+      "title": "Year/month",
+      "type": "categorical"
+    },
+    {
+      "key": "tsne_x",
+      "title": "t-SNE 1",
+      "type": "continuous"
+    },
+    {
+      "key": "tsne_y",
+      "title": "t-SNE 2",
+      "type": "continuous"
+    },
+    {
+      "key": "tsne_cluster",
+      "title": "t-SNE cluster",
+      "type": "categorical"
+    }
+  ],
+  "geo_resolutions": [
+    "division",
+    "country",
+    "region"
+  ],
+  "display_defaults": {
+    "map_triplicate": true,
+    "color_by": "clade_membership"
+  },
+  "filters": [
+    "clade_membership",
+    "subclade",
+    "region",
+    "country",
+    "division",
+    "submitting_lab",
+    "recency",
+    "epiweek",
+    "year_month",
+    "tsne_cluster"
+  ],
+  "panels": [
+    "tree",
+    "map",
+    "entropy",
+    "frequencies"
+  ]
+}