Merge pull request #195 from nextstrain/use-proposed-subclades

Add proposed subclades to public and private builds
nextstrain · Nov 7, 2024 · 3477eac · 3477eac
2 parents 39a4cd9 + 6df5c2c
commit 3477eac
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Showing 24 changed files with 347 additions and 197 deletions.
diff --git a/Snakefile b/Snakefile
@@ -48,18 +48,18 @@ subclade_url_by_lineage_and_segment = {
     }
 }
 
-emerging_subclade_url_by_lineage_and_segment = {
+proposed_subclade_url_by_lineage_and_segment = {
     "h1n1pdm": {
-        "ha": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/main/.auto-generated/subclades.tsv",
-        "na": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_NA/main/.auto-generated/subclades.tsv",
+        "ha": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/main/.auto-generated/subclade-proposals.tsv",
+        "na": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_NA/main/.auto-generated/subclade-proposals.tsv",
     },
     "h3n2": {
-        "ha": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/emerging/.auto-generated/subclades.tsv",
-        "na": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_A-H3N2_NA/main/.auto-generated/subclades.tsv",
+        "ha": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/main/.auto-generated/subclade-proposals.tsv",
+        "na": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_A-H3N2_NA/main/.auto-generated/subclade-proposals.tsv",
     },
     "vic": {
-        "ha": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_B-Vic_HA/main/.auto-generated/subclades.tsv",
-        "na": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_B-Vic_NA/main/.auto-generated/subclades.tsv",
+        "ha": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_B-Vic_HA/main/.auto-generated/subclade-proposals.tsv",
+        "na": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_B-Vic_NA/main/.auto-generated/subclade-proposals.tsv",
     }
 }
 

diff --git a/config/h1n1pdm/ha/auspice_config.json b/config/h1n1pdm/ha/auspice_config.json
@@ -51,58 +51,85 @@
       "scale": [
         [
           "C.1",
-          "#492AB5"
+          "#3F52CD"
         ],
         [
           "C.1.1",
-          "#3F4CCB"
+          "#4681CA"
         ],
         [
-          "C.1.2",
-          "#4271CE"
+          "C.1.8",
+          "#57A1AD"
+        ],
+        [
+          "C.1.9",
+          "#70B487"
+        ],
+        [
+          "D",
+          "#90BC65"
+        ],
+        [
+          "D.1",
+          "#B4BD4C"
         ],
         [
-          "C.1.5",
-          "#4C8FC0"
+          "D.2",
+          "#D3B240"
         ],
         [
-          "C.1.7",
-          "#5AA5A8"
+          "D.3",
+          "#E59638"
         ],
         [
-          "C.1.7.1",
-          "#6DB38A"
+          "D.4",
+          "#E4642E"
+        ]
+      ]
+    },
+    {
+      "key": "proposed_subclade",
+      "title": "Proposed subclade",
+      "type": "categorical",
+      "scale": [
+        [
+          "C.1",
+          "#3F52CD"
         ],
         [
-          "C.1.7.2",
-          "#85BA6F"
+          "C.1.1",
+          "#4681CA"
         ],
         [
           "C.1.8",
-          "#A0BE59"
+          "#57A1AD"
         ],
         [
           "C.1.9",
-          "#BBBC49"
+          "#70B487"
         ],
         [
           "D",
-          "#D2B340"
+          "#90BC65"
         ],
         [
           "D.1",
-          "#E19F3A"
+          "#B4BD4C"
         ],
         [
           "D.2",
-          "#E68033"
+          "#D3B240"
         ],
         [
           "D.3",
-          "#E2562B"
+          "#E59638"
         ],
         [
           "D.4",
+          "#E4642E"
+        ],
+        [
+          "D.5",
           "#DB2823"
         ]
       ]
@@ -210,7 +237,8 @@
   ],
   "display_defaults": {
     "map_triplicate": true,
-    "color_by": "clade_membership",
+    "color_by": "subclade",
+    "branch_label": "Subclade",
     "tip_label": "gisaid_strain"
   },
   "filters": [

diff --git a/config/h1n1pdm/na/auspice_config.json b/config/h1n1pdm/na/auspice_config.json
@@ -49,41 +49,36 @@
       "title": "Subclade",
       "type": "categorical",
       "scale": [
-        [
-          "C",
-          "#3E5DD0"
-        ],
-        [
-          "C.3",
-          "#4A8CC2"
-        ],
         [
           "C.4",
-          "#60AA9E"
-        ],
-        [
-          "C.5.1.1",
-          "#80B974"
-        ],
-        [
-          "C.5.2",
-          "#A6BE55"
+          "#4E94BD"
         ],
         [
           "C.5.3",
-          "#CBB742"
+          "#81BA72"
         ],
         [
           "C.5.3.1",
-          "#E29D39"
+          "#C8B944"
+        ]
+      ]
+    },
+    {
+      "key": "proposed_subclade",
+      "title": "Proposed subclade",
+      "type": "categorical",
+      "scale": [
+        [
+          "C.4",
+          "#4E94BD"
         ],
         [
-          "C.5.3.2",
-          "#E56A2F"
+          "C.5.3",
+          "#81BA72"
         ],
         [
-          "C.5.3.3",
-          "#DB2823"
+          "C.5.3.1",
+          "#C8B944"
         ]
       ]
     },
@@ -175,7 +170,8 @@
   ],
   "display_defaults": {
     "map_triplicate": true,
-    "color_by": "clade_membership",
+    "color_by": "subclade",
+    "branch_label": "Subclade",
     "tip_label": "gisaid_strain"
   },
   "filters": [

diff --git a/config/h3n2/ha/auspice_config.json b/config/h3n2/ha/auspice_config.json
@@ -76,8 +76,8 @@
       ]
     },
     {
-      "key": "emerging_subclade",
-      "title": "Emerging subclade",
+      "key": "proposed_subclade",
+      "title": "Proposed subclade",
       "type": "categorical",
       "scale": [
         [
@@ -227,7 +227,8 @@
   ],
   "display_defaults": {
     "map_triplicate": true,
-    "color_by": "clade_membership",
+    "color_by": "subclade",
+    "branch_label": "Subclade",
     "tip_label": "gisaid_strain"
   },
   "filters": [

diff --git a/config/h3n2/na/auspice_config.json b/config/h3n2/na/auspice_config.json
@@ -67,6 +67,29 @@
         ]
       ]
     },
+    {
+      "key": "proposed_subclade",
+      "title": "Proposed subclade",
+      "type": "categorical",
+      "scale": [
+        [
+          "B.4",
+          "#4A8CC2"
+        ],
+        [
+          "B.4.1",
+          "#71B486"
+        ],
+        [
+          "B.4.2",
+          "#ABBD52"
+        ],
+        [
+          "B.4.3",
+          "#DEA73C"
+        ]
+      ]
+    },
     {
       "key": "haplotype",
       "title": "Derived haplotype",
@@ -160,7 +183,8 @@
   ],
   "display_defaults": {
     "map_triplicate": true,
-    "color_by": "clade_membership",
+    "color_by": "subclade",
+    "branch_label": "Subclade",
     "tip_label": "gisaid_strain"
   },
   "filters": [

diff --git a/config/vic/ha/auspice_config.json b/config/vic/ha/auspice_config.json
@@ -44,7 +44,7 @@
       "title": "Clade",
       "type": "categorical"
     },
-    {
+        {
       "key": "subclade",
       "title": "Subclade",
       "type": "categorical",
@@ -79,6 +79,41 @@
         ]
       ]
     },
+    {
+      "key": "proposed_subclade",
+      "title": "Proposed subclade",
+      "type": "categorical",
+      "scale": [
+        [
+          "C.2",
+          "#4272CE"
+        ],
+        [
+          "C.3",
+          "#58A2AC"
+        ],
+        [
+          "C.5",
+          "#7DB877"
+        ],
+        [
+          "C.5.1",
+          "#AEBD50"
+        ],
+        [
+          "C.5.4",
+          "#D8AE3E"
+        ],
+        [
+          "C.5.6",
+          "#E67A32"
+        ],
+        [
+          "C.5.7",
+          "#DB2823"
+        ]
+      ]
+    },
     {
       "key": "cTiter",
       "title": "Antigenic advance (tree model)",
@@ -167,7 +202,8 @@
   ],
   "display_defaults": {
     "map_triplicate": true,
-    "color_by": "clade_membership",
+    "color_by": "subclade",
+    "branch_label": "Subclade",
     "tip_label": "gisaid_strain"
   },
   "filters": [