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Add proposed subclades to public and private builds #195

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merged 8 commits into from
Nov 7, 2024
Merged

Add proposed subclades to public and private builds #195

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d172bb7
Use proposed subclades in public/private builds
huddlej Nov 6, 2024
400f573
Use proposed subclades from Nextclade annotations
huddlej Nov 6, 2024
13167da
Plot proposed subclades in titer figures
huddlej Oct 28, 2024
d39e2ea
Use proposed subclades in measurements panels
huddlej Nov 6, 2024
c7b3d42
Display subclades by default public builds
huddlej Nov 7, 2024
77388e1
Revert to subclade as default branch label
huddlej Nov 7, 2024
3088a3b
Use underscore instead of spaces in branch label
huddlej Nov 7, 2024
6df5c2c
Use correct branch label value for subclade
huddlej Nov 7, 2024
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14 changes: 7 additions & 7 deletions Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
}
}

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66 changes: 47 additions & 19 deletions config/h1n1pdm/ha/auspice_config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
]
]
Expand Down Expand Up @@ -210,7 +237,8 @@
],
"display_defaults": {
"map_triplicate": true,
"color_by": "clade_membership",
"color_by": "subclade",
"branch_label": "Subclade",
"tip_label": "gisaid_strain"
},
"filters": [
Expand Down
44 changes: 20 additions & 24 deletions config/h1n1pdm/na/auspice_config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
]
]
},
Expand Down Expand Up @@ -175,7 +170,8 @@
],
"display_defaults": {
"map_triplicate": true,
"color_by": "clade_membership",
"color_by": "subclade",
"branch_label": "Subclade",
"tip_label": "gisaid_strain"
},
"filters": [
Expand Down
7 changes: 4 additions & 3 deletions config/h3n2/ha/auspice_config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -76,8 +76,8 @@
]
},
{
"key": "emerging_subclade",
"title": "Emerging subclade",
"key": "proposed_subclade",
"title": "Proposed subclade",
"type": "categorical",
"scale": [
[
Expand Down Expand Up @@ -227,7 +227,8 @@
],
"display_defaults": {
"map_triplicate": true,
"color_by": "clade_membership",
"color_by": "subclade",
"branch_label": "Subclade",
"tip_label": "gisaid_strain"
},
"filters": [
Expand Down
26 changes: 25 additions & 1 deletion config/h3n2/na/auspice_config.json
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -160,7 +183,8 @@
],
"display_defaults": {
"map_triplicate": true,
"color_by": "clade_membership",
"color_by": "subclade",
"branch_label": "Subclade",
"tip_label": "gisaid_strain"
},
"filters": [
Expand Down
40 changes: 38 additions & 2 deletions config/vic/ha/auspice_config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@
"title": "Clade",
"type": "categorical"
},
{
{
"key": "subclade",
"title": "Subclade",
"type": "categorical",
Expand Down Expand Up @@ -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)",
Expand Down Expand Up @@ -167,7 +202,8 @@
],
"display_defaults": {
"map_triplicate": true,
"color_by": "clade_membership",
"color_by": "subclade",
"branch_label": "Subclade",
"tip_label": "gisaid_strain"
},
"filters": [
Expand Down
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