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chore: upgrade Vega-Lite spec from v5 to v6
Update the schema URL to use Vega-Lite v6 to match the installed vega-lite package version (6.4.1). The spec is backward compatible and renders correctly with no changes needed.
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‎public/learn/featured-analyses/evolutionary-dynamics-of-coding-overlaps-in-measles/nucleotide-changes-vega-spec.json‎

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@@ -1,9 +1,19 @@
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{
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"config": { "view": { "continuousWidth": 300, "continuousHeight": 300 } },
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"config": {
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"view": {
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"continuousWidth": 300,
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"continuousHeight": 300
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}
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},
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"vconcat": [
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{
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"data": { "name": "data-a1ad66d96417cbab667365597f608ba0" },
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"mark": { "type": "tick", "thickness": 4 },
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"data": {
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"name": "data-a1ad66d96417cbab667365597f608ba0"
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},
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"mark": {
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"type": "tick",
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"thickness": 4
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},
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"encoding": {
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"color": {
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"field": "effect_bin",
@@ -16,33 +26,85 @@
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},
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"opacity": {
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"field": "samples",
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"scale": { "range": [0.35, 1] },
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"scale": {
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"range": [0.35, 1]
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},
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"title": "Samples",
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"type": "quantitative"
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},
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"size": {
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"field": "af_range",
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"scale": { "range": [6, 28] },
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"scale": {
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"range": [6, 28]
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},
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"title": "AF range (max-min)",
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"type": "quantitative"
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},
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"tooltip": [
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{ "field": "var_id", "type": "nominal" },
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{ "field": "chr", "type": "nominal" },
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{ "field": "genome_pos", "type": "quantitative" },
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{ "field": "ref", "type": "nominal" },
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{ "field": "alt", "type": "nominal" },
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{ "field": "product", "type": "nominal" },
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{ "field": "gene", "type": "nominal" },
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{ "field": "effect_bin", "type": "nominal" },
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{ "field": "samples", "type": "quantitative" },
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{ "field": "af", "type": "quantitative" },
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{ "field": "af_min", "type": "quantitative" },
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{ "field": "af_max", "type": "quantitative" },
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{ "field": "ref_codon", "type": "nominal" },
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{ "field": "new_codon", "type": "nominal" },
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{ "field": "ref_aa", "type": "nominal" },
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{ "field": "new_aa", "type": "nominal" }
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{
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"field": "var_id",
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"type": "nominal"
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},
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{
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"field": "chr",
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"type": "nominal"
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},
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{
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"field": "genome_pos",
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"type": "quantitative"
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},
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{
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"field": "ref",
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"type": "nominal"
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},
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{
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"field": "alt",
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"type": "nominal"
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},
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{
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"field": "product",
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"type": "nominal"
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},
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{
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"field": "gene",
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"type": "nominal"
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},
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{
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"field": "effect_bin",
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"type": "nominal"
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},
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{
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"field": "samples",
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"type": "quantitative"
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},
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{
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"field": "af",
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"type": "quantitative"
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},
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{
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"field": "af_min",
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"type": "quantitative"
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},
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{
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"field": "af_max",
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"type": "quantitative"
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},
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{
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"field": "ref_codon",
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"type": "nominal"
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},
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{
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"field": "new_codon",
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"type": "nominal"
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},
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{
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"field": "ref_aa",
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"type": "nominal"
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},
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{
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"field": "new_aa",
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"type": "nominal"
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}
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],
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"x": {
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"field": "genome_pos",
@@ -64,31 +126,65 @@
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{
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"layer": [
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{
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"mark": { "type": "rect" },
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"mark": {
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"type": "rect"
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},
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"encoding": {
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"color": {
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"field": "aa_label",
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"title": "Amino acid",
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"type": "nominal"
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},
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"tooltip": [
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{ "field": "CHROM", "type": "nominal" },
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{ "field": "product", "type": "nominal" },
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{ "field": "gene", "type": "nominal" },
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{ "field": "genome_pos", "type": "quantitative" },
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{ "field": "cds_nt_index", "type": "quantitative" },
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{ "field": "codon_index", "type": "quantitative" },
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{ "field": "codon_pos", "type": "quantitative" },
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{ "field": "codon", "type": "nominal" },
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{ "field": "aa_label", "type": "nominal" },
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{ "field": "base", "type": "nominal" }
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{
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"field": "CHROM",
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"type": "nominal"
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},
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{
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"field": "product",
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"type": "nominal"
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},
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{
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"field": "gene",
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"type": "nominal"
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},
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{
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"field": "genome_pos",
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"type": "quantitative"
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},
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{
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"field": "cds_nt_index",
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"type": "quantitative"
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},
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{
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"field": "codon_index",
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"type": "quantitative"
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},
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{
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"field": "codon_pos",
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"type": "quantitative"
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},
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{
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"field": "codon",
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"type": "nominal"
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},
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{
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"field": "aa_label",
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"type": "nominal"
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},
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{
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"field": "base",
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"type": "nominal"
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}
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],
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"x": {
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"field": "genome_pos",
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"title": "Genome position (1-based)",
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"type": "quantitative"
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},
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"x2": { "field": "x2" },
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"x2": {
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"field": "x2"
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},
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"y": {
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"field": "product",
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"sort": [
@@ -117,8 +213,14 @@
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"strokeWidth": 1
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},
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"encoding": {
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"text": { "field": "base", "type": "nominal" },
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"x": { "field": "x_mid", "type": "quantitative" },
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"text": {
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"field": "base",
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"type": "nominal"
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},
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"x": {
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"field": "x_mid",
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"type": "quantitative"
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},
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"y": {
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"field": "product",
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"sort": [
@@ -136,7 +238,9 @@
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}
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}
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],
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"data": { "name": "data-8fb1d001c9584e6ee761d2bf63274f5c" },
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"data": {
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"name": "data-8fb1d001c9584e6ee761d2bf63274f5c"
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},
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"height": 144,
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"title": "Per-nucleotide amino acid context by product (centered nucleotide labels)",
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"width": 756
@@ -145,20 +249,31 @@
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"params": [
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{
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"name": "param_2",
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"select": { "type": "interval", "encodings": ["x", "y"] },
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"select": {
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"type": "interval",
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"encodings": ["x", "y"]
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},
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"bind": "scales",
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"views": ["view_6"]
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},
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{
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"name": "xzoom",
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"select": { "type": "interval", "encodings": ["x"] },
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"select": {
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"type": "interval",
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"encodings": ["x"]
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},
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"bind": "scales",
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"views": ["view_5", "view_6"]
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}
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],
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"resolve": { "scale": { "color": "independent", "x": "shared" } },
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"resolve": {
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"scale": {
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"color": "independent",
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"x": "shared"
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}
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},
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"spacing": 6,
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"$schema": "https://vega.github.io/schema/vega-lite/v5.20.1.json",
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"$schema": "https://vega.github.io/schema/vega-lite/v6.json",
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"datasets": {
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"data-a1ad66d96417cbab667365597f608ba0": [
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{

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