diff --git a/backend/alignment.go b/backend/alignment.go
index aed2a9c..20c510a 100644
--- a/backend/alignment.go
+++ b/backend/alignment.go
@@ -190,6 +190,16 @@ type FastaEntry struct {
type SearchResult struct {
Database string `json:"db"`
Alignments interface{} `json:"alignments"`
+ TaxonomyReport interface{} `json:"taxonomyreport"`
+}
+
+type TaxonomyReport struct {
+ Proportion float64 `json:"proportion"`
+ CladeReads int `json:"clade_reads"`
+ TaxonReads int `json:"taxon_reads"`
+ Rank string `json:"rank"`
+ TaxonID string `json:"taxon_id"`
+ ScientificName string `json:"name"`
}
func dbpaths(path string) (string, string) {
@@ -320,13 +330,71 @@ func ReadAlignments[T any, U interface{ ~uint32 | ~int64 }](id Id, entries []U,
all = append(all, results)
}
reader.Delete()
+
+ // Read the taxonomy report
+ taxonomyReportPath := filepath.Join(base, "alis_" + db + "_report")
+ taxonomyReport, _ := ReadTaxonomyReport(taxonomyReportPath)
+
base := filepath.Base(name)
- res = append(res, SearchResult{strings.TrimPrefix(base, "alis_"), all})
+ res = append(res, SearchResult{
+ strings.TrimPrefix(base, "alis_"),
+ all,
+ taxonomyReport, // Include taxonomy report
+ })
}
return res, nil
}
+func ReadTaxonomyReport(filePath string) ([]TaxonomyReport, error) {
+ file, err := os.Open(filePath)
+ if err != nil {
+ // Return an empty report for any error
+ return []TaxonomyReport{}, nil
+ }
+ defer file.Close()
+
+ var reports []TaxonomyReport
+ scanner := bufio.NewScanner(file)
+
+ for scanner.Scan() {
+ line := scanner.Text()
+ fields := strings.Split(line, "\t")
+ if len(fields) < 6 {
+ // Skip invalid lines
+ continue
+ }
+
+ // Parse the fields
+ proportion, err := strconv.ParseFloat(fields[0], 64)
+ if err != nil {
+ continue
+ }
+
+ cladeReads, err := strconv.Atoi(fields[1])
+ if err != nil {
+ continue
+ }
+
+ taxonReads, err := strconv.Atoi(fields[2])
+ if err != nil {
+ continue
+ }
+
+ report := TaxonomyReport{
+ Proportion: proportion,
+ CladeReads: cladeReads,
+ TaxonReads: taxonReads,
+ Rank: fields[3],
+ TaxonID: fields[4],
+ ScientificName: strings.TrimSpace(fields[5]),
+ }
+ reports = append(reports, report)
+ }
+
+ return reports, nil
+}
+
func Alignments(id Id, entry []int64, databases []string, jobsbase string) ([]SearchResult, error) {
return ReadAlignments[AlignmentEntry, int64](id, entry, databases, jobsbase)
}
diff --git a/frontend/ResultView.vue b/frontend/ResultView.vue
index 348f7ac..faeac32 100644
--- a/frontend/ResultView.vue
+++ b/frontend/ResultView.vue
@@ -96,6 +96,7 @@
{{ entry.db }} {{ entry.alignments ? Object.values(entry.alignments).length : 0 }} hits
+
Graphical
@@ -106,7 +107,9 @@
-
+
+
+
@@ -251,6 +254,7 @@
import Panel from './Panel.vue';
import AlignmentPanel from './AlignmentPanel.vue';
import Ruler from './Ruler.vue';
+import SankeyDiagram from './SankeyDiagram.vue';
import { debounce } from './lib/debounce';
@@ -265,7 +269,7 @@ function getAbsOffsetTop($el) {
export default {
name: 'ResultView',
- components: { Panel, AlignmentPanel, Ruler },
+ components: { Panel, AlignmentPanel, Ruler, SankeyDiagram },
data() {
return {
alignment: null,
@@ -424,7 +428,6 @@ src: url(assets/InconsolataClustal2.woff2),
}
}
-
.theme--dark {
.result-table {
a:not([href]) {
diff --git a/frontend/SankeyDiagram.vue b/frontend/SankeyDiagram.vue
new file mode 100644
index 0000000..945a43b
--- /dev/null
+++ b/frontend/SankeyDiagram.vue
@@ -0,0 +1,583 @@
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/frontend/rankUtils.js b/frontend/rankUtils.js
new file mode 100644
index 0000000..92068dc
--- /dev/null
+++ b/frontend/rankUtils.js
@@ -0,0 +1,75 @@
+/** Full rank order used for sorting/ordering of hierarchy */
+export const rankOrderFull = [
+ "superkingdom",
+ "kingdom",
+ "subkingdom",
+ "superphylum",
+ "phylum",
+ "subphylum",
+ "superclass",
+ "class",
+ "subclass",
+ "superorder",
+ "order",
+ "suborder",
+ "infraorder",
+ "parvorder",
+ "superfamily",
+ "family",
+ "subfamily",
+ "supergenus",
+ "genus",
+ "subgenus",
+ "superspecies",
+ "species",
+ "subspecies",
+ "no rank",
+ "clade",
+];
+
+/** Ranks displays as levels/columns on sankey diagram
+ * Include 'no rank' for nodes displayed on sankey */
+export const sankeyRankColumns = ["superkingdom", "kingdom", "phylum", "class", "order", "family", "genus", "species"];
+
+const rankColors = [
+ // Superkingdom
+ "#57291F",
+ "#E63A06",
+ "#EE9595",
+ // Superphylum
+ "#FF6200",
+ "#FF9200",
+ "#F7B267",
+ // Superclass
+ "#E8B600",
+ "#FFD000",
+ "#E6DB6A",
+ // Superorder
+ "#044036",
+ "#0A7A26",
+ "#46A74B",
+ "#86B614",
+ "#ABE188",
+ // Superfamily
+ "#0065A2",
+ "#00A5E3",
+ "#77D0D0",
+ // Supergenus
+ "#520073",
+ "#9C47B0",
+ "#C792C7",
+ // Superspecies
+ "#FD4BB9",
+ "#F389F3",
+ "#FAB3E3",
+ // No rank
+ "#8A9BA7",
+ // Clade
+ "#696B73",
+];
+
+/** Function to retrieve color corresponding to rank */
+export function getRankColor(rank) {
+ const rankIndex = rankOrderFull.indexOf(rank);
+ return rankColors[rankIndex % rankColors.length];
+}
diff --git a/package-lock.json b/package-lock.json
index 31b903b..97aa259 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,13 +1,17 @@
{
"name": "mmseqs-app",
- "version": "1.7.0",
+ "version": "1.8.0",
"lockfileVersion": 2,
"requires": true,
"packages": {
"": {
"name": "mmseqs-app",
- "version": "1.7.0",
+ "version": "1.8.0",
"license": "GPL-3.0-or-later",
+ "dependencies": {
+ "d3": "^7.9.0",
+ "d3-sankey": "^0.12.3"
+ },
"devDependencies": {
"@babel/core": "^7.22.11",
"@babel/plugin-proposal-object-rest-spread": "^7.20.7",
@@ -5056,6 +5060,456 @@
"node": ">=4"
}
},
+ "node_modules/d3": {
+ "version": "7.9.0",
+ "resolved": "https://registry.npmjs.org/d3/-/d3-7.9.0.tgz",
+ "integrity": "sha512-e1U46jVP+w7Iut8Jt8ri1YsPOvFpg46k+K8TpCb0P+zjCkjkPnV7WzfDJzMHy1LnA+wj5pLT1wjO901gLXeEhA==",
+ "license": "ISC",
+ "dependencies": {
+ "d3-array": "3",
+ "d3-axis": "3",
+ "d3-brush": "3",
+ "d3-chord": "3",
+ "d3-color": "3",
+ "d3-contour": "4",
+ "d3-delaunay": "6",
+ "d3-dispatch": "3",
+ "d3-drag": "3",
+ "d3-dsv": "3",
+ "d3-ease": "3",
+ "d3-fetch": "3",
+ "d3-force": "3",
+ "d3-format": "3",
+ "d3-geo": "3",
+ "d3-hierarchy": "3",
+ "d3-interpolate": "3",
+ "d3-path": "3",
+ "d3-polygon": "3",
+ "d3-quadtree": "3",
+ "d3-random": "3",
+ "d3-scale": "4",
+ "d3-scale-chromatic": "3",
+ "d3-selection": "3",
+ "d3-shape": "3",
+ "d3-time": "3",
+ "d3-time-format": "4",
+ "d3-timer": "3",
+ "d3-transition": "3",
+ "d3-zoom": "3"
+ },
+ "engines": {
+ "node": ">=12"
+ }
+ },
+ "node_modules/d3-array": {
+ "version": "3.2.4",
+ "resolved": "https://registry.npmjs.org/d3-array/-/d3-array-3.2.4.tgz",
+ "integrity": "sha512-tdQAmyA18i4J7wprpYq8ClcxZy3SC31QMeByyCFyRt7BVHdREQZ5lpzoe5mFEYZUWe+oq8HBvk9JjpibyEV4Jg==",
+ "license": "ISC",
+ "dependencies": {
+ "internmap": "1 - 2"
+ },
+ "engines": {
+ "node": ">=12"
+ }
+ },
+ "node_modules/d3-axis": {
+ "version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/d3-axis/-/d3-axis-3.0.0.tgz",
+ "integrity": "sha512-IH5tgjV4jE/GhHkRV0HiVYPDtvfjHQlQfJHs0usq7M30XcSBvOotpmH1IgkcXsO/5gEQZD43B//fc7SRT5S+xw==",
+ "license": "ISC",
+ "engines": {
+ "node": ">=12"
+ }
+ },
+ "node_modules/d3-brush": {
+ "version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/d3-brush/-/d3-brush-3.0.0.tgz",
+ "integrity": "sha512-ALnjWlVYkXsVIGlOsuWH1+3udkYFI48Ljihfnh8FZPF2QS9o+PzGLBslO0PjzVoHLZ2KCVgAM8NVkXPJB2aNnQ==",
+ "license": "ISC",
+ "dependencies": {
+ "d3-dispatch": "1 - 3",
+ "d3-drag": "2 - 3",
+ "d3-interpolate": "1 - 3",
+ "d3-selection": "3",
+ "d3-transition": "3"
+ },
+ "engines": {
+ "node": ">=12"
+ }
+ },
+ "node_modules/d3-chord": {
+ "version": "3.0.1",
+ "resolved": "https://registry.npmjs.org/d3-chord/-/d3-chord-3.0.1.tgz",
+ "integrity": "sha512-VE5S6TNa+j8msksl7HwjxMHDM2yNK3XCkusIlpX5kwauBfXuyLAtNg9jCp/iHH61tgI4sb6R/EIMWCqEIdjT/g==",
+ "license": "ISC",
+ "dependencies": {
+ "d3-path": "1 - 3"
+ },
+ "engines": {
+ "node": ">=12"
+ }
+ },
+ "node_modules/d3-color": {
+ "version": "3.1.0",
+ "resolved": "https://registry.npmjs.org/d3-color/-/d3-color-3.1.0.tgz",
+ "integrity": "sha512-zg/chbXyeBtMQ1LbD/WSoW2DpC3I0mpmPdW+ynRTj/x2DAWYrIY7qeZIHidozwV24m4iavr15lNwIwLxRmOxhA==",
+ "license": "ISC",
+ "engines": {
+ "node": ">=12"
+ }
+ },
+ "node_modules/d3-contour": {
+ "version": "4.0.2",
+ "resolved": "https://registry.npmjs.org/d3-contour/-/d3-contour-4.0.2.tgz",
+ "integrity": "sha512-4EzFTRIikzs47RGmdxbeUvLWtGedDUNkTcmzoeyg4sP/dvCexO47AaQL7VKy/gul85TOxw+IBgA8US2xwbToNA==",
+ "license": "ISC",
+ "dependencies": {
+ "d3-array": "^3.2.0"
+ },
+ "engines": {
+ "node": ">=12"
+ }
+ },
+ "node_modules/d3-delaunay": {
+ "version": "6.0.4",
+ "resolved": "https://registry.npmjs.org/d3-delaunay/-/d3-delaunay-6.0.4.tgz",
+ "integrity": "sha512-mdjtIZ1XLAM8bm/hx3WwjfHt6Sggek7qH043O8KEjDXN40xi3vx/6pYSVTwLjEgiXQTbvaouWKynLBiUZ6SK6A==",
+ "license": "ISC",
+ "dependencies": {
+ "delaunator": "5"
+ },
+ "engines": {
+ "node": ">=12"
+ }
+ },
+ "node_modules/d3-dispatch": {
+ "version": "3.0.1",
+ "resolved": "https://registry.npmjs.org/d3-dispatch/-/d3-dispatch-3.0.1.tgz",
+ "integrity": "sha512-rzUyPU/S7rwUflMyLc1ETDeBj0NRuHKKAcvukozwhshr6g6c5d8zh4c2gQjY2bZ0dXeGLWc1PF174P2tVvKhfg==",
+ "license": "ISC",
+ "engines": {
+ "node": ">=12"
+ }
+ },
+ "node_modules/d3-drag": {
+ "version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/d3-drag/-/d3-drag-3.0.0.tgz",
+ "integrity": "sha512-pWbUJLdETVA8lQNJecMxoXfH6x+mO2UQo8rSmZ+QqxcbyA3hfeprFgIT//HW2nlHChWeIIMwS2Fq+gEARkhTkg==",
+ "license": "ISC",
+ "dependencies": {
+ "d3-dispatch": "1 - 3",
+ "d3-selection": "3"
+ },
+ "engines": {
+ "node": ">=12"
+ }
+ },
+ "node_modules/d3-dsv": {
+ "version": "3.0.1",
+ "resolved": "https://registry.npmjs.org/d3-dsv/-/d3-dsv-3.0.1.tgz",
+ "integrity": "sha512-UG6OvdI5afDIFP9w4G0mNq50dSOsXHJaRE8arAS5o9ApWnIElp8GZw1Dun8vP8OyHOZ/QJUKUJwxiiCCnUwm+Q==",
+ "license": "ISC",
+ "dependencies": {
+ "commander": "7",
+ "iconv-lite": "0.6",
+ "rw": "1"
+ },
+ "bin": {
+ "csv2json": "bin/dsv2json.js",
+ "csv2tsv": "bin/dsv2dsv.js",
+ "dsv2dsv": "bin/dsv2dsv.js",
+ "dsv2json": "bin/dsv2json.js",
+ "json2csv": "bin/json2dsv.js",
+ "json2dsv": "bin/json2dsv.js",
+ "json2tsv": "bin/json2dsv.js",
+ "tsv2csv": "bin/dsv2dsv.js",
+ "tsv2json": "bin/dsv2json.js"
+ },
+ "engines": {
+ "node": ">=12"
+ }
+ },
+ "node_modules/d3-dsv/node_modules/commander": {
+ "version": "7.2.0",
+ "resolved": "https://registry.npmjs.org/commander/-/commander-7.2.0.tgz",
+ "integrity": "sha512-QrWXB+ZQSVPmIWIhtEO9H+gwHaMGYiF5ChvoJ+K9ZGHG/sVsa6yiesAD1GC/x46sET00Xlwo1u49RVVVzvcSkw==",
+ "license": "MIT",
+ "engines": {
+ "node": ">= 10"
+ }
+ },
+ "node_modules/d3-ease": {
+ "version": "3.0.1",
+ "resolved": "https://registry.npmjs.org/d3-ease/-/d3-ease-3.0.1.tgz",
+ "integrity": "sha512-wR/XK3D3XcLIZwpbvQwQ5fK+8Ykds1ip7A2Txe0yxncXSdq1L9skcG7blcedkOX+ZcgxGAmLX1FrRGbADwzi0w==",
+ "license": "BSD-3-Clause",
+ "engines": {
+ "node": ">=12"
+ }
+ },
+ "node_modules/d3-fetch": {
+ "version": "3.0.1",
+ "resolved": "https://registry.npmjs.org/d3-fetch/-/d3-fetch-3.0.1.tgz",
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+ "license": "ISC",
+ "dependencies": {
+ "d3-dsv": "1 - 3"
+ },
+ "engines": {
+ "node": ">=12"
+ }
+ },
+ "node_modules/d3-force": {
+ "version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/d3-force/-/d3-force-3.0.0.tgz",
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+ "license": "ISC",
+ "dependencies": {
+ "d3-dispatch": "1 - 3",
+ "d3-quadtree": "1 - 3",
+ "d3-timer": "1 - 3"
+ },
+ "engines": {
+ "node": ">=12"
+ }
+ },
+ "node_modules/d3-format": {
+ "version": "3.1.0",
+ "resolved": "https://registry.npmjs.org/d3-format/-/d3-format-3.1.0.tgz",
+ "integrity": "sha512-YyUI6AEuY/Wpt8KWLgZHsIU86atmikuoOmCfommt0LYHiQSPjvX2AcFc38PX0CBpr2RCyZhjex+NS/LPOv6YqA==",
+ "license": "ISC",
+ "engines": {
+ "node": ">=12"
+ }
+ },
+ "node_modules/d3-geo": {
+ "version": "3.1.1",
+ "resolved": "https://registry.npmjs.org/d3-geo/-/d3-geo-3.1.1.tgz",
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+ "license": "ISC",
+ "dependencies": {
+ "d3-array": "2.5.0 - 3"
+ },
+ "engines": {
+ "node": ">=12"
+ }
+ },
+ "node_modules/d3-hierarchy": {
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+ "license": "ISC",
+ "engines": {
+ "node": ">=12"
+ }
+ },
+ "node_modules/d3-interpolate": {
+ "version": "3.0.1",
+ "resolved": "https://registry.npmjs.org/d3-interpolate/-/d3-interpolate-3.0.1.tgz",
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+ "license": "ISC",
+ "dependencies": {
+ "d3-color": "1 - 3"
+ },
+ "engines": {
+ "node": ">=12"
+ }
+ },
+ "node_modules/d3-path": {
+ "version": "3.1.0",
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+ "license": "ISC",
+ "engines": {
+ "node": ">=12"
+ }
+ },
+ "node_modules/d3-polygon": {
+ "version": "3.0.1",
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+ "license": "ISC",
+ "engines": {
+ "node": ">=12"
+ }
+ },
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+ "version": "3.0.1",
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+ "license": "ISC",
+ "engines": {
+ "node": ">=12"
+ }
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+ "version": "3.0.1",
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+ "license": "ISC",
+ "engines": {
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+ }
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+ "version": "0.12.3",
+ "resolved": "https://registry.npmjs.org/d3-sankey/-/d3-sankey-0.12.3.tgz",
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+ "license": "BSD-3-Clause",
+ "dependencies": {
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+ }
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+ "dependencies": {
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+ "license": "BSD-3-Clause",
+ "dependencies": {
+ "d3-path": "1"
+ }
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+ "resolved": "https://registry.npmjs.org/d3-timer/-/d3-timer-3.0.1.tgz",
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+ "integrity": "sha512-ApKvfjsSR6tg06xrL434C0WydLr7JewBB3V+/39RMHsaXTOG0zmt/OAXeng5M5LBm0ojmxJrpomQVZ1aPvBL4w==",
+ "requires": {
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+ "d3-dispatch": "1 - 3",
+ "d3-ease": "1 - 3",
+ "d3-interpolate": "1 - 3",
+ "d3-timer": "1 - 3"
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+ "d3-zoom": {
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+ "resolved": "https://registry.npmjs.org/d3-zoom/-/d3-zoom-3.0.0.tgz",
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+ "requires": {
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+ "d3-drag": "2 - 3",
+ "d3-interpolate": "1 - 3",
+ "d3-selection": "2 - 3",
+ "d3-transition": "2 - 3"
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"dashdash": {
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"resolved": "https://registry.npmjs.org/dashdash/-/dashdash-1.14.1.tgz",
@@ -17697,6 +18486,14 @@
"slash": "^3.0.0"
}
},
+ "delaunator": {
+ "version": "5.0.1",
+ "resolved": "https://registry.npmjs.org/delaunator/-/delaunator-5.0.1.tgz",
+ "integrity": "sha512-8nvh+XBe96aCESrGOqMp/84b13H9cdKbG5P2ejQCh4d4sK9RL4371qou9drQjMhvnPmhWl5hnmqbEE0fXr9Xnw==",
+ "requires": {
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+ }
+ },
"delayed-stream": {
"version": "1.0.0",
"resolved": "https://registry.npmjs.org/delayed-stream/-/delayed-stream-1.0.0.tgz",
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- "dev": true,
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}
@@ -19827,6 +20623,11 @@
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"dev": true
},
+ "internmap": {
+ "version": "2.0.3",
+ "resolved": "https://registry.npmjs.org/internmap/-/internmap-2.0.3.tgz",
+ "integrity": "sha512-5Hh7Y1wQbvY5ooGgPbDaL5iYLAPzMTUrjMulskHLH6wnv/A+1q5rgEaiuqEjB+oxGXIVZs1FF+R/KPN3ZSQYYg=="
+ },
"interpret": {
"version": "2.2.0",
"resolved": "https://registry.npmjs.org/interpret/-/interpret-2.2.0.tgz",
@@ -21911,6 +22712,11 @@
"sprintf-js": "^1.1.2"
}
},
+ "robust-predicates": {
+ "version": "3.0.2",
+ "resolved": "https://registry.npmjs.org/robust-predicates/-/robust-predicates-3.0.2.tgz",
+ "integrity": "sha512-IXgzBWvWQwE6PrDI05OvmXUIruQTcoMDzRsOd5CDvHCVLcLHMTSYvOK5Cm46kWqlV3yAbuSpBZdJ5oP5OUoStg=="
+ },
"run-parallel": {
"version": "1.2.0",
"resolved": "https://registry.npmjs.org/run-parallel/-/run-parallel-1.2.0.tgz",
@@ -21920,6 +22726,11 @@
"queue-microtask": "^1.2.2"
}
},
+ "rw": {
+ "version": "1.3.3",
+ "resolved": "https://registry.npmjs.org/rw/-/rw-1.3.3.tgz",
+ "integrity": "sha512-PdhdWy89SiZogBLaw42zdeqtRJ//zFd2PgQavcICDUgJT5oW10QCRKbJ6bg4r0/UY2M6BWd5tkxuGFRvCkgfHQ=="
+ },
"safe-buffer": {
"version": "5.1.2",
"resolved": "https://registry.npmjs.org/safe-buffer/-/safe-buffer-5.1.2.tgz",
@@ -21929,8 +22740,7 @@
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"resolved": "https://registry.npmjs.org/safer-buffer/-/safer-buffer-2.1.2.tgz",
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- "dev": true
+ "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg=="
},
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diff --git a/package.json b/package.json
index efee910..d72bc38 100644
--- a/package.json
+++ b/package.json
@@ -146,5 +146,9 @@
"webpack-dev-server": "^4.15.1",
"webpack-hot-middleware": "^2.25.4",
"webpack-subresource-integrity": "^5.1.0"
+ },
+ "dependencies": {
+ "d3": "^7.9.0",
+ "d3-sankey": "^0.12.3"
}
}