@platforma-open/milaboratories.top-antibodies.workflow 1.3.0 → 1.3.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/.turbo/turbo-build.log +1 -5
- package/CHANGELOG.md +9 -0
- package/dist/tengo/lib/pf-spectratype-conv.lib.tengo +27 -27
- package/dist/tengo/lib/pf-vj-usage-conv.lib.tengo +26 -26
- package/dist/tengo/lib/sampled-cols-conv.lib.tengo +19 -30
- package/dist/tengo/tpl/main.plj.gz +0 -0
- package/package.json +6 -6
- package/src/main.tpl.tengo +1 -40
- package/src/pf-spectratype-conv.lib.tengo +27 -27
- package/src/pf-vj-usage-conv.lib.tengo +26 -26
- package/src/sampled-cols-conv.lib.tengo +19 -30
- package/dist/tengo/lib/pf-umap-conv.lib.tengo +0 -43
- package/dist/tengo/lib/sampled-cols-umap-conv.lib.tengo +0 -38
- package/src/pf-umap-conv.lib.tengo +0 -43
- package/src/sampled-cols-umap-conv.lib.tengo +0 -38
package/.turbo/turbo-build.log
CHANGED
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@@ -1,21 +1,17 @@
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WARN Issue while reading "/home/runner/work/top-antibodies/top-antibodies/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
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> @platforma-open/milaboratories.top-antibodies.workflow@1.3.
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> @platforma-open/milaboratories.top-antibodies.workflow@1.3.1 build /home/runner/work/top-antibodies/top-antibodies/workflow
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> rm -rf dist && pl-tengo check && pl-tengo build
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Processing "src/main.tpl.tengo"...
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Processing "src/pf-spectratype-conv.lib.tengo"...
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Processing "src/pf-umap-conv.lib.tengo"...
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Processing "src/pf-vj-usage-conv.lib.tengo"...
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Processing "src/sampled-cols-conv.lib.tengo"...
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Processing "src/sampled-cols-umap-conv.lib.tengo"...
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No syntax errors found.
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info: Compiling 'dist'...
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info: - writing /home/runner/work/top-antibodies/top-antibodies/workflow/dist/tengo/lib/pf-spectratype-conv.lib.tengo
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info: - writing /home/runner/work/top-antibodies/top-antibodies/workflow/dist/tengo/lib/pf-umap-conv.lib.tengo
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info: - writing /home/runner/work/top-antibodies/top-antibodies/workflow/dist/tengo/lib/pf-vj-usage-conv.lib.tengo
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info: - writing /home/runner/work/top-antibodies/top-antibodies/workflow/dist/tengo/lib/sampled-cols-conv.lib.tengo
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info: - writing /home/runner/work/top-antibodies/top-antibodies/workflow/dist/tengo/lib/sampled-cols-umap-conv.lib.tengo
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info: - writing /home/runner/work/top-antibodies/top-antibodies/workflow/dist/tengo/tpl/main.plj.gz
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info: Template Pack build done.
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info: Template Pack build done.
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package/CHANGELOG.md
CHANGED
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# @platforma-open/milaboratories.top-antibodies.workflow
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## 1.3.1
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### Patch Changes
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- Updated dependencies [b280c5c]
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- @platforma-open/milaboratories.top-antibodies.sample-clonotypes@1.0.2
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- @platforma-open/milaboratories.top-antibodies.spectratype@1.3.1
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- @platforma-open/milaboratories.top-antibodies.umap@1.0.2
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## 1.3.0
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### Minor Changes
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@@ -2,55 +2,55 @@ ll := import("@platforma-sdk/workflow-tengo:ll")
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getColumns := func() {
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return {
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axes: [
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{
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column: "chain",
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spec: {
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name: "pl7.app/vdj/chain",
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type: "String",
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annotations: { "pl7.app/label": "CDR3 chain" }
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}
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},
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column: "cdr3Length",
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spec: {
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name: "pl7.app/vdj/sequenceLength",
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type: "Int",
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domain: {
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"pl7.app/vdj/feature": "CDR3",
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"pl7.app/alphabet": "aminoacid"
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},
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annotations: { "pl7.app/label": "CDR3 aa Length" }
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}
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{
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column: "vGene",
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spec: {
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name: "pl7.app/vdj/geneHit",
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type: "String",
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domain: { "pl7.app/vdj/reference": "VGene" },
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annotations: {
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"pl7.app/label": "Best V gene"
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}
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}
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}
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],
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columns: [
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{
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column: "count",
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spec: {
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name: "pl7.app/vdj/vSpectratype",
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valueType: "Int",
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domain: {
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"pl7.app/vdj/feature": "CDR3",
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"pl7.app/alphabet": "aminoacid"
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},
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annotations: { "pl7.app/label": "CDR3 V Spectratype" }
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}
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}
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],
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storageFormat: "Binary",
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partitionKeyLength: 0
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}
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}
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getColumns := func() {
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return {
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axes: [
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column: "chain",
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spec: {
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name: "pl7.app/vdj/chain",
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type: "String",
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annotations: { "pl7.app/label": "CDR3 chain" }
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}
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},
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column: "vGene",
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spec: {
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name: "pl7.app/vdj/geneHit",
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type: "String",
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domain: { "pl7.app/vdj/reference": "VGene" },
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annotations: {
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"pl7.app/label": "Best V gene"
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}
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column: "jGene",
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spec: {
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name: "pl7.app/vdj/geneHit",
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type: "String",
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domain: { "pl7.app/vdj/reference": "JGene" },
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annotations: {
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"pl7.app/label": "Best J gene"
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}
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}
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],
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columns: [
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column: "count",
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spec: {
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name: "pl7.app/vdj/vjGeneUsage",
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valueType: "Int",
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annotations: { "pl7.app/label": "V/J usage" }
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}
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}
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],
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storageFormat: "Binary",
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partitionKeyLength: 0
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}
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}
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ll := import("@platforma-sdk/workflow-tengo:ll")
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getColumns := func(datasetSpec
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axes := [
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{
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"column": "clonotypeKey",
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"spec": datasetSpec.axesSpec[1]
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}]
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if len(linkerAxisSpec) > 0 {
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for key, val in linkerAxisSpec {
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axes = axes + [
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{
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"column": key,
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}
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}
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getColumns := func(datasetSpec) {
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}],
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columns: [
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column: "top",
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id: "link",
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allowNA: false,
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spec: {
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name: "pl7.app/vdj/sampling-column",
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valueType: "Int",
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domain: {},
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annotations: {
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"pl7.app/table/visibility": "optional",
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"pl7.app/isSubset": "true"
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partitionKeyLength: 0
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}
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}
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Binary file
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package/package.json
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{
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"name": "@platforma-open/milaboratories.top-antibodies.workflow",
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"version": "1.3.
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"version": "1.3.1",
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"type": "module",
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"description": "Block Workflow",
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"dependencies": {
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"@platforma-sdk/workflow-tengo": "^4.6.
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"@platforma-open/milaboratories.top-antibodies.
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"@platforma-open/milaboratories.top-antibodies.
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"@platforma-open/milaboratories.top-antibodies.
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"@platforma-sdk/workflow-tengo": "^4.6.2",
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"@platforma-open/milaboratories.top-antibodies.sample-clonotypes": "1.0.2",
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"@platforma-open/milaboratories.top-antibodies.umap": "1.0.2",
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"@platforma-open/milaboratories.top-antibodies.spectratype": "1.3.1"
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},
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"devDependencies": {
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"@platforma-sdk/tengo-builder": "^2.1.5",
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"@platforma-sdk/test": "^1.31.
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"@platforma-sdk/test": "^1.31.18",
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"vitest": "^2.1.8"
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},
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"scripts": {
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package/src/main.tpl.tengo
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xsv := import("@platforma-sdk/workflow-tengo:pframes.xsv")
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pframes := import("@platforma-sdk/workflow-tengo:pframes")
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sampledColsConv := import(":sampled-cols-conv")
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sampledColsUmapConv := import(":sampled-cols-umap-conv")
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spectratypeConv := import(":pf-spectratype-conv")
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vjUsageConv := import(":pf-vj-usage-conv")
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slices := import("@platforma-sdk/workflow-tengo:slices")
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umapConv := import(":pf-umap-conv")
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wf.prepare(func(args){
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// We need a table with cluster ID (optional) | clonotype id | selected ranking columns
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topClonotypesCsv = sampleClones.getFile("sampledClonotypes_top.csv")
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// Store outputs
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sampledColsParams := sampledColsConv.getColumns(datasetSpec
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sampledColsParams := sampledColsConv.getColumns(datasetSpec)
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sampledColumnsPf := xsv.importFile(topClonotypesCsv, "csv", sampledColsParams)
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outputs["sampledRows"] = pframes.exportFrame(sampledColumnsPf)
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// Prepare filter col subset for UMAP
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// Avoid taking cluster axis using other params
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sampledColsUmapParams := sampledColsUmapConv.getColumns(datasetSpec)
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sampledColsUmapPf := xsv.importFile(topClonotypesCsv, "csv", sampledColsUmapParams)
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outputs["sampledRowsUmap"] = pframes.exportFrame(sampledColsUmapPf)
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}
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////////// UMAP //////////
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// Generate input TSV with Clonotype ID and aa sequence
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umapTable := pframes.tsvFileBuilder()
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umapTable.setAxisHeader(datasetSpec.axesSpec[1].name, "clonotypeKey")
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for col in columns.getColumns("aaSequence") {
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if isSingleCell {
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chainLabel := col.spec.domain["pl7.app/vdj/scClonotypeChain"]
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umapTable.add(col, {header: "aaSequence." + chainLabel})
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} else {
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chainLabel := col.spec.axesSpec[0].domain["pl7.app/vdj/chain"]
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umapTable.add(col, {header: "aaSequence." + chainLabel})
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}
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}
|
|
172
|
-
umapTable = umapTable.build()
|
|
173
|
-
|
|
174
|
-
// UMAP script should go here
|
|
175
|
-
umapClones := exec.builder().
|
|
176
|
-
software(assets.importSoftware("@platforma-open/milaboratories.top-antibodies.umap:main")).
|
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177
|
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addFile("sequences.tsv", umapTable).
|
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|
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arg("-i").arg("sequences.tsv").
|
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179
|
-
arg("-u").arg("umap.tsv").
|
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180
|
-
saveFile("umap.tsv").
|
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|
-
printErrStreamToStdout().
|
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-
saveStdoutContent().
|
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|
-
cache(24 * 60 * 60 * 1000).
|
|
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|
-
run()
|
|
185
|
-
|
|
186
|
-
|
|
187
|
-
umapPf := xsv.importFile(umapClones.getFile("umap.tsv"), "tsv", umapConv.getColumns(datasetSpec))
|
|
188
|
-
outputs["umap"] = pframes.exportFrame(umapPf)
|
|
189
150
|
|
|
190
151
|
////////// CDR3 Length Calculation //////////
|
|
191
152
|
|
|
@@ -2,55 +2,55 @@ ll := import("@platforma-sdk/workflow-tengo:ll")
|
|
|
2
2
|
|
|
3
3
|
getColumns := func() {
|
|
4
4
|
return {
|
|
5
|
-
|
|
5
|
+
axes: [
|
|
6
6
|
{
|
|
7
|
-
|
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8
|
-
|
|
9
|
-
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10
|
-
|
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11
|
-
|
|
7
|
+
column: "chain",
|
|
8
|
+
spec: {
|
|
9
|
+
name: "pl7.app/vdj/chain",
|
|
10
|
+
type: "String",
|
|
11
|
+
annotations: { "pl7.app/label": "CDR3 chain" }
|
|
12
12
|
}
|
|
13
13
|
},
|
|
14
14
|
{
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15
|
-
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-
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17
|
-
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18
|
-
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19
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-
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15
|
+
column: "cdr3Length",
|
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16
|
+
spec: {
|
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17
|
+
name: "pl7.app/vdj/sequenceLength",
|
|
18
|
+
type: "Int",
|
|
19
|
+
domain: {
|
|
20
20
|
"pl7.app/vdj/feature": "CDR3",
|
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21
21
|
"pl7.app/alphabet": "aminoacid"
|
|
22
22
|
},
|
|
23
|
-
|
|
23
|
+
annotations: { "pl7.app/label": "CDR3 aa Length" }
|
|
24
24
|
}
|
|
25
25
|
},
|
|
26
26
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{
|
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27
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-
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-
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29
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-
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30
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-
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31
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-
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32
|
-
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27
|
+
column: "vGene",
|
|
28
|
+
spec: {
|
|
29
|
+
name: "pl7.app/vdj/geneHit",
|
|
30
|
+
type: "String",
|
|
31
|
+
domain: { "pl7.app/vdj/reference": "VGene" },
|
|
32
|
+
annotations: {
|
|
33
33
|
"pl7.app/label": "Best V gene"
|
|
34
34
|
}
|
|
35
35
|
}
|
|
36
36
|
}
|
|
37
37
|
],
|
|
38
|
-
|
|
38
|
+
columns: [
|
|
39
39
|
{
|
|
40
|
-
|
|
41
|
-
|
|
42
|
-
|
|
43
|
-
|
|
44
|
-
|
|
40
|
+
column: "count",
|
|
41
|
+
spec: {
|
|
42
|
+
name: "pl7.app/vdj/vSpectratype",
|
|
43
|
+
valueType: "Int",
|
|
44
|
+
domain: {
|
|
45
45
|
"pl7.app/vdj/feature": "CDR3",
|
|
46
46
|
"pl7.app/alphabet": "aminoacid"
|
|
47
47
|
},
|
|
48
|
-
|
|
48
|
+
annotations: { "pl7.app/label": "CDR3 V Spectratype" }
|
|
49
49
|
}
|
|
50
50
|
}
|
|
51
51
|
],
|
|
52
|
-
|
|
53
|
-
|
|
52
|
+
storageFormat: "Binary",
|
|
53
|
+
partitionKeyLength: 0
|
|
54
54
|
}
|
|
55
55
|
}
|
|
56
56
|
|
|
@@ -2,50 +2,50 @@ ll := import("@platforma-sdk/workflow-tengo:ll")
|
|
|
2
2
|
|
|
3
3
|
getColumns := func() {
|
|
4
4
|
return {
|
|
5
|
-
|
|
5
|
+
axes: [
|
|
6
6
|
{
|
|
7
|
-
|
|
8
|
-
|
|
9
|
-
|
|
10
|
-
|
|
11
|
-
|
|
7
|
+
column: "chain",
|
|
8
|
+
spec: {
|
|
9
|
+
name: "pl7.app/vdj/chain",
|
|
10
|
+
type: "String",
|
|
11
|
+
annotations: { "pl7.app/label": "CDR3 chain" }
|
|
12
12
|
}
|
|
13
13
|
},
|
|
14
14
|
{
|
|
15
|
-
|
|
16
|
-
|
|
17
|
-
|
|
18
|
-
|
|
19
|
-
|
|
20
|
-
|
|
15
|
+
column: "vGene",
|
|
16
|
+
spec: {
|
|
17
|
+
name: "pl7.app/vdj/geneHit",
|
|
18
|
+
type: "String",
|
|
19
|
+
domain: { "pl7.app/vdj/reference": "VGene" },
|
|
20
|
+
annotations: {
|
|
21
21
|
"pl7.app/label": "Best V gene"
|
|
22
22
|
}
|
|
23
23
|
}
|
|
24
24
|
},
|
|
25
25
|
{
|
|
26
|
-
|
|
27
|
-
|
|
28
|
-
|
|
29
|
-
|
|
30
|
-
|
|
31
|
-
|
|
26
|
+
column: "jGene",
|
|
27
|
+
spec: {
|
|
28
|
+
name: "pl7.app/vdj/geneHit",
|
|
29
|
+
type: "String",
|
|
30
|
+
domain: { "pl7.app/vdj/reference": "JGene" },
|
|
31
|
+
annotations: {
|
|
32
32
|
"pl7.app/label": "Best J gene"
|
|
33
33
|
}
|
|
34
34
|
}
|
|
35
35
|
}
|
|
36
36
|
],
|
|
37
|
-
|
|
37
|
+
columns: [
|
|
38
38
|
{
|
|
39
|
-
|
|
40
|
-
|
|
41
|
-
|
|
42
|
-
|
|
43
|
-
|
|
39
|
+
column: "count",
|
|
40
|
+
spec: {
|
|
41
|
+
name: "pl7.app/vdj/vjGeneUsage",
|
|
42
|
+
valueType: "Int",
|
|
43
|
+
annotations: { "pl7.app/label": "V/J usage" }
|
|
44
44
|
}
|
|
45
45
|
}
|
|
46
46
|
],
|
|
47
|
-
|
|
48
|
-
|
|
47
|
+
storageFormat: "Binary",
|
|
48
|
+
partitionKeyLength: 0
|
|
49
49
|
}
|
|
50
50
|
}
|
|
51
51
|
|
|
@@ -1,42 +1,31 @@
|
|
|
1
1
|
ll := import("@platforma-sdk/workflow-tengo:ll")
|
|
2
2
|
|
|
3
|
-
getColumns := func(datasetSpec
|
|
4
|
-
axes := [
|
|
5
|
-
{
|
|
6
|
-
"column": "clonotypeKey",
|
|
7
|
-
"spec": datasetSpec.axesSpec[1]
|
|
8
|
-
}]
|
|
9
|
-
|
|
10
|
-
if len(linkerAxisSpec) > 0 {
|
|
11
|
-
for key, val in linkerAxisSpec {
|
|
12
|
-
axes = axes + [
|
|
13
|
-
{
|
|
14
|
-
"column": key,
|
|
15
|
-
"spec": val
|
|
16
|
-
}]
|
|
17
|
-
}
|
|
18
|
-
|
|
19
|
-
}
|
|
3
|
+
getColumns := func(datasetSpec) {
|
|
20
4
|
return {
|
|
21
|
-
|
|
22
|
-
|
|
5
|
+
axes: [
|
|
6
|
+
{
|
|
7
|
+
column: "clonotypeKey",
|
|
8
|
+
spec: datasetSpec.axesSpec[1]
|
|
9
|
+
}],
|
|
10
|
+
columns: [
|
|
23
11
|
{
|
|
24
|
-
|
|
25
|
-
|
|
26
|
-
|
|
27
|
-
|
|
28
|
-
|
|
29
|
-
|
|
30
|
-
|
|
31
|
-
|
|
12
|
+
column: "top",
|
|
13
|
+
id: "link",
|
|
14
|
+
allowNA: false,
|
|
15
|
+
spec: {
|
|
16
|
+
name: "pl7.app/vdj/sampling-column",
|
|
17
|
+
valueType: "Int",
|
|
18
|
+
domain: {},
|
|
19
|
+
annotations: {
|
|
32
20
|
"pl7.app/label": "Sampling column",
|
|
33
|
-
"pl7.app/table/visibility": "optional"
|
|
21
|
+
"pl7.app/table/visibility": "optional",
|
|
22
|
+
"pl7.app/isSubset": "true"
|
|
34
23
|
}
|
|
35
24
|
}
|
|
36
25
|
}
|
|
37
26
|
],
|
|
38
|
-
|
|
39
|
-
|
|
27
|
+
storageFormat: "Binary",
|
|
28
|
+
partitionKeyLength: 0
|
|
40
29
|
}
|
|
41
30
|
}
|
|
42
31
|
|
|
@@ -1,43 +0,0 @@
|
|
|
1
|
-
ll := import("@platforma-sdk/workflow-tengo:ll")
|
|
2
|
-
|
|
3
|
-
getColumns := func(datasetSpec) {
|
|
4
|
-
return {
|
|
5
|
-
"axes": [
|
|
6
|
-
{
|
|
7
|
-
"column": "clonotypeKey",
|
|
8
|
-
"spec": datasetSpec.axesSpec[1]
|
|
9
|
-
}
|
|
10
|
-
],
|
|
11
|
-
"columns": [
|
|
12
|
-
{
|
|
13
|
-
"column": "UMAP1",
|
|
14
|
-
"id": "umap1",
|
|
15
|
-
"allowNA": false,
|
|
16
|
-
"spec": {
|
|
17
|
-
"name": "pl7.app/vdj/umap1",
|
|
18
|
-
"valueType": "Double",
|
|
19
|
-
"annotations": {
|
|
20
|
-
"pl7.app/label": "UMAP Dim1"
|
|
21
|
-
}
|
|
22
|
-
}
|
|
23
|
-
},
|
|
24
|
-
{
|
|
25
|
-
"column": "UMAP2",
|
|
26
|
-
"id": "umap2",
|
|
27
|
-
"allowNA": false,
|
|
28
|
-
"spec": {
|
|
29
|
-
"name": "pl7.app/vdj/umap2",
|
|
30
|
-
"valueType": "Double",
|
|
31
|
-
"annotations": {
|
|
32
|
-
"pl7.app/label": "UMAP Dim2"
|
|
33
|
-
}
|
|
34
|
-
}
|
|
35
|
-
}],
|
|
36
|
-
"storageFormat": "Binary",
|
|
37
|
-
"partitionKeyLength": 0
|
|
38
|
-
}
|
|
39
|
-
}
|
|
40
|
-
|
|
41
|
-
export ll.toStrict({
|
|
42
|
-
getColumns: getColumns
|
|
43
|
-
})
|
|
@@ -1,38 +0,0 @@
|
|
|
1
|
-
ll := import("@platforma-sdk/workflow-tengo:ll")
|
|
2
|
-
|
|
3
|
-
|
|
4
|
-
|
|
5
|
-
getColumns := func(datasetSpec) {
|
|
6
|
-
axes := [
|
|
7
|
-
{
|
|
8
|
-
"column": "clonotypeKey",
|
|
9
|
-
"spec": datasetSpec.axesSpec[1]
|
|
10
|
-
}]
|
|
11
|
-
|
|
12
|
-
return {
|
|
13
|
-
"axes": axes,
|
|
14
|
-
"columns": [
|
|
15
|
-
{
|
|
16
|
-
"column": "top",
|
|
17
|
-
"id": "link2", // temporal change
|
|
18
|
-
"allowNA": false,
|
|
19
|
-
"spec": {
|
|
20
|
-
"name": "pl7.app/vdj/sampling-column-umap",
|
|
21
|
-
"valueType": "Int",
|
|
22
|
-
"domain": {},
|
|
23
|
-
"annotations": {
|
|
24
|
-
"pl7.app/label": "Top clonotypes",
|
|
25
|
-
"pl7.app/table/visibility": "optional",
|
|
26
|
-
"pl7.app/isSubset": "true"
|
|
27
|
-
}
|
|
28
|
-
}
|
|
29
|
-
}
|
|
30
|
-
],
|
|
31
|
-
"storageFormat": "Binary",
|
|
32
|
-
"partitionKeyLength": 0
|
|
33
|
-
}
|
|
34
|
-
}
|
|
35
|
-
|
|
36
|
-
export ll.toStrict({
|
|
37
|
-
getColumns: getColumns
|
|
38
|
-
})
|
|
@@ -1,43 +0,0 @@
|
|
|
1
|
-
ll := import("@platforma-sdk/workflow-tengo:ll")
|
|
2
|
-
|
|
3
|
-
getColumns := func(datasetSpec) {
|
|
4
|
-
return {
|
|
5
|
-
"axes": [
|
|
6
|
-
{
|
|
7
|
-
"column": "clonotypeKey",
|
|
8
|
-
"spec": datasetSpec.axesSpec[1]
|
|
9
|
-
}
|
|
10
|
-
],
|
|
11
|
-
"columns": [
|
|
12
|
-
{
|
|
13
|
-
"column": "UMAP1",
|
|
14
|
-
"id": "umap1",
|
|
15
|
-
"allowNA": false,
|
|
16
|
-
"spec": {
|
|
17
|
-
"name": "pl7.app/vdj/umap1",
|
|
18
|
-
"valueType": "Double",
|
|
19
|
-
"annotations": {
|
|
20
|
-
"pl7.app/label": "UMAP Dim1"
|
|
21
|
-
}
|
|
22
|
-
}
|
|
23
|
-
},
|
|
24
|
-
{
|
|
25
|
-
"column": "UMAP2",
|
|
26
|
-
"id": "umap2",
|
|
27
|
-
"allowNA": false,
|
|
28
|
-
"spec": {
|
|
29
|
-
"name": "pl7.app/vdj/umap2",
|
|
30
|
-
"valueType": "Double",
|
|
31
|
-
"annotations": {
|
|
32
|
-
"pl7.app/label": "UMAP Dim2"
|
|
33
|
-
}
|
|
34
|
-
}
|
|
35
|
-
}],
|
|
36
|
-
"storageFormat": "Binary",
|
|
37
|
-
"partitionKeyLength": 0
|
|
38
|
-
}
|
|
39
|
-
}
|
|
40
|
-
|
|
41
|
-
export ll.toStrict({
|
|
42
|
-
getColumns: getColumns
|
|
43
|
-
})
|
|
@@ -1,38 +0,0 @@
|
|
|
1
|
-
ll := import("@platforma-sdk/workflow-tengo:ll")
|
|
2
|
-
|
|
3
|
-
// modified from sampled-cols-conv.lib.tengo
|
|
4
|
-
|
|
5
|
-
getColumns := func(datasetSpec) {
|
|
6
|
-
axes := [
|
|
7
|
-
{
|
|
8
|
-
"column": "clonotypeKey",
|
|
9
|
-
"spec": datasetSpec.axesSpec[1]
|
|
10
|
-
}]
|
|
11
|
-
|
|
12
|
-
return {
|
|
13
|
-
"axes": axes,
|
|
14
|
-
"columns": [
|
|
15
|
-
{
|
|
16
|
-
"column": "top",
|
|
17
|
-
"id": "link2", // temporal change
|
|
18
|
-
"allowNA": false,
|
|
19
|
-
"spec": {
|
|
20
|
-
"name": "pl7.app/vdj/sampling-column-umap",
|
|
21
|
-
"valueType": "Int",
|
|
22
|
-
"domain": {},
|
|
23
|
-
"annotations": {
|
|
24
|
-
"pl7.app/label": "Top clonotypes",
|
|
25
|
-
"pl7.app/table/visibility": "optional",
|
|
26
|
-
"pl7.app/isSubset": "true"
|
|
27
|
-
}
|
|
28
|
-
}
|
|
29
|
-
}
|
|
30
|
-
],
|
|
31
|
-
"storageFormat": "Binary",
|
|
32
|
-
"partitionKeyLength": 0
|
|
33
|
-
}
|
|
34
|
-
}
|
|
35
|
-
|
|
36
|
-
export ll.toStrict({
|
|
37
|
-
getColumns: getColumns
|
|
38
|
-
})
|