genome-spy-python 0.1.0__py3-none-any.whl

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Files changed (64) hide show
  1. genome_spy/__init__.py +199 -0
  2. genome_spy/_chart_authoring.py +231 -0
  3. genome_spy/_conditions.py +72 -0
  4. genome_spy/_embed.py +87 -0
  5. genome_spy/_expressions.py +271 -0
  6. genome_spy/_parameters.py +267 -0
  7. genome_spy/_render.py +207 -0
  8. genome_spy/_utils.py +75 -0
  9. genome_spy/_widget.py +262 -0
  10. genome_spy/api.py +198 -0
  11. genome_spy/arrow.py +155 -0
  12. genome_spy/channels.py +193 -0
  13. genome_spy/chart.py +1240 -0
  14. genome_spy/data.py +56 -0
  15. genome_spy/data_transformers.py +267 -0
  16. genome_spy/datasets/__init__.py +189 -0
  17. genome_spy/datasets/_airway.py +219 -0
  18. genome_spy/datasets/_annotations.py +37 -0
  19. genome_spy/datasets/_gistic.py +43 -0
  20. genome_spy/datasets/_grammar.py +66 -0
  21. genome_spy/datasets/_hapmap.py +180 -0
  22. genome_spy/datasets/_mutation.py +289 -0
  23. genome_spy/datasets/_oncoprint.py +523 -0
  24. genome_spy/datasets/data/airway_metadata.csv +9 -0
  25. genome_spy/datasets/data/airway_scaledcounts.csv +38695 -0
  26. genome_spy/datasets/data/brca.maf.gz +0 -0
  27. genome_spy/datasets/data/hapmap_gwas.csv +14413 -0
  28. genome_spy/datasets/data/mutation_impact_reference.json +27 -0
  29. genome_spy/datasets/data/oncoprint_dataset3.json +266 -0
  30. genome_spy/datasets/data/p53_sequence_comparison.json.gz +0 -0
  31. genome_spy/datasets/data/pik3ca_mutations.json +1 -0
  32. genome_spy/datasets/data/pik3ca_tcga_brca_lollipop.json +38 -0
  33. genome_spy/datasets/data/refseq_gene_bodies.csv.gz +0 -0
  34. genome_spy/datasets/data/tal1_alphagenome_reference.json.gz +0 -0
  35. genome_spy/datasets/data/tcga.tsv +146 -0
  36. genome_spy/datasets/data/tcga_laml.maf.gz +0 -0
  37. genome_spy/datasets/data/tcga_laml_annot.tsv +201 -0
  38. genome_spy/datasets/data/tcga_laml_combined_oncoplot.json.gz +0 -0
  39. genome_spy/datasets/data/tcga_ov_gistic_lesions.tsv.gz +0 -0
  40. genome_spy/datasets/data/tcga_ov_gistic_scores.tsv.gz +0 -0
  41. genome_spy/helpers.py +185 -0
  42. genome_spy/jupyter.py +5 -0
  43. genome_spy/py.typed +0 -0
  44. genome_spy/schema/__init__.py +784 -0
  45. genome_spy/schema/_kwds.py +1394 -0
  46. genome_spy/schema/_typing.py +186 -0
  47. genome_spy/schema/capabilities.json +593 -0
  48. genome_spy/schema/channels.py +8943 -0
  49. genome_spy/schema/composition.py +1064 -0
  50. genome_spy/schema/core.py +51821 -0
  51. genome_spy/schema/ergonomics.py +2056 -0
  52. genome_spy/schema/expressions.py +476 -0
  53. genome_spy/schema/genome-spy-schema.json +33657 -0
  54. genome_spy/schema/lazy.py +326 -0
  55. genome_spy/schema/mixins.py +11684 -0
  56. genome_spy/schemapi.py +264 -0
  57. genome_spy/static/widget.js +345 -0
  58. genome_spy_python-0.1.0.dist-info/METADATA +185 -0
  59. genome_spy_python-0.1.0.dist-info/RECORD +64 -0
  60. genome_spy_python-0.1.0.dist-info/WHEEL +4 -0
  61. genome_spy_python-0.1.0.dist-info/licenses/LICENSE +21 -0
  62. genome_spy_python-0.1.0.dist-info/licenses/LICENSES/ALTAIR-BSD-3-Clause.txt +27 -0
  63. genome_spy_python-0.1.0.dist-info/licenses/LICENSES/GALLERY-DATA-MIT.txt +22 -0
  64. genome_spy_python-0.1.0.dist-info/licenses/THIRD_PARTY_NOTICES.md +42 -0
genome_spy/datasets/data/mutation_impact_reference.json ADDED
@@ -0,0 +1,27 @@
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+ {
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+ "assembly": "synthetic-v1",
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+ "chrom": "chrSynthetic",
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+ "description": "Deterministic reference window for the Marimo mutation-impact prototype.",
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+ "rows": [
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+ {"position": 100, "base": "A", "value": 0.25},
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+ {"position": 101, "base": "C", "value": 0.4},
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+ {"position": 102, "base": "G", "value": 0.55},
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+ {"position": 103, "base": "T", "value": 0.7},
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+ {"position": 104, "base": "T", "value": 0.3},
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+ {"position": 105, "base": "C", "value": 0.45},
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+ {"position": 106, "base": "G", "value": 0.6},
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+ {"position": 107, "base": "A", "value": 0.75},
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+ {"position": 108, "base": "G", "value": 0.35},
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+ {"position": 109, "base": "T", "value": 0.5},
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+ {"position": 110, "base": "A", "value": 0.65},
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+ {"position": 111, "base": "C", "value": 0.25},
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+ {"position": 112, "base": "C", "value": 0.4},
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+ {"position": 113, "base": "G", "value": 0.55},
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+ {"position": 114, "base": "T", "value": 0.7},
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+ {"position": 115, "base": "A", "value": 0.3},
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+ {"position": 116, "base": "T", "value": 0.45},
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+ {"position": 117, "base": "G", "value": 0.6},
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+ {"position": 118, "base": "C", "value": 0.75},
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+ {"position": 119, "base": "A", "value": 0.35}
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+ ]
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+ }
genome_spy/datasets/data/oncoprint_dataset3.json ADDED
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+ [{
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+ "sample": "TCGA-23-1027-01",
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+ "gene": "BRCA1",
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+ "alteration": "E23fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-25-1632-01",
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+ "gene": "BRCA1",
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+ "alteration": "L1216fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-23-1026-01",
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+ "gene": "BRCA1",
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+ "alteration": "G813fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-13-0804-01",
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+ "gene": "BRCA1",
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+ "alteration": "C47W",
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+ "type": "MISSENSE"
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+ }, {
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+ "sample": "TCGA-24-2298-01",
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+ "gene": "BRCA1",
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+ "alteration": "Q1395fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-61-2008-01",
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+ "gene": "BRCA1",
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+ "alteration": "W1815*",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-09-2045-01",
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+ "gene": "BRCA1",
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+ "alteration": "Q1779fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-04-1356-01",
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+ "gene": "BRCA1",
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+ "alteration": "V722fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-25-1630-01",
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+ "gene": "BRCA1",
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+ "alteration": "K519fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-24-1470-01",
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+ "gene": "BRCA1",
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+ "alteration": "L1676fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-13-0730-01",
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+ "gene": "BRCA1",
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+ "alteration": "R1835*",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-13-0883-01",
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+ "gene": "BRCA1",
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+ "alteration": "Q1756fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-25-2401-01",
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+ "gene": "BRCA1",
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+ "alteration": "Q1756fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-13-0903-01",
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+ "gene": "BRCA1",
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+ "alteration": "R504fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-13-0887-01",
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+ "gene": "BRCA1",
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+ "alteration": "E23fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-13-1494-01",
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+ "gene": "BRCA1",
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+ "alteration": "K45_splice",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-09-2051-01",
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+ "gene": "BRCA1",
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+ "alteration": "Q1756fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-23-2078-01",
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+ "gene": "BRCA1",
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+ "alteration": "E23fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-23-2079-01",
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+ "gene": "BRCA1",
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+ "alteration": "E23fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-10-0931-01",
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+ "gene": "BRCA1",
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+ "alteration": "E23fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-59-2348-01",
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+ "gene": "BRCA1",
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+ "alteration": "E797*",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-23-2077-01",
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+ "gene": "BRCA1",
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+ "alteration": "Q1756fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-09-1669-01",
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+ "gene": "BRCA1",
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+ "alteration": "E1345fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-23-2081-01",
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+ "gene": "BRCA1",
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+ "alteration": "Q1756fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-13-1408-01",
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+ "gene": "BRCA1",
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+ "alteration": "E23fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-13-1489-01",
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+ "gene": "BRCA1",
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+ "alteration": "N1265fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-25-1318-01",
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+ "gene": "BRCA2",
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+ "alteration": "L1491fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-13-0793-01",
138
+ "gene": "BRCA2",
139
+ "alteration": "T3085fs",
140
+ "type": "TRUNC"
141
+ }, {
142
+ "sample": "TCGA-24-1463-01",
143
+ "gene": "BRCA2",
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+ "alteration": "G602fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-13-0913-01",
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+ "gene": "BRCA2",
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+ "alteration": "E1857fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-04-1367-01",
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+ "gene": "BRCA2",
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+ "alteration": "E294*",
155
+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-24-1562-01",
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+ "gene": "BRCA2",
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+ "alteration": "K3326*",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-04-1331-01",
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+ "gene": "BRCA2",
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+ "alteration": "C711*",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-24-1103-01",
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+ "gene": "BRCA2",
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+ "alteration": "K1638E",
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+ "type": "MISSENSE"
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+ }, {
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+ "sample": "TCGA-13-0885-01",
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+ "gene": "BRCA2",
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+ "alteration": "K1406fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-13-0890-01",
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+ "gene": "BRCA2",
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+ "alteration": "V1229fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-13-1512-01",
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+ "gene": "BRCA2",
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+ "alteration": "K3326*",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-23-1030-01",
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+ "gene": "BRCA2",
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+ "alteration": "T1354M",
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+ "type": "MISSENSE"
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+ }, {
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+ "sample": "TCGA-23-1026-01",
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+ "gene": "BRCA2",
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+ "alteration": "K3326*",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-25-1634-01",
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+ "gene": "BRCA2",
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+ "alteration": "E2878_splice",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-24-1555-01",
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+ "gene": "BRCA2",
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+ "alteration": "T2607fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-13-0886-01",
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+ "gene": "BRCA2",
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+ "alteration": "S1982fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-13-0792-01",
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+ "gene": "BRCA2",
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+ "alteration": "E1143D",
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+ "type": "MISSENSE"
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+ }, {
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+ "sample": "TCGA-24-2293-01",
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+ "gene": "BRCA2",
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+ "alteration": "R2520*",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-23-1120-01",
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+ "gene": "BRCA2",
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+ "alteration": "L3277fs",
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+ "type": "TRUNC"
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+ }, {
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+ "sample": "TCGA-25-2396-01",
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+ "gene": null,
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+ }, {
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+ "sample": "TCGA-25-2397-01",
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+ "gene": null,
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+ }, {
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+ "sample": "TCGA-25-2398-01",
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genome_spy/datasets/data/pik3ca_mutations.json ADDED
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genome_spy/datasets/data/pik3ca_tcga_brca_lollipop.json ADDED
@@ -0,0 +1,38 @@
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+ {
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+ ],
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+ "domains": [
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+ {"start": 765, "end": 1051, "label": "Kinase", "description": "PI3K/PI4K catalytic"}
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+ ]
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+ }