gsMap3D 0.1.0a1__py3-none-any.whl

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Files changed (74) hide show
  1. gsMap/__init__.py +13 -0
  2. gsMap/__main__.py +4 -0
  3. gsMap/cauchy_combination_test.py +342 -0
  4. gsMap/cli.py +355 -0
  5. gsMap/config/__init__.py +72 -0
  6. gsMap/config/base.py +296 -0
  7. gsMap/config/cauchy_config.py +79 -0
  8. gsMap/config/dataclasses.py +235 -0
  9. gsMap/config/decorators.py +302 -0
  10. gsMap/config/find_latent_config.py +276 -0
  11. gsMap/config/format_sumstats_config.py +54 -0
  12. gsMap/config/latent2gene_config.py +461 -0
  13. gsMap/config/ldscore_config.py +261 -0
  14. gsMap/config/quick_mode_config.py +242 -0
  15. gsMap/config/report_config.py +81 -0
  16. gsMap/config/spatial_ldsc_config.py +334 -0
  17. gsMap/config/utils.py +286 -0
  18. gsMap/find_latent/__init__.py +3 -0
  19. gsMap/find_latent/find_latent_representation.py +312 -0
  20. gsMap/find_latent/gnn/distribution.py +498 -0
  21. gsMap/find_latent/gnn/encoder_decoder.py +186 -0
  22. gsMap/find_latent/gnn/gcn.py +85 -0
  23. gsMap/find_latent/gnn/gene_former.py +164 -0
  24. gsMap/find_latent/gnn/loss.py +18 -0
  25. gsMap/find_latent/gnn/st_model.py +125 -0
  26. gsMap/find_latent/gnn/train_step.py +177 -0
  27. gsMap/find_latent/st_process.py +781 -0
  28. gsMap/format_sumstats.py +446 -0
  29. gsMap/generate_ldscore.py +1018 -0
  30. gsMap/latent2gene/__init__.py +18 -0
  31. gsMap/latent2gene/connectivity.py +781 -0
  32. gsMap/latent2gene/entry_point.py +141 -0
  33. gsMap/latent2gene/marker_scores.py +1265 -0
  34. gsMap/latent2gene/memmap_io.py +766 -0
  35. gsMap/latent2gene/rank_calculator.py +590 -0
  36. gsMap/latent2gene/row_ordering.py +182 -0
  37. gsMap/latent2gene/row_ordering_jax.py +159 -0
  38. gsMap/ldscore/__init__.py +1 -0
  39. gsMap/ldscore/batch_construction.py +163 -0
  40. gsMap/ldscore/compute.py +126 -0
  41. gsMap/ldscore/constants.py +70 -0
  42. gsMap/ldscore/io.py +262 -0
  43. gsMap/ldscore/mapping.py +262 -0
  44. gsMap/ldscore/pipeline.py +615 -0
  45. gsMap/pipeline/quick_mode.py +134 -0
  46. gsMap/report/__init__.py +2 -0
  47. gsMap/report/diagnosis.py +375 -0
  48. gsMap/report/report.py +100 -0
  49. gsMap/report/report_data.py +1832 -0
  50. gsMap/report/static/js_lib/alpine.min.js +5 -0
  51. gsMap/report/static/js_lib/tailwindcss.js +83 -0
  52. gsMap/report/static/template.html +2242 -0
  53. gsMap/report/three_d_combine.py +312 -0
  54. gsMap/report/three_d_plot/three_d_plot_decorate.py +246 -0
  55. gsMap/report/three_d_plot/three_d_plot_prepare.py +202 -0
  56. gsMap/report/three_d_plot/three_d_plots.py +425 -0
  57. gsMap/report/visualize.py +1409 -0
  58. gsMap/setup.py +5 -0
  59. gsMap/spatial_ldsc/__init__.py +0 -0
  60. gsMap/spatial_ldsc/io.py +656 -0
  61. gsMap/spatial_ldsc/ldscore_quick_mode.py +912 -0
  62. gsMap/spatial_ldsc/spatial_ldsc_jax.py +382 -0
  63. gsMap/spatial_ldsc/spatial_ldsc_multiple_sumstats.py +439 -0
  64. gsMap/utils/__init__.py +0 -0
  65. gsMap/utils/generate_r2_matrix.py +610 -0
  66. gsMap/utils/jackknife.py +518 -0
  67. gsMap/utils/manhattan_plot.py +643 -0
  68. gsMap/utils/regression_read.py +177 -0
  69. gsMap/utils/torch_utils.py +23 -0
  70. gsmap3d-0.1.0a1.dist-info/METADATA +168 -0
  71. gsmap3d-0.1.0a1.dist-info/RECORD +74 -0
  72. gsmap3d-0.1.0a1.dist-info/WHEEL +4 -0
  73. gsmap3d-0.1.0a1.dist-info/entry_points.txt +2 -0
  74. gsmap3d-0.1.0a1.dist-info/licenses/LICENSE +21 -0
gsMap/latent2gene/__init__.py ADDED
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+ """
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+ latent2gene subpackage for gsMap
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+
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+ This package contains all components for converting latent representations to gene marker scores:
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+ - Rank calculation from latent representations
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+ - Connectivity matrix building (spatial → anchor → homogeneous)
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+ - Marker score calculation
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+ - Memory-mapped storage utilities
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+ """
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+
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+ from .connectivity import ConnectivityMatrixBuilder
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+ from .entry_point import run_latent_to_gene
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+ from .marker_scores import MarkerScoreCalculator
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+ from .rank_calculator import RankCalculator
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+
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+ __all__ = [
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+ 'run_latent_to_gene'
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+ ]