scFates 1.2.2__tar.gz → 1.2.4__tar.gz

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.
Files changed (61) hide show
  1. {scfates-1.2.2/scFates.egg-info → scfates-1.2.4}/PKG-INFO +2 -2
  2. {scfates-1.2.2 → scfates-1.2.4}/pyproject.toml +1 -1
  3. {scfates-1.2.2 → scfates-1.2.4}/scFates/tools/dendrogram.py +11 -6
  4. {scfates-1.2.2 → scfates-1.2.4/scFates.egg-info}/PKG-INFO +2 -2
  5. {scfates-1.2.2 → scfates-1.2.4}/scFates.egg-info/requires.txt +1 -1
  6. {scfates-1.2.2 → scfates-1.2.4}/LICENSE +0 -0
  7. {scfates-1.2.2 → scfates-1.2.4}/MANIFEST.in +0 -0
  8. {scfates-1.2.2 → scfates-1.2.4}/README.md +0 -0
  9. {scfates-1.2.2 → scfates-1.2.4}/scFates/__init__.py +0 -0
  10. {scfates-1.2.2 → scfates-1.2.4}/scFates/datasets/__init__.py +0 -0
  11. {scfates-1.2.2 → scfates-1.2.4}/scFates/datasets/_datasets.py +0 -0
  12. {scfates-1.2.2 → scfates-1.2.4}/scFates/datasets/test.h5ad +0 -0
  13. {scfates-1.2.2 → scfates-1.2.4}/scFates/get/__init__.py +0 -0
  14. {scfates-1.2.2 → scfates-1.2.4}/scFates/get/get.py +0 -0
  15. {scfates-1.2.2 → scfates-1.2.4}/scFates/logging.py +0 -0
  16. {scfates-1.2.2 → scfates-1.2.4}/scFates/pl.py +0 -0
  17. {scfates-1.2.2 → scfates-1.2.4}/scFates/plot/__init__.py +0 -0
  18. {scfates-1.2.2 → scfates-1.2.4}/scFates/plot/binned_pseudotime_meta.py +0 -0
  19. {scfates-1.2.2 → scfates-1.2.4}/scFates/plot/covariate.py +0 -0
  20. {scfates-1.2.2 → scfates-1.2.4}/scFates/plot/dendrogram.py +0 -0
  21. {scfates-1.2.2 → scfates-1.2.4}/scFates/plot/features.py +0 -0
  22. {scfates-1.2.2 → scfates-1.2.4}/scFates/plot/linearity_deviation.py +0 -0
  23. {scfates-1.2.2 → scfates-1.2.4}/scFates/plot/matrix.py +0 -0
  24. {scfates-1.2.2 → scfates-1.2.4}/scFates/plot/milestones.py +0 -0
  25. {scfates-1.2.2 → scfates-1.2.4}/scFates/plot/module_inclusion.py +0 -0
  26. {scfates-1.2.2 → scfates-1.2.4}/scFates/plot/modules.py +0 -0
  27. {scfates-1.2.2 → scfates-1.2.4}/scFates/plot/palette_tools.py +0 -0
  28. {scfates-1.2.2 → scfates-1.2.4}/scFates/plot/palettes.py +0 -0
  29. {scfates-1.2.2 → scfates-1.2.4}/scFates/plot/slide_cors.py +0 -0
  30. {scfates-1.2.2 → scfates-1.2.4}/scFates/plot/synchro_path.py +0 -0
  31. {scfates-1.2.2 → scfates-1.2.4}/scFates/plot/test_association.py +0 -0
  32. {scfates-1.2.2 → scfates-1.2.4}/scFates/plot/test_fork.py +0 -0
  33. {scfates-1.2.2 → scfates-1.2.4}/scFates/plot/trajectory.py +0 -0
  34. {scfates-1.2.2 → scfates-1.2.4}/scFates/plot/utils.py +0 -0
  35. {scfates-1.2.2 → scfates-1.2.4}/scFates/pp.py +0 -0
  36. {scfates-1.2.2 → scfates-1.2.4}/scFates/preprocessing/__init__.py +0 -0
  37. {scfates-1.2.2 → scfates-1.2.4}/scFates/preprocessing/diffusion.py +0 -0
  38. {scfates-1.2.2 → scfates-1.2.4}/scFates/preprocessing/pagoda2.py +0 -0
  39. {scfates-1.2.2 → scfates-1.2.4}/scFates/settings.py +0 -0
  40. {scfates-1.2.2 → scfates-1.2.4}/scFates/tests/test_w_plots.py +0 -0
  41. {scfates-1.2.2 → scfates-1.2.4}/scFates/tl.py +0 -0
  42. {scfates-1.2.2 → scfates-1.2.4}/scFates/tools/__init__.py +0 -0
  43. {scfates-1.2.2 → scfates-1.2.4}/scFates/tools/_test_monocle3.R +0 -0
  44. {scfates-1.2.2 → scfates-1.2.4}/scFates/tools/bifurcation_tools.py +0 -0
  45. {scfates-1.2.2 → scfates-1.2.4}/scFates/tools/cluster.py +0 -0
  46. {scfates-1.2.2 → scfates-1.2.4}/scFates/tools/conversion.py +0 -0
  47. {scfates-1.2.2 → scfates-1.2.4}/scFates/tools/correlation_tools.py +0 -0
  48. {scfates-1.2.2 → scfates-1.2.4}/scFates/tools/covariate.py +0 -0
  49. {scfates-1.2.2 → scfates-1.2.4}/scFates/tools/fit.py +0 -0
  50. {scfates-1.2.2 → scfates-1.2.4}/scFates/tools/graph_fitting.py +0 -0
  51. {scfates-1.2.2 → scfates-1.2.4}/scFates/tools/graph_operations.py +0 -0
  52. {scfates-1.2.2 → scfates-1.2.4}/scFates/tools/linearity_deviation.py +0 -0
  53. {scfates-1.2.2 → scfates-1.2.4}/scFates/tools/pseudotime.py +0 -0
  54. {scfates-1.2.2 → scfates-1.2.4}/scFates/tools/root.py +0 -0
  55. {scfates-1.2.2 → scfates-1.2.4}/scFates/tools/slide_cors.py +0 -0
  56. {scfates-1.2.2 → scfates-1.2.4}/scFates/tools/test_association.py +0 -0
  57. {scfates-1.2.2 → scfates-1.2.4}/scFates/tools/utils.py +0 -0
  58. {scfates-1.2.2 → scfates-1.2.4}/scFates.egg-info/SOURCES.txt +0 -0
  59. {scfates-1.2.2 → scfates-1.2.4}/scFates.egg-info/dependency_links.txt +0 -0
  60. {scfates-1.2.2 → scfates-1.2.4}/scFates.egg-info/top_level.txt +0 -0
  61. {scfates-1.2.2 → scfates-1.2.4}/setup.cfg +0 -0
{scfates-1.2.2/scFates.egg-info → scfates-1.2.4}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: scFates
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- Version: 1.2.2
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+ Version: 1.2.4
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  Summary: scanpy compatible python suite for fast tree inference and advanced pseudotime downstream analysis
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  Author: Louis Faure
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  Project-URL: Repository, https://github.com/LouisFaure/scFates
@@ -26,7 +26,7 @@ Requires-Dist: typing_extensions
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  Requires-Dist: scikit-learn
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  Requires-Dist: scikit-misc
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  Requires-Dist: simpleppt>=1.1.3
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- Requires-Dist: elpigraph-python==0.3.2
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+ Requires-Dist: elpigraph-python>=0.3.4
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  Requires-Dist: networkx>3.0
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  Requires-Dist: igraph>=0.9.6
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  Requires-Dist: adjustText>=0.7.3
{scfates-1.2.2 → scfates-1.2.4}/pyproject.toml RENAMED
@@ -31,7 +31,7 @@ dependencies = [
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  "scikit-learn",
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  "scikit-misc",
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  "simpleppt>=1.1.3",
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- "elpigraph-python==0.3.2",
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+ "elpigraph-python>=0.3.4",
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  "networkx>3.0",
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  "igraph>=0.9.6",
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  "adjustText>=0.7.3",
{scfates-1.2.2 → scfates-1.2.4}/scFates/tools/dendrogram.py RENAMED
@@ -82,12 +82,17 @@ def dendrogram(adata: anndata.AnnData, crowdedness: float = 1):
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  df["seg_pos"] = df.seg.astype(str)
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  df["t"] = -df.t
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- for i, x in enumerate(newseg):
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- df.loc[df.seg == newseg.index[i], "seg_pos"] = x
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-
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- df.seg_pos = df.seg_pos.astype("category").cat.rename_categories(
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- range(len(df.seg_pos.unique()))
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- )
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+ # Sort newseg BEFORE assigning positions to cells
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+ # This ensures the categorical mapping matches the dendrogram segment order
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+ newseg_sorted = newseg.iloc[newseg.argsort()]
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+
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+ # Create mapping from segment ID to sorted position index
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+ seg_to_pos = {seg_id: i for i, seg_id in enumerate(newseg_sorted.index)}
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+
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+ # Assign positions to cells based on sorted order
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+ for seg_id, pos_idx in seg_to_pos.items():
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+ df.loc[df.seg == seg_id, "seg_pos"] = pos_idx
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+
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  df.seg_pos = df.seg_pos.astype(int).astype("category")
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  dend = stripplot(
{scfates-1.2.2 → scfates-1.2.4/scFates.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: scFates
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- Version: 1.2.2
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+ Version: 1.2.4
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  Summary: scanpy compatible python suite for fast tree inference and advanced pseudotime downstream analysis
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  Author: Louis Faure
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  Project-URL: Repository, https://github.com/LouisFaure/scFates
@@ -26,7 +26,7 @@ Requires-Dist: typing_extensions
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  Requires-Dist: scikit-learn
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  Requires-Dist: scikit-misc
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  Requires-Dist: simpleppt>=1.1.3
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- Requires-Dist: elpigraph-python==0.3.2
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+ Requires-Dist: elpigraph-python>=0.3.4
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  Requires-Dist: networkx>3.0
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  Requires-Dist: igraph>=0.9.6
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  Requires-Dist: adjustText>=0.7.3
{scfates-1.2.2 → scfates-1.2.4}/scFates.egg-info/requires.txt RENAMED
@@ -17,7 +17,7 @@ typing_extensions
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  scikit-learn
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  scikit-misc
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  simpleppt>=1.1.3
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- elpigraph-python==0.3.2
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+ elpigraph-python>=0.3.4
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  networkx>3.0
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  igraph>=0.9.6
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  adjustText>=0.7.3
{scfates-1.2.2 → scfates-1.2.4}/LICENSE RENAMED
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{scfates-1.2.2 → scfates-1.2.4}/MANIFEST.in RENAMED
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{scfates-1.2.2 → scfates-1.2.4}/README.md RENAMED
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{scfates-1.2.2 → scfates-1.2.4}/scFates/__init__.py RENAMED
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{scfates-1.2.2 → scfates-1.2.4}/scFates/get/__init__.py RENAMED
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{scfates-1.2.2 → scfates-1.2.4}/scFates/get/get.py RENAMED
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{scfates-1.2.2 → scfates-1.2.4}/scFates/logging.py RENAMED
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{scfates-1.2.2 → scfates-1.2.4}/scFates/pl.py RENAMED
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{scfates-1.2.2 → scfates-1.2.4}/scFates/plot/matrix.py RENAMED
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{scfates-1.2.2 → scfates-1.2.4}/scFates/plot/modules.py RENAMED
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{scfates-1.2.2 → scfates-1.2.4}/scFates/plot/utils.py RENAMED
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{scfates-1.2.2 → scfates-1.2.4}/scFates/pp.py RENAMED
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{scfates-1.2.2 → scfates-1.2.4}/scFates/settings.py RENAMED
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{scfates-1.2.2 → scfates-1.2.4}/scFates/tl.py RENAMED
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{scfates-1.2.2 → scfates-1.2.4}/scFates/tools/fit.py RENAMED
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{scfates-1.2.2 → scfates-1.2.4}/scFates/tools/root.py RENAMED
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{scfates-1.2.2 → scfates-1.2.4}/scFates/tools/utils.py RENAMED
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{scfates-1.2.2 → scfates-1.2.4}/setup.cfg RENAMED
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