SURE-tools 2.0.6__tar.gz → 2.0.8__tar.gz

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Files changed (26) hide show
  1. {sure_tools-2.0.6 → sure_tools-2.0.8}/PKG-INFO +1 -1
  2. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE/SURE.py +11 -1
  3. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE/flow/plot_quiver.py +1 -1
  4. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE_tools.egg-info/PKG-INFO +1 -1
  5. {sure_tools-2.0.6 → sure_tools-2.0.8}/setup.py +1 -1
  6. {sure_tools-2.0.6 → sure_tools-2.0.8}/LICENSE +0 -0
  7. {sure_tools-2.0.6 → sure_tools-2.0.8}/README.md +0 -0
  8. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE/__init__.py +0 -0
  9. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE/assembly/__init__.py +0 -0
  10. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE/assembly/assembly.py +0 -0
  11. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE/assembly/atlas.py +0 -0
  12. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE/atac/__init__.py +0 -0
  13. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE/atac/utils.py +0 -0
  14. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE/codebook/__init__.py +0 -0
  15. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE/codebook/codebook.py +0 -0
  16. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE/flow/__init__.py +0 -0
  17. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE/utils/__init__.py +0 -0
  18. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE/utils/custom_mlp.py +0 -0
  19. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE/utils/queue.py +0 -0
  20. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE/utils/utils.py +0 -0
  21. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE_tools.egg-info/SOURCES.txt +0 -0
  22. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE_tools.egg-info/dependency_links.txt +0 -0
  23. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE_tools.egg-info/entry_points.txt +0 -0
  24. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE_tools.egg-info/requires.txt +0 -0
  25. {sure_tools-2.0.6 → sure_tools-2.0.8}/SURE_tools.egg-info/top_level.txt +0 -0
  26. {sure_tools-2.0.6 → sure_tools-2.0.8}/setup.cfg +0 -0
{sure_tools-2.0.6 → sure_tools-2.0.8}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: SURE-tools
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- Version: 2.0.6
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+ Version: 2.0.8
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  Summary: Succinct Representation of Single Cells
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  Home-page: https://github.com/ZengFLab/SURE
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  Author: Feng Zeng
{sure_tools-2.0.6 → sure_tools-2.0.8}/SURE/SURE.py RENAMED
@@ -814,7 +814,7 @@ class SURE(nn.Module):
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  return A
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  def _cell_move(self, xs, factor_idx, perturb):
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- zns = self.encoder_zn(xs)
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+ zns,_ = self.encoder_zn(xs)
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  if type(factor_idx) == str:
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  factor_idx = np.where(self.cell_factor_names==factor_idx)
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@@ -850,6 +850,16 @@ class SURE(nn.Module):
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  Z = np.concatenate(Z)
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  return Z
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+ def get_metacell_move(self, factor_idx, perturb):
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+ zs = self._get_codebook()
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+ ps = convert_to_tensor(perturb, device=self.get_device())
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+
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+ if type(factor_idx) == str:
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+ factor_idx = np.where(self.cell_factor_names==factor_idx)
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+
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+ ms = self.cell_factor_effect[factor_idx]([zs,ps])
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+ return tensor_to_numpy(ms)
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+
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  def preprocess(self, xs, threshold=0):
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  if self.loss_func == 'bernoulli':
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  ad = sc.AnnData(xs)
{sure_tools-2.0.6 → sure_tools-2.0.8}/SURE/flow/plot_quiver.py RENAMED
@@ -32,7 +32,7 @@ def plot_quiver(z_points, delta_z, method='umap', figsize=(6,4), dpi=200):
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  sc.pp.neighbors(ad)
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  sc.tl.umap(ad)
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  z_2d = ad[:z_points.shape[0]].obsm['X_umap']
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- delta_z_2d = ad[z_points.shape[0]:] - z_2d
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+ delta_z_2d = ad[z_points.shape[0]:].obsm['X_umap'] - z_2d
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  dim_names = ['UMAP1', 'UMAP2']
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  # 绘制quiver图
{sure_tools-2.0.6 → sure_tools-2.0.8}/SURE_tools.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: SURE-tools
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- Version: 2.0.6
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+ Version: 2.0.8
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  Summary: Succinct Representation of Single Cells
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  Home-page: https://github.com/ZengFLab/SURE
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  Author: Feng Zeng
{sure_tools-2.0.6 → sure_tools-2.0.8}/setup.py RENAMED
@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
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  setup(
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  name='SURE-tools',
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- version='2.0.6',
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+ version='2.0.8',
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  description='Succinct Representation of Single Cells',
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  long_description=long_description,
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  long_description_content_type="text/markdown",
{sure_tools-2.0.6 → sure_tools-2.0.8}/LICENSE RENAMED
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{sure_tools-2.0.6 → sure_tools-2.0.8}/README.md RENAMED
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{sure_tools-2.0.6 → sure_tools-2.0.8}/SURE/__init__.py RENAMED
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{sure_tools-2.0.6 → sure_tools-2.0.8}/setup.cfg RENAMED
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