Release v1.4.0

Main feature changes

• Shiny web application for in silico perturbation and least square action path analyses PR 582.
  

• More 3D plots PR 597

  • 3D scatters with Plotly and Pyvista dyn.pl.scatters_interactive().

• 3D vectors and topography with Plotly and Pyvista dyn.pl.cell_wise_vectors_3d(), dyn.pl.topography_3d().

• 3D animation with Pyvista dyn.mv.PyvistaAnim().

• The tools module has been reorganized PR 625

  • Deprecate files dynamo_fitting.py, dynamo_bk.py, dynamics_deprecated.py, utils_moments_deprecated.py.
  • Deprecate legacy functions in construct_velocity_tree.py,pseudotime.py, moments.py, clustering.py.
  • Merge utils_markers.py and markers.py.
  • Merge time_series.py (learns a direct principal graph by integrating the transition matrix between and DDRTree)
    and construct_velocity_tree.py(Integrate pseudotime ordering with velocity to automatically assign the direction
    of the learned trajectory.) to DDRTree_graph.py.
  • Reorganize some functions to utils in the following file: time_series.py, multiomics.py.
  • Rename: DDRTree_py.py to DDRTree.py, psl_py.py to psl.py.

download pdf version of the module graph

• Saved the velocity parameters in adata.varm instead of adata.var PR 579.

• DDRtree based pseudotime and graph learning PR 564 dyn.tl.order_cells(), dyn.tl.construct_velocity_tree().

• Integrated hnswlib fast nearest neighbors method PR 552.

• A helper function to convert the AnnData object from Dynamo to Scvelo, or vice versa PR 551.

• Deprecate infomap clustering PR 555.

Detailed change log and release notes can be found in our Readthedocs.