More 3D plots

dynamo/movie/__init__.py

@@ -1,4 +1,4 @@
 """Mapping Vector Field of Single Cells
 """
 
-from .fate import StreamFuncAnim, animate_fates
+from .fate import PyvistaAnim, StreamFuncAnim, StreamFuncAnim3D, animate_fates

dynamo/movie/utils.py

@@ -1,10 +1,30 @@
-from typing import Union
+from typing import Optional, Union
 
+import numpy as np
 
-def remove_particles(pts: list, xlim: Union[tuple, list], ylim: Union[tuple, list]):
+
+def remove_particles(
+    pts: np.ndarray,
+    xlim: Union[tuple, list],
+    ylim: Union[tuple, list],
+    zlim: Optional[Union[tuple, list]] = None,
+) -> np.ndarray:
+    """Remove particles that fall outside specified coordinate ranges.
+
+    Args:
+        pts: an array of points.
+        xlim: X-coordinate limits specified as a tuple or list of two values: (min_x, max_x).
+        ylim: Y-coordinate limits specified as a tuple or list of two values: (min_y, max_y).
+        zlim: Z-coordinate limits specified as a tuple or list of two values: (min_z, max_z). If not provided (default),
+            only 2D filtering based on xlim and ylim is performed.
+
+    Returns:
+        An array of points that fall within the specified coordinate ranges.
+    """
     if len(pts) == 0:
         return []
     outside_xlim = (pts[:, 0] < xlim[0]) | (pts[:, 0] > xlim[1])
     outside_ylim = (pts[:, 1] < ylim[0]) | (pts[:, 1] > ylim[1])
-    keep = ~(outside_xlim | outside_ylim)
+    outside_zlim = np.full(outside_xlim.shape, False) if zlim is None else (pts[:, 2] < ylim[0]) | (pts[:, 2] > ylim[1])
+    keep = ~(outside_xlim | outside_ylim | outside_zlim)
     return pts[keep]

dynamo/plot/__init__.py

@@ -31,7 +31,7 @@
     variance_explained,
 )
 from .pseudotime import plot_dim_reduced_direct_graph
-from .scatters import scatters
+from .scatters import scatters, scatters_interactive
 from .scPotential import show_landscape
 from .sctransform import sctransform_plot_fit, plot_residual_var
 from .scVectorField import (  # , plot_LIC_gray
@@ -61,6 +61,7 @@
     plot_separatrix,
     plot_traj,
     topography,
+    topography_3D,
 )
 
 # from .theme import points
@@ -81,6 +82,7 @@
     "quiver_autoscaler",
     "save_fig",
     "scatters",
+    "scatters_interactive",
     "basic_stats",
     "show_fraction",
     "feature_genes",
@@ -116,6 +118,7 @@
     "plot_separatrix",
     "plot_traj",
     "topography",
+    "topography_3D",
     "speed",
     "acceleration",
     "curl",