update functions related to three_d_plot

Author: YifanLu2000

spateo/plotting/static/three_d_plot/three_dims_plots.py

@@ -182,7 +182,7 @@ def three_d_plot(
     model: Union[PolyData, UnstructuredGrid, MultiBlock],
     key: Union[str, list] = None,
     filename: Optional[str] = None,
-    jupyter: Union[bool, Literal["panel", "none", "pythreejs", "static", "ipygany"]] = False,
+    jupyter: Union[bool, Literal["panel", "none", "pythreejs", "static", "ipygany", "html"]] = False,
     off_screen: bool = False,
     window_size: tuple = (512, 512),
     background: str = "white",
@@ -346,7 +346,7 @@ def three_d_multi_plot(
     model: Union[PolyData, UnstructuredGrid, MultiBlock],
     key: Union[str, list] = None,
     filename: Optional[str] = None,
-    jupyter: Union[bool, Literal["panel", "none", "pythreejs", "static", "ipygany"]] = False,
+    jupyter: Union[bool, Literal["panel", "none", "pythreejs", "static", "ipygany", "html"]] = False,
     off_screen: bool = False,
     shape: Union[str, list, tuple] = None,
     window_size: Optional[tuple] = None,
@@ -576,7 +576,7 @@ def three_d_animate(
     stable_kwargs: Optional[dict] = None,
     key: Optional[str] = None,
     filename: str = "animate.mp4",
-    jupyter: Union[bool, Literal["panel", "none", "pythreejs", "static", "ipygany"]] = False,
+    jupyter: Union[bool, Literal["panel", "none", "pythreejs", "static", "ipygany", "html"]] = False,
     off_screen: bool = False,
     window_size: tuple = (512, 512),
     background: str = "white",

spateo/plotting/static/three_d_plot/three_dims_plotter.py

@@ -73,7 +73,7 @@ def create_plotter(
 
 
 def _set_jupyter(
-    jupyter: Union[bool, Literal["trame", "panel", "none", "static"]] = False,
+    jupyter: Union[bool, Literal["trame", "panel", "none", "static", "html"]] = False,
     off_screen: bool = False,
 ):
     if jupyter is False:
@@ -82,7 +82,7 @@ def _set_jupyter(
     elif jupyter is True:
         off_screen1, off_screen2 = True, off_screen
         jupyter_backend = "static"
-    elif jupyter in ["trame", "panel", "none", "static"]:
+    elif jupyter in ["trame", "panel", "none", "static", "html"]:
         off_screen1, off_screen2 = True, off_screen
         jupyter_backend = jupyter
     else:
@@ -535,7 +535,7 @@ def output_plotter(
     filename: Optional[str] = None,
     view_up: tuple = (0.5, 0.5, 1),
     framerate: int = 15,
-    jupyter: Union[bool, Literal["trame", "panel", "none", "static"]] = False,
+    jupyter: Union[bool, Literal["trame", "panel", "none", "static", "html"]] = False,
 ):
     """
     Output plotter as image, gif file or mp4 file.

spateo/tdr/models/models_migration/line_model.py

@@ -95,10 +95,10 @@ def construct_lines(
         plot_cmap: Recommended colormap parameter values for plotting.
     """
 
-    padding = np.array([2] * edges.shape[0], int)
-    edges_w_padding = np.vstack((padding, edges.T)).T
-    model = pv.PolyData(points, edges_w_padding)
-
+    # padding = np.array([2] * edges.shape[0], int)
+    # edges_w_padding = np.vstack((padding, edges.T)).T
+    # model = pv.PolyData(points, edges_w_padding)
+    model = pv.PolyData(points, lines=pv.CellArray.from_regular_cells(np.array(edges)))
     labels = np.asarray([label] * points.shape[0]) if isinstance(label, str) else np.asarray(label)
     assert len(labels) == points.shape[0], "The number of labels is not equal to the number of points."
     plot_cmap = None

spateo/tdr/models/models_migration/morphopath_model.py

@@ -157,7 +157,7 @@ def construct_genesis(
 def construct_trajectory_X(
     cells_states: Union[np.ndarray, List[np.ndarray]],
     init_states: Optional[np.ndarray] = None,
-    n_sampling: Optional[int] = None,
+    n_sampling: Optional[Union[int, np.ndarray]] = None,
     sampling_method: str = "trn",
     key_added: str = "trajectory",
     label: Optional[Union[str, list, np.ndarray]] = None,
@@ -202,13 +202,15 @@ def construct_trajectory_X(
     else:
         raise ValueError("`label` value is wrong.")
 
-    if not (n_sampling is None):
+    if (n_sampling is not None) and (isinstance(n_sampling, int)):
         index_arr = sample(
             arr=index_arr,
             n=n_sampling,
             method=sampling_method,
             X=init_states,
         )
+    elif (n_sampling is not None) and (isinstance(n_sampling, np.ndarray)):
+        index_arr = n_sampling
     else:
         if index_arr.shape[0] > 200:
             lm.main_warning(
@@ -244,6 +246,7 @@ def construct_trajectory_X(
 
     streamlines, plot_cmap = construct_lines(
         points=np.concatenate(trajectories_points, axis=0),
+        # points=trajectories_points,
         edges=np.concatenate(trajectories_edges, axis=0),
         key_added=key_added,
         label=np.asarray(trajectories_labels),
@@ -271,7 +274,7 @@ def construct_trajectory_X(
 def construct_trajectory(
     adata: AnnData,
     fate_key: str = "fate_develop",
-    n_sampling: Optional[int] = None,
+    n_sampling: Optional[Union[int, np.ndarray]] = None,
     sampling_method: str = "trn",
     key_added: str = "trajectory",
     label: Optional[Union[str, list, np.ndarray]] = None,