Merge pull request #177 from BiomedicalMachineLearning/dev_psts

Dev psts

Author: duypham2108

HISTORY.rst

@@ -2,6 +2,8 @@
 History
 =======
 
+0.4.8 (2022-06-15)
+------------------
 0.4.7 (2022-03-28)
 ------------------
 0.4.6 (2022-03-09)

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.4.7
+current_version = 0.4.8
 commit = True
 tag = True
 

setup.py

@@ -49,6 +49,6 @@
     test_suite="tests",
     tests_require=test_requirements,
     url="https://github.com/BiomedicalMachineLearning/stLearn",
-    version="0.4.7",
+    version="0.4.8",
     zip_safe=False,
 )

stlearn/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = """Genomics and Machine Learning lab"""
 __email__ = "duy.pham@uq.edu.au"
-__version__ = "0.4.7"
+__version__ = "0.4.8"
 
 
 from . import add

stlearn/plotting/classes.py

@@ -640,6 +640,12 @@ def __init__(
         text_box_size: Optional[float] = 5,
         color_bar_size: Optional[float] = 10,
         bbox_to_anchor: Optional[Tuple[float, float]] = (1, 1),
+        # trajectory
+        trajectory_node_size: Optional[int] = 10,
+        trajectory_alpha: Optional[float] = 1.0,
+        trajectory_width: Optional[float] = 2.5,
+        trajectory_edge_color: Optional[str] = "#f4efd3",
+        trajectory_arrowsize: Optional[int] = 17,
     ):
         super().__init__(
             adata=adata,
@@ -683,6 +689,13 @@ def __init__(
         if show_subcluster:
             self._add_sub_clusters()
         if show_trajectories:
+
+            self.trajectory_node_size = trajectory_node_size
+            self.trajectory_alpha = trajectory_alpha
+            self.trajectory_width = trajectory_width
+            self.trajectory_edge_color = trajectory_edge_color
+            self.trajectory_arrowsize = trajectory_arrowsize
+
             self._add_trajectories()
 
         if crop:
@@ -913,23 +926,23 @@ def _add_trajectories(self):
             nx.draw_networkx_edges(
                 G,
                 pos=centroid_dict,
-                node_size=10,
-                alpha=1.0,
-                width=2.5,
-                edge_color="#f4efd3",
-                arrowsize=17,
+                node_size=self.trajectory_node_size,
+                alpha=self.trajectory_alpha,
+                width=self.trajectory_width,
+                edge_color=self.trajectory_edge_color,
+                arrowsize=self.trajectory_arrowsize,
                 arrowstyle="<|-",
                 connectionstyle="arc3,rad=0.2",
             )
         else:
             nx.draw_networkx_edges(
                 G,
                 pos=centroid_dict,
-                node_size=10,
-                alpha=1.0,
-                width=2.5,
-                edge_color="#f4efd3",
-                arrowsize=17,
+                node_size=self.trajectory_node_size,
+                alpha=self.trajectory_alpha,
+                width=self.trajectory_width,
+                edge_color=self.trajectory_edge_color,
+                arrowsize=self.trajectory_arrowsize,
                 arrowstyle="-|>",
                 connectionstyle="arc3,rad=0.2",
             )

stlearn/plotting/cluster_plot.py

@@ -53,6 +53,12 @@ def cluster_plot(
     text_box_size: Optional[float] = 5,
     color_bar_size: Optional[float] = 10,
     bbox_to_anchor: Optional[Tuple[float, float]] = (1, 1),
+    # trajectory
+    trajectory_node_size: Optional[int] = 10,
+    trajectory_alpha: Optional[float] = 1.0,
+    trajectory_width: Optional[float] = 2.5,
+    trajectory_edge_color: Optional[str] = "#f4efd3",
+    trajectory_arrowsize: Optional[int] = 17,
 ) -> Optional[AnnData]:
 
     """\
@@ -106,6 +112,11 @@ def cluster_plot(
         text_box_size=text_box_size,
         color_bar_size=color_bar_size,
         bbox_to_anchor=bbox_to_anchor,
+        trajectory_node_size=trajectory_node_size,
+        trajectory_alpha=trajectory_alpha,
+        trajectory_width=trajectory_width,
+        trajectory_edge_color=trajectory_edge_color,
+        trajectory_arrowsize=trajectory_arrowsize,
     )