Monte Carlo pseudotime trajectories

.gitignore

@@ -110,3 +110,4 @@ ENV/
 
 # IDE settings
 .vscode/
+.idea/

docs/genetools.rst

@@ -36,6 +36,14 @@ genetools.stats module
     :undoc-members:
     :show-inheritance:
 
+genetools.trajectory module
+---------------------------
+
+.. automodule:: genetools.trajectory
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 
 Module contents
 ---------------

genetools/__init__.py

@@ -5,6 +5,6 @@
 __version__ = "0.4.0"
 
 # We want genetools.[submodule].[function] to be accessible simply by importing genetools, without having to import genetools.[submodule]
-from . import helpers, plots, scanpy_helpers, stats
+from . import helpers, plots, scanpy_helpers, stats, trajectory
 
-__all__ = ["helpers", "plots", "scanpy_helpers", "stats"]
+__all__ = ["helpers", "plots", "scanpy_helpers", "stats", "trajectory"]

genetools/helpers.py

@@ -60,6 +60,28 @@ def merge_into_left(left, right, **kwargs):
     return df
 
 
+def sample_cells_from_clusters(obs_df, n_cells, cluster_key, cluster_names):
+    """[summary]
+
+    :param obs_df: [description]
+    :type obs_df: [type]
+    :param n_cells: [description]
+    :type n_cells: [type]
+    :param cluster_key: [description]
+    :type cluster_key: [type]
+    :param cluster_names: [description]
+    :type cluster_names: [type]
+    :return: [description]
+    :rtype: [type]
+    """
+    return (
+        obs_df[obs_df[cluster_key].isin(cluster_names)]
+        .index.to_series()
+        .sample(n_cells)
+        .values
+    )
+
+
 def horizontal_concat(df_left, df_right):
     """Concatenate df_right horizontally to df_left, with no checks for whether the indexes match, but confirming final shape.