updates

01_data.ipynb

@@ -35,6 +35,10 @@
    "outputs": [],
    "source": [
     "# | export\n",
+    "\n",
+    "## helper functions\n",
+    "import roux.lib.df as rd #noqa\n",
+    "\n",
     "def get_net_data(\n",
     "    adata,\n",
     "    n: int = 5,  # number of nodes per subset/group\n",

02_graph.ipynb

@@ -45,9 +45,10 @@
     "from IPython.display import display\n",
     "import pandas as pd\n",
     "\n",
+    "## helper functions\n",
+    "import roux.lib.df as rd #noqa\n",
     "from roux.lib.str import linebreaker\n",
     "\n",
-    "\n",
     "def center_subset_label(\n",
     "    ds1: pd.Series,\n",
     ") -> pd.Series:\n",

03_hypergraph.ipynb

@@ -39,6 +39,8 @@
     "import pandas as pd\n",
     "from roux.lib.io import read_dict\n",
     "\n",
+    "import roux.lib.df as rd #noqa\n",
+    "\n",
     "def get_degreeby_subset(\n",
     "    nodes: pd.DataFrame,\n",
     "    edges: pd.DataFrame,\n",

index.ipynb

@@ -16,10 +16,10 @@
     "warnings.filterwarnings(\"ignore\", category=UserWarning)\n",
     "\n",
     "from pathlib import Path\n",
-    "\n",
     "import pandas as pd\n",
-    "import roux.lib.df as rd\n",
-    "\n",
+    "## helper functions\n",
+    "import roux.lib.df as rd #noqa\n",
+    "## functions from parag\n",
     "from parag.utils import export_plot\n",
     "\n",
     "## parameters\n",

parag/core.py

@@ -4,6 +4,9 @@
 __all__ = ['get_net_data']
 
 # %% ../01_data.ipynb 3
+## helper functions
+import roux.lib.df as rd #noqa
+
 def get_net_data(
     adata,
     n: int = 5,  # number of nodes per subset/group
@@ -19,6 +22,7 @@ def get_net_data(
     """
     import logging
     import pandas as pd
+    import roux.lib.df as rd
 
     ## nodes
     logging.info("processing nodes:")
@@ -29,7 +33,7 @@ def get_net_data(
         ],
         axis=1,
     )
-    if n is not None:
+    if not n is None:
         df1 = (
             df01.log()
             .groupby("bulk_labels", as_index=False, observed=False)

parag/graph.py

@@ -8,13 +8,16 @@
 
 logging.basicConfig(level=logging.INFO)
 import pandas as pd
-from roux.lib.io import read_dict, to_dict
+from roux.lib.io import read_dict, to_dict, read_ps, read_table, to_table
 import roux.lib.df as rd  # noqa
 
+from IPython.display import display
+import pandas as pd
 
+## helper functions
+import roux.lib.df as rd #noqa
 from roux.lib.str import linebreaker
 
-
 def center_subset_label(
     ds1: pd.Series,
 ) -> pd.Series:
@@ -102,7 +105,7 @@ def get_preprocessed(
             }
         )
     )
-    if testn is not None:
+    if not testn is None:
         df1 = df1.head(testn)
         logging.warning(f"testing {testn} nodes")
     if verbose:
@@ -327,7 +330,7 @@ def to_net(
         # _col_node_name=_col_node_id
     if col_subset_name is None:
         col_subset_name = col_subset_id
-    if nodes_path is not None and edges_path is not None:
+    if not nodes_path is None and not edges_path is None:
         df1 = pd.DataFrame(read_dict(nodes_path))
         df2 = pd.DataFrame(read_dict(edges_path))
     else:

parag/hypergraph.py

@@ -8,6 +8,8 @@
 import pandas as pd
 from roux.lib.io import read_dict
 
+import roux.lib.df as rd #noqa
+
 def get_degreeby_subset(
     nodes: pd.DataFrame,
     edges: pd.DataFrame,
@@ -102,7 +104,7 @@ def plot_degreeby_subset(
         col_target=col_target,
         col_subset_id=col_subset_id,
     )
-    if order is not None:
+    if not order is None:
         degreebysubset = degreebysubset.set_index("source").loc[order, :].reset_index()
     # degreebysubset.head(1)
 
@@ -119,6 +121,7 @@ def plot_degreeby_subset(
     #     import seaborn as sns # for the matching color palette
     #     cmap_subsets=sns.color_palette("colorblind")
 
+    from roux.viz.colors import get_ncolors
 
     if hue_order is None:
         subsets = degreebysubset.set_index("source").columns.tolist()

parag/utils.py

@@ -64,7 +64,7 @@ def display_plot(
         method (str, optional): method. Defaults to 'vega'.
     """
 
-    if defaults is not None:
+    if not defaults is None:
         spec = _set_defaults(
             spec,
             defaults,