Remove highest_frac_genes by cleanup() before saving and remove long nxviz warning

dynamo/configuration.py

@@ -137,6 +137,33 @@ def allowed_X_layer_names():
     def init_uns_pp_namespace(adata: AnnData):
         adata.uns[DynamoAdataKeyManager.UNS_PP_KEY] = {}
 
+    def get_vf_dict(adata, basis="", vf_key="VecFld"):
+        if basis is not None:
+            if len(basis) > 0:
+                vf_key = "%s_%s" % (vf_key, basis)
+
+        if vf_key not in adata.uns.keys():
+            raise ValueError(
+                f"Vector field function {vf_key} is not included in the adata object! "
+                f"Try firstly running dyn.vf.VectorField(adata, basis='{basis}')"
+            )
+
+        vf_dict = adata.uns[vf_key]
+        return vf_dict
+
+    def vecfld_from_adata(adata, basis="", vf_key="VecFld"):
+        vf_dict = DynamoAdataKeyManager.get_vf_dict(adata, basis=basis, vf_key=vf_key)
+
+        method = vf_dict["method"]
+        if method.lower() == "sparsevfc":
+            func = lambda x: vector_field_function(x, vf_dict)
+        elif method.lower() == "dynode":
+            func = lambda x: dynode_vector_field_function(x, vf_dict)
+        else:
+            raise ValueError(f"current only support two methods, SparseVFC and dynode")
+
+        return vf_dict, func
+
 
 # TODO discuss alias naming convention
 DKM = DynamoAdataKeyManager
@@ -786,5 +813,7 @@ def set_pub_style_mpltex():
 
 # initialize DynamoSaveConfig and DynamoVisConfig mode defaults
 DynamoAdataConfig.update_data_store_mode("full")
-main_info("setting visualization default mode in dynamo. Your customized matplotlib settings might be overritten.")
+main_info(
+    "[dynamo import initialization] setting visualization default mode in dynamo. Your customized matplotlib settings might be overritten."
+)
 DynamoVisConfig.set_default_mode()

dynamo/data_io.py

@@ -300,6 +300,8 @@ def cleanup(adata, del_prediction=False, del_2nd_moments=False):
         adata.uns.pop("kinetics_heatmap")
     if "hdbscan" in adata.uns_keys():
         adata.uns.pop("hdbscan")
+    if "highest_frac_genes" in adata.uns_keys():
+        adata.uns.pop("highest_frac_genes")
 
     VF_keys = [i if i.startswith("VecFld") else None for i in adata.uns_keys()]
     for i in VF_keys:

dynamo/plot/networks.py

@@ -1,10 +1,14 @@
+# nxviz prints long warning messages regarding nxviz's own version update information
+import warnings
+
 import networkx as nx
 import numpy as np
 import nxviz as nv
-import nxviz.annotate
 import pandas as pd
 from matplotlib.axes import Axes
 
+warnings.filterwarnings("ignore", module="nxviz")
+
 from ..tools.utils import flatten, index_gene, update_dict
 from .utils import save_fig, set_colorbar
 from .utils_graph import ArcPlot

dynamo/plot/scVectorField.py

@@ -1418,7 +1418,7 @@ def streamline_plot(
     cmap: Optional[str] = None,
     color_key: Union[dict, list] = None,
     color_key_cmap: Optional[str] = None,
-    background: Optional[str] = "white",
+    background: Optional[str] = None,
     ncols: int = 4,
     pointsize: Union[None, float] = None,
     figsize: tuple = (6, 4),

dynamo/plot/scatters.py

@@ -832,7 +832,8 @@ def _plot_basis_layer(cur_b, cur_l):
                     if deaxis:
                         deaxis_all(ax)
 
-                ax.set_title(cur_title)
+                ax.set_title(cur_title, color=font_color)
+                ax.tick_params(axis="both", colors=font_color)
 
                 axes_list.append(ax)
                 color_list.append(color_out)

dynamo/vectorfield/utils.py

@@ -13,6 +13,7 @@
 from scipy.spatial.distance import cdist, pdist
 from tqdm import tqdm
 
+from ..configuration import DKM
 from ..dynamo_logger import LoggerManager, main_info
 from ..tools.utils import (
     form_triu_matrix,
@@ -22,6 +23,8 @@
 )
 from .FixedPoints import FixedPoints
 
+get_vf_dict = DKM.get_vf_dict
+
 
 def is_outside_domain(x, domain):
     x = x[None, :] if x.ndim == 1 else x
@@ -225,21 +228,6 @@ def con_K_div_cur_free(x, y, sigma=0.8, eta=0.5):
     return G, df_kernel, cf_kernel
 
 
-def get_vf_dict(adata, basis="", vf_key="VecFld"):
-    if basis is not None:
-        if len(basis) > 0:
-            vf_key = "%s_%s" % (vf_key, basis)
-
-    if vf_key not in adata.uns.keys():
-        raise ValueError(
-            f"Vector field function {vf_key} is not included in the adata object! "
-            f"Try firstly running dyn.vf.VectorField(adata, basis='{basis}')"
-        )
-
-    vf_dict = adata.uns[vf_key]
-    return vf_dict
-
-
 def vecfld_from_adata(adata, basis="", vf_key="VecFld"):
     vf_dict = get_vf_dict(adata, basis=basis, vf_key=vf_key)