Fix edge colors

docs/source/notebooks/circles.py

@@ -96,10 +96,8 @@
 fig = plot.plot_plotly(
     colors=labels,
     cmap=["jet", "viridis", "cividis"],
-    node_size=[0.0, 0.5, 1.0, 1.5, 2.0],
+    node_size=[0.25 * x for x in range(9)],
     agg=np.nanmean,
-    width=600,
-    height=600,
 )
 
 fig.show(config={"scrollZoom": True}, renderer="notebook_connected")
@@ -119,10 +117,8 @@
 fig = plot.plot_plotly(
     colors=labels,
     cmap=["jet", "viridis", "cividis"],
-    node_size=[0.0, 0.5, 1.0, 1.5, 2.0],
+    node_size=[0.25 * x for x in range(9)],
     agg=np.nanstd,
-    width=600,
-    height=600,
 )
 
 fig.show(config={"scrollZoom": True}, renderer="notebook_connected")

docs/source/notebooks/digits.py

@@ -103,10 +103,8 @@ def mode(arr):
     colors=labels,
     cmap=["jet", "viridis", "cividis"],
     agg=mode,
-    node_size=[0.0, 0.5, 1.0, 1.5, 2.0],
+    node_size=[0.25 * x for x in range(9)],
     title="mode of digits",
-    width=600,
-    height=600,
 )
 
 fig.show(config={"scrollZoom": True}, renderer="notebook_connected")
@@ -134,10 +132,8 @@ def entropy(arr):
     colors=labels,
     cmap=["jet", "viridis", "cividis"],
     agg=entropy,
-    node_size=[0.0, 0.5, 1.0, 1.5, 2.0],
+    node_size=[0.25 * x for x in range(9)],
     title="entropy of digits",
-    width=600,
-    height=600,
 )
 
 fig.show(config={"scrollZoom": True}, renderer="notebook_connected")

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "tda-mapper"
-version = "0.11.1"
+version = "0.11.2"
 description = "A simple and efficient Python implementation of Mapper algorithm for Topological Data Analysis"
 readme = "README.md"
 authors = [{ name = "Luca Simi", email = "lucasimi90@gmail.com" }]

src/tdamapper/plot.py

@@ -103,9 +103,9 @@ def plot_matplotlib(
         node_size=1,
         agg=np.nanmean,
         title=None,
+        cmap="jet",
         width=512,
         height=512,
-        cmap="jet",
     ):
         """
         Draw a static plot using Matplotlib.
@@ -123,15 +123,15 @@ def plot_matplotlib(
         :type agg: Callable, optional
         :param title: The title to be displayed alongside the figure.
         :type title: str, optional
+        :param cmap: The name of a colormap used to map `colors` data values,
+            aggregated by `agg`, to actual RGBA colors. Defaults to 'jet'.
+        :type cmap: str, optional
         :param width: The desired width of the figure in pixels. Defaults to
             512.
         :type width: int, optional
         :param height: The desired height of the figure in pixels. Defaults to
             512
         :type height: int, optional
-        :param cmap: The name of a colormap used to map `colors` data values,
-            aggregated by `agg`, to actual RGBA colors. Defaults to 'jet'.
-        :type cmap: str, optional
 
         :return: A static matplotlib figure that can be displayed on screen
             and notebooks.
@@ -145,9 +145,9 @@ def plot_matplotlib(
             node_size=node_size,
             agg=agg,
             title=title,
+            cmap=cmap,
             width=width,
             height=height,
-            cmap=cmap,
         )
 
     def plot_plotly(
@@ -156,9 +156,9 @@ def plot_plotly(
         node_size=1,
         agg=np.nanmean,
         title=None,
-        width=512,
-        height=512,
         cmap="jet",
+        width=None,
+        height=None,
     ):
         """
         Draw an interactive plot using Plotly.
@@ -180,15 +180,13 @@ def plot_plotly(
             and title is a list of string, each item will be used as title for
             its corresponding colormap.
         :type title: str, list[str], optional
-        :param width: The desired width of the figure in pixels. Defaults to
-            512.
-        :type width: int, optional
-        :param height: The desired height of the figure in pixels. Defaults to
-            512.
-        :type height: int, optional
         :param cmap: The name of a colormap used to map `colors` data values,
             aggregated by `agg`, to actual RGBA colors. Defaults to 'jet'.
         :type cmap: str, optional
+        :param width: The desired width of the figure in pixels.
+        :type width: int, optional
+        :param height: The desired height of the figure in pixels.
+        :type height: int, optional
 
         :return: An interactive Plotly figure that can be displayed on screen
             and notebooks. For 3D embeddings, the figure requires a WebGL
@@ -201,9 +199,9 @@ def plot_plotly(
             node_size=node_size,
             agg=agg,
             title=title,
+            cmap=cmap,
             width=width,
             height=height,
-            cmap=cmap,
         )
 
     def plot_plotly_update(
@@ -213,9 +211,9 @@ def plot_plotly_update(
         node_size=None,
         agg=None,
         title=None,
+        cmap=None,
         width=None,
         height=None,
-        cmap=None,
     ):
         """
         Draw an interactive plot using Plotly on a previously rendered figure.
@@ -240,15 +238,15 @@ def plot_plotly_update(
         :param title: The title to be displayed alongside the figure. Defaults
             to None.
         :type title: str, optional
+        :param cmap: The name of a colormap used to map `colors` data values,
+            aggregated by `agg`, to actual RGBA colors. Defaults to None.
+        :type cmap: str, optional
         :param width: The desired width of the figure in pixels. Defaults to
             None.
         :type width: int, optional
         :param height: The desired height of the figure in pixels. Defaults to
             None.
         :type height: int, optional
-        :param cmap: The name of a colormap used to map `colors` data values,
-            aggregated by `agg`, to actual RGBA colors. Defaults to None.
-        :type cmap: str, optional
 
         :return: An interactive Plotly figure that can be displayed on screen
             and notebooks. For 3D embeddings, the figure requires a WebGL
@@ -262,9 +260,9 @@ def plot_plotly_update(
             node_size=node_size,
             agg=agg,
             title=title,
+            cmap=cmap,
             width=width,
             height=height,
-            cmap=cmap,
         )
 
     def plot_pyvis(
@@ -274,9 +272,9 @@ def plot_pyvis(
         node_size=1,
         agg=np.nanmean,
         title=None,
+        cmap="jet",
         width=512,
         height=512,
-        cmap="jet",
     ):
         """
         Draw an interactive HTML plot using PyVis.
@@ -298,15 +296,15 @@ def plot_pyvis(
         :param title: The title to be displayed alongside the figure. Defaults
             to None.
         :type title: str, optional
+        :param cmap: The name of a colormap used to map `colors` data values,
+            aggregated by `agg`, to actual RGBA colors. Defaults to 'jet'.
+        :type cmap: str, optional
         :param width: The desired width of the figure in pixels. Defaults to
             512.
         :type width: int, optional
         :param height: The desired height of the figure in pixels. Defaults to
             512.
         :type height: int, optional
-        :param cmap: The name of a colormap used to map `colors` data values,
-            aggregated by `agg`, to actual RGBA colors. Defaults to 'jet'.
-        :type cmap: str, optional
         """
         return plot_pyvis(
             self,
@@ -315,9 +313,9 @@ def plot_pyvis(
             node_size=node_size,
             agg=agg,
             title=title,
+            cmap=cmap,
             width=width,
             height=height,
-            cmap=cmap,
         )