Merge pull request #232 from lucasimi/fix-edge-colors

Fix edge colors

Author: lucasimi

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,
  )