Commit ef96cb44 authored by Maxime's avatar Maxime
Browse files

docs: improve function descriptions

parent 1c0abd19

phasik/drawing/drawing.py

+15 −6
Original line number Diff line number Diff line
@@ -32,14 +32,18 @@ def plot_events( 
    alpha=1,

    va="bottom",

):

    """Plot events as vertical lines on axes

    """Visualize the occurence of events as vertical lines.



    This function was designed to be used in complement to another function `plot_cluster_sets`

    that draws objects over time (horizontal axis). The vertical lines are drawn at the 

    horizontal value corresponding to the time of occurrence of the event.



    Parameters

    ----------

    events : list of tuples (time, name, line_style)

        time - time at which the event occurred

        name - the name of the event

        line_style - any string accepted by matplotlib.lines.Line2D.set_linestyle

        * time - time at which the event occurred

        * name - the name of the event

        * line_style - any string accepted by matplotlib.lines.Line2D.set_linestyle

    ax : matplotlib.Axes, optional

        Axes on which to plot the events

    text_y_pos : float, optional
@@ -61,6 +65,7 @@ def plot_events( 
    See Also

    --------

    plot_phases

    plot_cluster_sets

    """



    if ax is None:
@@ -152,7 +157,11 @@ def plot_events( 




def plot_phases(phases, ax=None, y_pos=None, ymin=0, ymax=1, t_offset=0):

    """Plot phases as shaded regions on axes

    """Visualize temporal phases as shaded intervals



    This function was designed to be used in complement to another function `plot_cluster_sets`

    that draws objects over time (horizontal axis). The phases are drawn as shaded regions 

    spanning the time interval corresponding to the phases.



    Parameters

    ----------
@@ -314,7 +323,7 @@ def threshold_plot( 




def plot_edge_series(temporal_network, edges, ax=None, **kwargs):

    """Plot timeseries of edge weights, for the specified edges

    """Draw time series of edge weights, for the specified edges



    Parameters

    ----------

phasik/drawing/drawing_clusters.py

+22 −6
Original line number Diff line number Diff line
@@ -89,7 +89,7 @@ def plot_randindex_bars_over_methods_and_sizes( 
                heights,

                width,

                label=method,

                **kwargs

                **kwargs,

            )



    ax.set_xticks(xticks)
@@ -105,7 +105,7 @@ def plot_cluster_set( 
    cmap=mpl.colormaps["tab10"],

    number_of_colors=10,

    colors=None,

    **kwargs

    **kwargs,

):

    """Plots this cluster set as a scatter graph
@@ -156,7 +156,7 @@ def plot_cluster_set( 
        cmap=cmap,

        vmin=1,

        vmax=number_of_colors,

        **kwargs

        **kwargs,

    )



    return ax
@@ -297,7 +297,9 @@ def plot_dendrogram( 
    return ax





def plot_average_silhouettes(cluster_sets, ax=None, c="k", marker="o", ls="-", **kwargs):

def plot_average_silhouettes(

    cluster_sets, ax=None, c="k", marker="o", ls="-", **kwargs

):

    """Plot the average silhouettes across this range of cluster sets



    Parameters
@@ -317,7 +319,14 @@ def plot_average_silhouettes(cluster_sets, ax=None, c="k", marker="o", ls="-", * 


    if ax is None:

        ax = plt.gca()

    ax.plot(cluster_sets.silhouettes_average, cluster_sets.ns_max, c=c, marker=marker, ls=ls, **kwargs)

    ax.plot(

        cluster_sets.silhouettes_average,

        cluster_sets.ns_max,

        c=c,

        marker=marker,

        ls=ls,

        **kwargs,

    )

    ax.set_xlabel("Average silhouette")



    return ax
@@ -343,7 +352,14 @@ def plot_ns_clusters(cluster_sets, ax=None, c="k", marker="o", ls="-", **kwargs) 


    if ax is None:

        ax = plt.gca()

    ax.plot(cluster_sets.n_clusters, cluster_sets.ns_max, c=c, marker=marker, ls=ls, **kwargs)

    ax.plot(

        cluster_sets.n_clusters,

        cluster_sets.ns_max,

        c=c,

        marker=marker,

        ls=ls,

        **kwargs,

    )



    return ax

phasik/drawing/drawing_networks.py

+24 −64
Original line number Diff line number Diff line
@@ -69,14 +69,15 @@ def standard_label_params(color): 
def draw_graph(

    graph,

    ax=None,

    label_nodes=True,

    color="mediumseagreen",

    pos=None,

    color="mediumseagreen",

    edge_widths=None,

    edge_colors=None,

    edge_cmap=None,

    edge_vmin=None,

    edge_vmax=None,

    label_nodes=True,

    colorbar=True,

):

    """Basic graph drawing function
@@ -86,12 +87,10 @@ def draw_graph( 
        Graph to visualise

    ax : matplotlib.Axes, optional

        Axes on which to draw the graph

    label_nodes : bool, optional

        Whether to label the nodes or just leave them as small circles (default True)

    pos : dict

        Dictionary of node positions of the form {node_id : (x, y)}

    color : str, optional

        Color to use for the graph nodes and edges (default 'mediumseagreen')

    pos : dict

        Dictionary of node positions

    edge_widths: float or array of floats

        Line width of edges

    edge_colors: color or array of colors
@@ -103,10 +102,15 @@ def draw_graph( 
        Colormap for mapping intensities of edges

    edge_vmin,edge_vmax: floats, optional

        Minimum and maximum for edge colormap scaling

    label_nodes : bool, optional

        Whether to label the nodes or just leave them as small circles (default True)

    colorbar : bool, optional

        Wether to draw a colorbar



    Returns

    -------

    None

    matplotlib.axes.Axes

        The axis object to draw on

    """



    if ax is None:
@@ -115,62 +119,6 @@ def draw_graph( 
    if pos is None:

        pos = nx.spring_layout(graph)



    _draw_graph(

        graph,

        pos,

        ax,

        label_nodes,

        color,

        edge_widths,

        edge_colors,

        edge_cmap,

        edge_vmin,

        edge_vmax,

    )





def _draw_graph(

    graph,

    pos,

    ax,

    label_nodes,

    color,

    edge_widths=1,

    edge_colors="k",

    edge_cmap=None,

    edge_vmin=None,

    edge_vmax=None,

):

    """Plots a networkx.Graph with a predefined style



    Parameters

    ----------

    graph : networkx.Graph

        Graph to visualise

    pos : dict

        Dictionary of positions used by plotting function in networkx

    ax : maplotlib.axis

        Axes on which to plot

    label_nodes : bool

        If True, plot node labels

    color : str

        Color used for nodes and edges

    edge_widths: float or array of floats

        Line width of edges

    edge_colors: color or array of colors

        Edge color. Can be a single color or a sequence of colors with the same length as

        edgelist. Color can be string or rgb (or rgba) tuple of floats from 0-1.

        If numeric values are specified they will be mapped to colors using the edge_cmap

        and edge_vmin,edge_vmax parameters.

    edge_cmap: Matplotlib colormap, optional

        Colormap for mapping intensities of edges

    edge_vmin,edge_vmax: floats, optional

        Minimum and maximum for edge colormap scaling



    Returns

    -------



    """

    params_nodes = standard_node_params(color)

    params_edges = standard_edge_params(color)

    params_labels = standard_label_params(color)
@@ -193,10 +141,13 @@ def _draw_graph( 
    if label_nodes:

        nx.draw_networkx_labels(graph, ax=ax, pos=pos, **params_labels)



    if colorbar:

        if edge_colors is not None:

            if len(edge_colors) == len(graph.edges):

                plt.colorbar(im, ax=ax, label="edge color scale")



    return ax





def highlight_subgraphs(graphs, colors, ax=None, pos=None, label_nodes=True):

    """Draw multiple nested subgraphs on the same axes
@@ -226,7 +177,16 @@ def highlight_subgraphs(graphs, colors, ax=None, pos=None, label_nodes=True): 
        pos = nx.spring_layout(graphs[0])



    for graph, color in zip(graphs, colors):

        _draw_graph(graph, pos, ax, label_nodes, color, edge_colors=color)

        draw_graph(

            graph=graph,

            pos=pos,

            ax=ax,

            label_nodes=label_nodes,

            color=color,

            edge_colors=color,

        )



    return 





def animate_temporal_network(