src/cluster_plotters.py

#!/usr/bin/env python
"""
Functions which plot confidence elipses around clusters.
"""

import matplotlib.pyplot as plt
from matplotlib.patches import Ellipse
import matplotlib
import matplotlib.transforms as transforms
import numpy as np
import pandas as pd

def confidence_ellipse(x, y, ax, n_std=3.0, facecolor='none', **kwargs):
    """
    Create a plot of the covariance confidence ellipse of *x* and *y*.

    Parameters
    ----------
    x, y : array-like, shape (n, )
        Input data.

    ax : matplotlib.axes.Axes
        The axes object to draw the ellipse into.

    n_std : float
        The number of standard deviations to determine the ellipse's radiuses.

    **kwargs
        Forwarded to `~matplotlib.patches.Ellipse`

    Returns
    -------
    matplotlib.patches.Ellipse
    """
    if x.size != y.size:
        raise ValueError("x and y must be the same size")

    cov = np.cov(x, y)
    pearson = cov[0, 1]/np.sqrt(cov[0, 0] * cov[1, 1])
    # Using a special case to obtain the eigenvalues of this
    # two-dimensional dataset.
    ell_radius_x = np.sqrt(1 + pearson)
    ell_radius_y = np.sqrt(1 - pearson)
    ellipse = Ellipse((0, 0), width=ell_radius_x * 2, height=ell_radius_y * 2,
                      facecolor=facecolor, **kwargs)

    # Calculating the standard deviation of x from
    # the squareroot of the variance and multiplying
    # with the given number of standard deviations.
    scale_x = np.sqrt(cov[0, 0]) * n_std
    mean_x = np.mean(x)

    # calculating the standard deviation of y ...
    scale_y = np.sqrt(cov[1, 1]) * n_std
    mean_y = np.mean(y)

    transf = transforms.Affine2D() \
        .rotate_deg(45) \
        .scale(scale_x, scale_y) \
        .translate(mean_x, mean_y)

    ellipse.set_transform(transf + ax.transData)
    return ax.add_patch(ellipse)

def plot_cluster_ellipses(df, ax=None, color=None, annotation_color=None, color_map=None):
    if ax is None:
        fig, ax  = plt.subplots(figsize=(13,13))

 
    unique_label,cluster_rep_index, counts = np.unique(df.labels, return_index=True, return_counts=True)
    cmap = plt.get_cmap('turbo')
    norm = matplotlib.colors.Normalize(vmin=min(df.labels), vmax=max(df.labels))
    
    for label, rep_id in zip(unique_label, cluster_rep_index):
        if label != -1:
            if color_map:
                color = cmap(norm(label))
                annotation_color = cmap(norm(label))
            

            cluster_x_y = df[df.labels==label][["fx", "fy"]].to_numpy() 
            confidence_ellipse(cluster_x_y[:, 0], cluster_x_y[:, 1], ax, edgecolor=color, n_std=3)
            ax.annotate(label, cluster_x_y.mean(0)+[-7,0],color=annotation_color,alpha=1, weight='normal', ha='center', va='center', size=9)
    return ax

def plot_groups(df, column, ax=None, values=None):
    import colorcet as cc
    
    if ax is None:
        fig, ax = plt.subplots(figsize=(13,13))
    if column not in df.columns:
        raise IndexError(f"Column {column} is not in the dataframe")
    
    if not values:
        values = df[column].unique()

    for i, value in enumerate(values):
        indices = df[column]==value
        if (value == -1) and (column=="labels"):
            ax.scatter(df.fx[indices], df.fy[indices],s=1, c="black", label=value)
        else:
            ax.scatter(df.fx[indices], df.fy[indices],s=4, c=cc.glasbey[i%len(cc.glasbey)], label=value)

    if len(values) > len(cc.glasbey):
        print(f"Colors used multiple times since number of categories exceeds {len(cc.glasbey)}.")
    
    return ax