psynlig.heatmap

The psynlig.heatmap module defines methods for generaing a heat map to show Pearson correlation coefficients for pairs of variables.

Example usage

To generate the following heat map:

../_images/wine1.png

the method psynlig.heatmap.plot_heatmap() is used:

# Copyright (c) 2020, Anders Lervik.
# Distributed under the MIT License. See LICENSE for more info.
"""An example of generating a heat map of correlations."""
from matplotlib import pyplot as plt
import pandas as pd
from sklearn.datasets import load_wine as load_data
from psynlig import plot_correlation_heatmap
plt.style.use('seaborn-talk')


data_set = load_data()
data = pd.DataFrame(data_set['data'], columns=data_set['feature_names'])
kwargs = {
    'heatmap': {
        'vmin': -1,
        'vmax': 1,
        'cmap': 'viridis',
    }
}
plot_correlation_heatmap(data, textcolors=['white', 'black'], **kwargs)
plt.show()

psynlig.heatmap source code

A module defining helper methods for creating a heat map.

psynlig.heatmap.annotate_heatmap(img, data=None, val_fmt='{x:.2f}', textcolors=None, **kwargs)[source]

Annotate a heatmap with values.

Parameters

  • img (object like matplotlib.image.AxesImage) – The heat map image to be labeled.

  • data (object like numpy.ndarray, optional) – Data used to annotate the heat map. If not given, the data in the heat map image (img) is used.

  • val_fmt (string, optional) – The format of the annotations inside the heat map.

  • textcolors (list of strings, optional) – Colors used for the text. The number of colors provided defines a binning for the data values, and values are colored with the corresponding color. If no colors are provided, all are colored black.

  • **kwargs (dict, optional) – Extra arguments used for creating text labels.

psynlig.heatmap.create_bubbles(data, img, axi)[source]

Create bubbles for a heat map.

Parameters
psynlig.heatmap.heatmap(data, row_labels, col_labels, axi=None, fig=None, cbar_kw=None, cbarlabel='', bubble=False, **kwargs)[source]

Create a heat map from a numpy array and two lists of labels.

Parameters

  • data (object like numpy.ndarray) – A 2D numpy array of shape (N, M).

  • row_labels (list of strings) – A list or array of length N with the labels for the rows.

  • col_labels (list of strings) – A list or array of length M with the labels for the columns.

  • axi (object like matplotlib.axes.Axes, optional) – An axis to plot the heat map. If not provided, a new axis will be created.

  • fig (object like matplotlib.figure.Figure, optional) – The figure where the axes resides in. If given, tight layout will be applied.

  • cbar_kw (dict, optional) – A dictionary with arguments to the creation of the color bar.

  • cbarlabel (string, optional) – The label for the color bar.

  • bubble (boolean, optional) – If True, we will draw bubbles indicating the size of the given data points.

  • **kwargs (dict, optional) – Additional arguments for drawing the heat map.

Returns

psynlig.heatmap.plot_annotated_heatmap(data, row_labels, col_labels, cbarlabel='', val_fmt='{x:.2f}', textcolors=None, bubble=False, annotate=True, **kwargs)[source]

Plot a heat map to investigate correlations.

Parameters

  • data (object like numpy.ndarray) – A 2D numpy array of shape (N, M).

  • row_labels (list of strings) – A list or array of length N with the labels for the rows.

  • col_labels (list of strings) – A list or array of length M with the labels for the columns.

  • cbarlabel (string, optional) – The label for the color bar.

  • val_fmt (string, optional) – The format of the annotations inside the heat map.

  • textcolors (list of strings, optional) – Colors used for the text. The number of colors provided defines a binning for the data values, and values are colored with the corresponding color. If no colors are provided, all are colored black.

  • bubble (boolean, optional) – If True, we will draw bubbles to indicate the size of the given data points.

  • annotate (boolean, optional) – If True, we will annotate the plot with values.

  • **kwargs (dict, optional) – Arguments used for drawing the heat map.

Returns

psynlig.heatmap.plot_correlation_heatmap(data, val_fmt='{x:.2f}', bubble=False, annotate=True, textcolors=None, **kwargs)[source]

Plot a heat map to investigate correlations.

Parameters

  • data (object like pandas.DataFrame) – The data we will generate a heat correlation map from.

  • val_fmt (string, optional) – The format of the annotations inside the heat map.

  • bubble (optional, boolean) – If True, we will draw bubbles to indicate the size of the given data points.

  • annotate (boolean, optional) – If True, we will annotate the plot with values.

  • textcolors (list of strings, optional) – Colors used for the text. The number of colors provided defines a binning for the data values, and values are colored with the corresponding color. If no colors are provided, all are colored black.

  • **kwargs (dict, optional) – Arguments used for drawing the heat map.

Returns