skbio.sequence.SubstitutionMatrix.plot

SubstitutionMatrix.plot(cmap=None, title='')

Create a heatmap of the dissimilarity matrix.

Parameters:

cmap: str or matplotlib.colors.Colormap, optional

Sets the color scheme of the heatmap If None, defaults to the colormap specified in the matplotlib rc file.

title: str, optional

Sets the title label of the heatmap (Default is blank)

Returns:

matplotlib.figure.Figure

Figure containing the heatmap and colorbar of the plotted dissimilarity matrix.

Examples

Define a dissimilarity matrix with five objects labeled A-E:

>>> from skbio.stats.distance import DissimilarityMatrix
>>> dm = DissimilarityMatrix([[0, 1, 2, 3, 4], [1, 0, 1, 2, 3],
...                           [2, 1, 0, 1, 2], [3, 2, 1, 0, 1],
...                           [4, 3, 2, 1, 0]],
...                          ['A', 'B', 'C', 'D', 'E'])

Plot the dissimilarity matrix as a heatmap:

>>> fig = dm.plot(cmap='Reds', title='Example heatmap')