mdciao.plots.plot_matrix

mdciao.plots.plot_matrix(mat, labels, pixelsize=1, transpose=False, grid=False, cmap='binary', colorbar=False)

Plot a matrix using imshow.

Matrx can be non-symmetric and rectangular, rows and columns need not represent the same residues or groups of residues

Parameters

  • mat (2D numpy.ndarray of shape (N,M)) – The matrix to be plotted, NaNs are allowed

  • labels (list of len(2) with x and y labels) – The length of each list has to be N, M for x, y respectively, else this method fails

  • pixelsize (int, default is 1) – The size in inches of the pixel representing the contact. Ultimately controls the size of the figure, because figsize = _np.array(mat.shape)*pixelsize

  • transpose (bool, default is False) –

  • grid (boolean, default is False) – overlap a grid of dashed lines

  • cmap (str, default is 'binary') – What matplotlib.cmap to use

  • colorbar (boolean, default is False) – whether to use a colorbar

  • transpose – Transpose the matrix when plotting

Returns

  • ax (Axes object)

  • pixelsize (float, size of the pixel) – Helpful in cases where this method is called with the default value, in case the value changes in the future