Ld

plot_ld_matrix(ldm, variant_subset=None, start_row=None, end_row=None, symmetric=False, cmap='OrRd', include_colorbar=True)

Plot a heatmap representing the LD matrix or portions of it.

Parameters:

Name	Type	Description	Default
ldm	LDMatrix	An instance of LDMatrix.	required
variant_subset		A list of variant rsIDs to subset the LD matrix.	None
start_row		The starting row index for the LD matrix plot.	None
end_row		The ending row index (not inclusive) for the LD matrix plot.	None
symmetric		If True, plot the symmetric version of the LD matrix. Otherwise, plot the upper triangular part.	False
cmap		The color map for the LD matrix plot.	'OrRd'
include_colorbar		If True, include a colorbar in the plot.	True

Source code in magenpy/plot/ld.py

def plot_ld_matrix(ldm: LDMatrix,
                   variant_subset=None,
                   start_row=None,
                   end_row=None,
                   symmetric=False,
                   cmap='OrRd',
                   include_colorbar=True):
    """
    Plot a heatmap representing the LD matrix or portions of it.

    :param ldm: An instance of `LDMatrix`.
    :param variant_subset: A list of variant rsIDs to subset the LD matrix.
    :param start_row: The starting row index for the LD matrix plot.
    :param end_row: The ending row index (not inclusive) for the LD matrix plot.
    :param symmetric: If True, plot the symmetric version of the LD matrix.
    Otherwise, plot the upper triangular part.
    :param cmap: The color map for the LD matrix plot.
    :param include_colorbar: If True, include a colorbar in the plot.
    """

    curr_mask = None

    if variant_subset is not None:
        curr_mask = ldm.get_mask()
        ldm.reset_mask()
        ldm.filter_snps(variant_subset)

    ld_mat = ldm.load_data(start_row=start_row,
                           end_row=end_row,
                           return_symmetric=symmetric,
                           return_square=True,
                           return_as_csr=True,
                           dtype=np.float32).todense()

    plt.imshow(ld_mat, cmap=cmap, vmin=-1., vmax=1.)

    if include_colorbar:
        plt.colorbar()

    # Reset the original mask:
    if curr_mask is not None:
        ldm.set_mask(curr_mask)

    plt.axis('off')