Plotting functions¶
Plotting functions for variant call data.
Variant location¶
-
allel.plot.
variant_locator
(pos, step=None, ax=None, start=None, stop=None, flip=False, line_kwargs=None)[source]¶ Plot lines indicating the physical genome location of variants from a single chromosome/contig. By default the top x axis is in variant index space, and the bottom x axis is in genome position space.
Parameters: pos : array_like
A sorted 1-dimensional array of genomic positions from a single chromosome/contig.
step : int, optional
Plot a line for every step variants.
ax : axes, optional
The axes on which to draw. If not provided, a new figure will be created.
start : int, optional
The start position for the region to draw.
stop : int, optional
The stop position for the region to draw.
flip : bool, optional
Flip the plot upside down.
line_kwargs : dict-like
Additional keyword arguments passed through to plt.Line2D.
Returns: ax : axes
The axes on which the plot was drawn
Pairwise distance¶
-
allel.plot.
pairwise_distance
(dist, labels=None, colorbar=True, ax=None, imshow_kwargs=None)[source]¶ Plot a pairwise distance matrix.
Parameters: dist : array_like
The distance matrix in condensed form.
labels : sequence of strings, optional
Sample labels for the axes.
colorbar : bool, optional
If True, add a colorbar to the current figure.
ax : axes, optional
The axes on which to draw. If not provided, a new figure will be created.
imshow_kwargs : dict-like, optional
Additional keyword arguments passed through to
matplotlib.pyplot.imshow()
.Returns: ax : axes
The axes on which the plot was drawn
Linkage disequilibrium¶
-
allel.plot.
pairwise_ld
(m, colorbar=True, ax=None, imshow_kwargs=None)[source]¶ Plot a matrix of linkage disequilibrium values between pairs of variants.
Parameters: m : array_like
LD matrix in condensed form.
colorbar : bool, optional
If True, add a colorbar to the current figure.
ax : axes, optional
The axes on which to draw. If not provided, a new figure will be created.
imshow_kwargs : dict-like, optional
Additional keyword arguments passed through to
matplotlib.pyplot.imshow()
.Returns: ax : axes
The axes on which the plot was drawn
Selection¶
-
allel.plot.
voight_painting
(painting, palette='colorblind', flank='right', ax=None, height_factor=0.01)[source]¶ Plot a painting of shared haplotype prefixes.
Parameters: painting : array_like, int, shape (n_variants, n_haplotypes)
Painting array.
ax : axes, optional
The axes on which to draw. If not provided, a new figure will be created.
palette : string, optional
A Seaborn palette name.
flank : {‘right’, ‘left’}, optional
If left, painting will be reversed along first axis.
height_factor : float, optional
If no axes provided, determine height of figure by multiplying height of painting array by this number.