Site frequency spectra¶

allel.
sfs
(dac, n=None)[source]¶ Compute the site frequency spectrum given derived allele counts at a set of biallelic variants.
Parameters:  dac : array_like, int, shape (n_variants,)
Array of derived allele counts.
 n : int, optional
The total number of chromosomes called.
Returns:  sfs : ndarray, int, shape (n_chromosomes,)
Array where the kth element is the number of variant sites with k derived alleles.

allel.
sfs_folded
(ac, n=None)[source]¶ Compute the folded site frequency spectrum given reference and alternate allele counts at a set of biallelic variants.
Parameters:  ac : array_like, int, shape (n_variants, 2)
Allele counts array.
 n : int, optional
The total number of chromosomes called.
Returns:  sfs_folded : ndarray, int, shape (n_chromosomes//2,)
Array where the kth element is the number of variant sites with a minor allele count of k.

allel.
sfs_scaled
(dac, n=None)[source]¶ Compute the site frequency spectrum scaled such that a constant value is expected across the spectrum for neutral variation and constant population size.
Parameters:  dac : array_like, int, shape (n_variants,)
Array of derived allele counts.
 n : int, optional
The total number of chromosomes called.
Returns:  sfs_scaled : ndarray, int, shape (n_chromosomes,)
An array where the value of the kth element is the number of variants with k derived alleles, multiplied by k.

allel.
sfs_folded_scaled
(ac, n=None)[source]¶ Compute the folded site frequency spectrum scaled such that a constant value is expected across the spectrum for neutral variation and constant population size.
Parameters:  ac : array_like, int, shape (n_variants, 2)
Allele counts array.
 n : int, optional
The total number of chromosomes called.
Returns:  sfs_folded_scaled : ndarray, int, shape (n_chromosomes//2,)
An array where the value of the kth element is the number of variants with minor allele count k, multiplied by the scaling factor (k * (n  k) / n).

allel.
joint_sfs
(dac1, dac2, n1=None, n2=None)[source]¶ Compute the joint site frequency spectrum between two populations.
Parameters:  dac1 : array_like, int, shape (n_variants,)
Derived allele counts for the first population.
 dac2 : array_like, int, shape (n_variants,)
Derived allele counts for the second population.
 n1, n2 : int, optional
The total number of chromosomes called in each population.
Returns:  joint_sfs : ndarray, int, shape (m_chromosomes, n_chromosomes)
Array where the (i, j)th element is the number of variant sites with i derived alleles in the first population and j derived alleles in the second population.

allel.
joint_sfs_folded
(ac1, ac2, n1=None, n2=None)[source]¶ Compute the joint folded site frequency spectrum between two populations.
Parameters:  ac1 : array_like, int, shape (n_variants, 2)
Allele counts for the first population.
 ac2 : array_like, int, shape (n_variants, 2)
Allele counts for the second population.
 n1, n2 : int, optional
The total number of chromosomes called in each population.
Returns:  joint_sfs_folded : ndarray, int, shape (n1//2 + 1, n2//2 + 1)
Array where the (i, j)th element is the number of variant sites with a minor allele count of i in the first population and j in the second population.

allel.
joint_sfs_scaled
(dac1, dac2, n1=None, n2=None)[source]¶ Compute the joint site frequency spectrum between two populations, scaled such that a constant value is expected across the spectrum for neutral variation, constant population size and unrelated populations.
Parameters:  dac1 : array_like, int, shape (n_variants,)
Derived allele counts for the first population.
 dac2 : array_like, int, shape (n_variants,)
Derived allele counts for the second population.
 n1, n2 : int, optional
The total number of chromosomes called in each population.
Returns:  joint_sfs_scaled : ndarray, int, shape (n1 + 1, n2 + 1)
Array where the (i, j)th element is the scaled frequency of variant sites with i derived alleles in the first population and j derived alleles in the second population.

allel.
joint_sfs_folded_scaled
(ac1, ac2, n1=None, n2=None)[source]¶ Compute the joint folded site frequency spectrum between two populations, scaled such that a constant value is expected across the spectrum for neutral variation, constant population size and unrelated populations.
Parameters:  ac1 : array_like, int, shape (n_variants, 2)
Allele counts for the first population.
 ac2 : array_like, int, shape (n_variants, 2)
Allele counts for the second population.
 n1, n2 : int, optional
The total number of chromosomes called in each population.
Returns:  joint_sfs_folded_scaled : ndarray, int, shape (n1//2 + 1, n2//2 + 1)
Array where the (i, j)th element is the scaled frequency of variant sites with a minor allele count of i in the first population and j in the second population.

allel.
fold_sfs
(s, n)[source]¶ Fold a site frequency spectrum.
Parameters:  s : array_like, int, shape (n_chromosomes,)
Site frequency spectrum
 n : int
Total number of chromosomes called.
Returns:  sfs_folded : ndarray, int
Folded site frequency spectrum

allel.
fold_joint_sfs
(s, n1, n2)[source]¶ Fold a joint site frequency spectrum.
Parameters:  s : array_like, int, shape (m_chromosomes, n_chromosomes)
Joint site frequency spectrum.
 n1, n2 : int, optional
The total number of chromosomes called in each population.
Returns:  joint_sfs_folded : ndarray, int
Folded joint site frequency spectrum.

allel.
scale_sfs
(s)[source]¶ Scale a site frequency spectrum.
Parameters:  s : array_like, int, shape (n_chromosomes,)
Site frequency spectrum.
Returns:  sfs_scaled : ndarray, int, shape (n_chromosomes,)
Scaled site frequency spectrum.

allel.
scale_sfs_folded
(s, n)[source]¶ Scale a folded site frequency spectrum.
Parameters:  s : array_like, int, shape (n_chromosomes//2,)
Folded site frequency spectrum.
 n : int
Number of chromosomes called.
Returns:  sfs_folded_scaled : ndarray, int, shape (n_chromosomes//2,)
Scaled folded site frequency spectrum.

allel.
scale_joint_sfs
(s)[source]¶ Scale a joint site frequency spectrum.
Parameters:  s : array_like, int, shape (n1, n2)
Joint site frequency spectrum.
Returns:  joint_sfs_scaled : ndarray, int, shape (n1, n2)
Scaled joint site frequency spectrum.

allel.
scale_joint_sfs_folded
(s, n1, n2)[source]¶ Scale a folded joint site frequency spectrum.
Parameters:  s : array_like, int, shape (m_chromosomes//2, n_chromosomes//2)
Folded joint site frequency spectrum.
 n1, n2 : int, optional
The total number of chromosomes called in each population.
Returns:  joint_sfs_folded_scaled : ndarray, int, shape (m_chromosomes//2, n_chromosomes//2)
Scaled folded joint site frequency spectrum.

allel.
plot_sfs
(s, yscale='log', bins=None, n=None, clip_endpoints=True, label=None, plot_kwargs=None, ax=None)[source]¶ Plot a site frequency spectrum.
Parameters:  s : array_like, int, shape (n_chromosomes,)
Site frequency spectrum.
 yscale : string, optional
Y axis scale.
 bins : int or array_like, int, optional
Allele count bins.
 n : int, optional
Number of chromosomes sampled. If provided, X axis will be plotted as allele frequency, otherwise as allele count.
 clip_endpoints : bool, optional
If True, do not plot first and last values from frequency spectrum.
 label : string, optional
Label for data series in plot.
 plot_kwargs : dictlike
Additional keyword arguments, passed through to ax.plot().
 ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
Returns:  ax : axes
The axes on which the plot was drawn.

allel.
plot_sfs_folded
(*args, **kwargs)[source]¶ Plot a folded site frequency spectrum.
Parameters:  s : array_like, int, shape (n_chromosomes/2,)
Site frequency spectrum.
 yscale : string, optional
Y axis scale.
 bins : int or array_like, int, optional
Allele count bins.
 n : int, optional
Number of chromosomes sampled. If provided, X axis will be plotted as allele frequency, otherwise as allele count.
 clip_endpoints : bool, optional
If True, do not plot first and last values from frequency spectrum.
 label : string, optional
Label for data series in plot.
 plot_kwargs : dictlike
Additional keyword arguments, passed through to ax.plot().
 ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
Returns:  ax : axes
The axes on which the plot was drawn.

allel.
plot_sfs_scaled
(*args, **kwargs)[source]¶ Plot a scaled site frequency spectrum.
Parameters:  s : array_like, int, shape (n_chromosomes,)
Site frequency spectrum.
 yscale : string, optional
Y axis scale.
 bins : int or array_like, int, optional
Allele count bins.
 n : int, optional
Number of chromosomes sampled. If provided, X axis will be plotted as allele frequency, otherwise as allele count.
 clip_endpoints : bool, optional
If True, do not plot first and last values from frequency spectrum.
 label : string, optional
Label for data series in plot.
 plot_kwargs : dictlike
Additional keyword arguments, passed through to ax.plot().
 ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
Returns:  ax : axes
The axes on which the plot was drawn.

allel.
plot_sfs_folded_scaled
(*args, **kwargs)[source]¶ Plot a folded scaled site frequency spectrum.
Parameters:  s : array_like, int, shape (n_chromosomes/2,)
Site frequency spectrum.
 yscale : string, optional
Y axis scale.
 bins : int or array_like, int, optional
Allele count bins.
 n : int, optional
Number of chromosomes sampled. If provided, X axis will be plotted as allele frequency, otherwise as allele count.
 clip_endpoints : bool, optional
If True, do not plot first and last values from frequency spectrum.
 label : string, optional
Label for data series in plot.
 plot_kwargs : dictlike
Additional keyword arguments, passed through to ax.plot().
 ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
Returns:  ax : axes
The axes on which the plot was drawn.

allel.
plot_joint_sfs
(s, ax=None, imshow_kwargs=None)[source]¶ Plot a joint site frequency spectrum.
Parameters:  s : array_like, int, shape (n_chromosomes_pop1, n_chromosomes_pop2)
Joint site frequency spectrum.
 ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
 imshow_kwargs : dictlike
Additional keyword arguments, passed through to ax.imshow().
Returns:  ax : axes
The axes on which the plot was drawn.

allel.
plot_joint_sfs_folded
(*args, **kwargs)[source]¶ Plot a joint site frequency spectrum.
Parameters:  s : array_like, int, shape (n_chromosomes_pop1/2, n_chromosomes_pop2/2)
Joint site frequency spectrum.
 ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
 imshow_kwargs : dictlike
Additional keyword arguments, passed through to ax.imshow().
Returns:  ax : axes
The axes on which the plot was drawn.

allel.
plot_joint_sfs_scaled
(*args, **kwargs)[source]¶ Plot a scaled joint site frequency spectrum.
Parameters:  s : array_like, int, shape (n_chromosomes_pop1, n_chromosomes_pop2)
Joint site frequency spectrum.
 ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
 imshow_kwargs : dictlike
Additional keyword arguments, passed through to ax.imshow().
Returns:  ax : axes
The axes on which the plot was drawn.

allel.
plot_joint_sfs_folded_scaled
(*args, **kwargs)[source]¶ Plot a scaled folded joint site frequency spectrum.
Parameters:  s : array_like, int, shape (n_chromosomes_pop1/2, n_chromosomes_pop2/2)
Joint site frequency spectrum.
 ax : axes, optional
Axes on which to draw. If not provided, a new figure will be created.
 imshow_kwargs : dictlike
Additional keyword arguments, passed through to ax.imshow().
Returns:  ax : axes
The axes on which the plot was drawn.