Index

C

calc_covariance_distance() (gpmap.summary.GPDataSummarizer method) calc_covariance_U_sites() (gpmap.summary.GPDataSummarizer method) calc_rate_matrix() (gpmap.randwalk.WMWalk method) calc_root_mean_squared_epistatic_coeff() (gpmap.summary.GPmapSummarizer method) calc_site_pairs_variance_perc() (gpmap.summary.GPmapSummarizer method) calc_sites_variance_perc() (gpmap.summary.GPmapSummarizer method)

calc_stationary_frequencies() (gpmap.randwalk.WMWalk method) calc_V_k_variance_components() (gpmap.summary.GPmapSummarizer method) calc_V_U_variance_components() (gpmap.summary.GPmapSummarizer method) calc_visualization() (gpmap.datasets.DataSet method) (gpmap.randwalk.WMWalk method) CodonSpace (class in gpmap.space) ConnectednessModelRegression (class in gpmap.inference)

D

DataSet (class in gpmap.datasets)

DiscreteSpace (class in gpmap.space) dsg_to_fig() (in module gpmap.plot.ds)

F

figure_allele_grid() (in module gpmap.plot.ds) (in module gpmap.plot.mpl) figure_Ns_grid() (in module gpmap.plot.mpl) figure_SeqDEFT_summary() (in module gpmap.plot.mpl)

fit() (gpmap.inference.ConnectednessModelRegression method) (gpmap.inference.LocalEpistasisRegression method) (gpmap.inference.MinimumEpistasisInterpolator method) (gpmap.inference.SeqDEFT method) (gpmap.inference.VCregression method)

G

generate_freq_reduced_code() (in module gpmap.seq) get_a_values() (gpmap.inference.LocalEpistasisRegression method) get_custom_codon_table() (in module gpmap.seq) get_decay_factors() (gpmap.inference.ConnectednessModelRegression method) get_edges_df() (gpmap.space.CodonSpace method) (gpmap.space.DiscreteSpace method) (gpmap.space.GridSpace method) (gpmap.space.SequenceSpace method) get_empirical_pred_correlations_df() (gpmap.inference.LocalEpistasisRegression method) get_genotypes_from_region() (in module gpmap.genotypes) get_lambda_U_values() (gpmap.inference.LocalEpistasisRegression method) get_neighbor_pairs() (gpmap.space.CodonSpace method) (gpmap.space.DiscreteSpace method) (gpmap.space.GridSpace method) (gpmap.space.SequenceSpace method)

get_neighbors() (gpmap.space.CodonSpace method) (gpmap.space.DiscreteSpace method) (gpmap.space.GridSpace method) (gpmap.space.SequenceSpace method) get_single_mutant_matrix() (gpmap.space.SequenceSpace method) get_state_idxs() (gpmap.space.CodonSpace method) (gpmap.space.DiscreteSpace method) (gpmap.space.GridSpace method) (gpmap.space.SequenceSpace method) get_variance_components() (gpmap.inference.VCregression method) GPDataSummarizer (class in gpmap.summary) GPmapSummarizer (class in gpmap.summary) GridSpace (class in gpmap.space)

L

list_available_datasets() (in module gpmap.datasets)

LocalEpistasisRegression (class in gpmap.inference)

M

make_contrasts() (gpmap.inference.ConnectednessModelRegression method) (gpmap.inference.LocalEpistasisRegression method) (gpmap.inference.MinimumEpistasisInterpolator method) (gpmap.inference.SeqDEFT method) (gpmap.inference.VCregression method)

marginalize_landscape_positions() (in module gpmap.genotypes) MinimumEpistasisInterpolator (class in gpmap.inference) msa_to_counts() (in module gpmap.seq)

P

plot() (gpmap.datasets.DataSet method) plot_correlation_distance() (in module gpmap.plot.mpl) plot_correlation_U_sites() (in module gpmap.plot.mpl) plot_edges() (in module gpmap.plot.ds) (in module gpmap.plot.mpl) plot_interaction_matrix() (in module gpmap.plot.mpl) plot_kth_variance_components() (in module gpmap.plot.mpl) plot_nodes() (in module gpmap.plot.ds) (in module gpmap.plot.mpl) plot_relaxation_times() (in module gpmap.plot.mpl)

plot_site_pairs_variance_components() (in module gpmap.plot.mpl) plot_sites_variance_components() (in module gpmap.plot.mpl) plot_visualization() (in module gpmap.plot.ds) (in module gpmap.plot.mpl) (in module gpmap.plot.ply) predict() (gpmap.inference.ConnectednessModelRegression method) (gpmap.inference.LocalEpistasisRegression method) (gpmap.inference.MinimumEpistasisInterpolator method) (gpmap.inference.SeqDEFT method) (gpmap.inference.VCregression method)

R

read_dataframe() (in module gpmap.utils)

read_edges() (in module gpmap.utils) remove_codon_incompatible_transitions() (gpmap.space.SequenceSpace method)

S

sample_prior() (gpmap.inference.ConnectednessModelRegression method) (gpmap.inference.LocalEpistasisRegression method) (gpmap.inference.MinimumEpistasisInterpolator method) (gpmap.inference.SeqDEFT method) (gpmap.inference.VCregression method) save() (gpmap.datasets.DataSet method) select_genotypes() (in module gpmap.genotypes) SeqDEFT (class in gpmap.inference)

SequenceSpace (class in gpmap.space) set_Ns() (gpmap.randwalk.WMWalk method) set_peaks() (gpmap.space.GridSpace method) simulate() (gpmap.inference.ConnectednessModelRegression method) (gpmap.inference.LocalEpistasisRegression method) (gpmap.inference.MinimumEpistasisInterpolator method) (gpmap.inference.SeqDEFT method) (gpmap.inference.VCregression method)

T

to_nucleotide_space() (gpmap.space.SequenceSpace method)

to_sequence_space() (gpmap.datasets.DataSet method)

V

VCregression (class in gpmap.inference)

W

WMWalk (class in gpmap.randwalk)

write_tables() (gpmap.randwalk.WMWalk method)