Index

A

alignment_distance() (in module pyckmeans.distance) all_elbows (pyckmeans.knee.KneeLocator property) all_elbows_y (pyckmeans.knee.KneeLocator property)

all_norm_elbows (pyckmeans.knee.KneeLocator property) all_norm_elbows_y (pyckmeans.knee.KneeLocator property) AVAILABLE_METRICS (pyckmeans.CKmeans attribute) (pyckmeans.core.ckmeans.CKmeans attribute)

B

bic_kmeans() (in module pyckmeans.core.ckmeans)

C

CKmeans (class in pyckmeans) (class in pyckmeans.core.ckmeans) CKmeansResult (class in pyckmeans.core.ckmeans) condensed_form() (in module pyckmeans.ordering)

copy() (pyckmeans.core.ckmeans.CKmeansResult method) (pyckmeans.core.wecr.WECRResult method) (pyckmeans.io.nucleotide_alignment.NucleotideAlignment method) (pyckmeans.NucleotideAlignment method)

D

default() (pyckmeans.core.utils.NumpyEncoder method) (pyckmeans.ordination.utils.NumpyEncoder method) distance() (pyckmeans.io.nucleotide_alignment.NucleotideAlignment method) (pyckmeans.NucleotideAlignment method)

distance_order() (in module pyckmeans.ordering) DistanceMatrix (class in pyckmeans) (class in pyckmeans.distance) drop_invariant_sites() (pyckmeans.io.nucleotide_alignment.NucleotideAlignment method) (pyckmeans.NucleotideAlignment method)

E

elbow (pyckmeans.knee.KneeLocator property)

elbow_y (pyckmeans.knee.KneeLocator property) encode_nucleotides() (in module pyckmeans.io.c_interop)

F

find_knee() (pyckmeans.knee.KneeLocator method) fit() (pyckmeans.CKmeans method) (pyckmeans.core.ckmeans.CKmeans method) (pyckmeans.core.multickmeans.MultiCKMeans method) (pyckmeans.core.wecr.WECR method) (pyckmeans.MultiCKMeans method) (pyckmeans.WECR method) from_bp_seqio_records() (pyckmeans.io.nucleotide_alignment.NucleotideAlignment class method) (pyckmeans.NucleotideAlignment class method) from_csv() (pyckmeans.distance.DistanceMatrix static method) (pyckmeans.DistanceMatrix static method) from_dict() (pyckmeans.core.ckmeans.CKmeansResult class method) (pyckmeans.core.wecr.WECRResult class method) (pyckmeans.ordination.PCOAResult class method)

from_dir() (pyckmeans.core.ckmeans.CKmeansResult class method) (pyckmeans.core.wecr.WECRResult class method) (pyckmeans.ordination.PCOAResult class method) from_file() (pyckmeans.io.nucleotide_alignment.NucleotideAlignment class method) (pyckmeans.NucleotideAlignment class method) from_json() (pyckmeans.core.ckmeans.CKmeansResult class method) (pyckmeans.core.wecr.WECRResult class method) (pyckmeans.ordination.PCOAResult class method) from_json_str() (pyckmeans.core.ckmeans.CKmeansResult class method) (pyckmeans.core.wecr.WECRResult class method) (pyckmeans.ordination.PCOAResult class method) from_phylip() (pyckmeans.distance.DistanceMatrix static method) (pyckmeans.DistanceMatrix static method)

G

get_cl() (pyckmeans.core.wecr.WECRResult method)

get_cl_affinity_propagation() (pyckmeans.core.wecr.WECRResult method) get_vectors() (pyckmeans.ordination.PCOAResult method)

I

IncompatibleNamesError, [1], [2], [3] InvalidAlignmentCharacterError InvalidAlignmentFileExtensionError InvalidAlignmentFileFormatError InvalidClusteringMetric InvalidConstraintsError InvalidCorrectionTypeError InvalidDistanceTypeError InvalidFastaAlignmentError

InvalidFilterError InvalidKError InvalidLinkageType InvalidMatrixShapeError InvalidOutFormatError InvalidPCOAResultError InvalidPhylipAlignmentError InvalidPhylipMatrixError InvalidReorderMethod InvalidSeqIORecordsError

J

jc_distance() (in module pyckmeans.distance.c_interop)

K

k2p_distance() (in module pyckmeans.distance.c_interop)

KneeLocator (class in pyckmeans.knee)

M

module pyckmeans pyckmeans.core pyckmeans.core.ckmeans pyckmeans.core.multickmeans pyckmeans.core.utils pyckmeans.core.wecr pyckmeans.distance pyckmeans.distance.c_interop pyckmeans.io pyckmeans.io.c_interop pyckmeans.io.csv pyckmeans.io.fasta pyckmeans.io.nucleotide_alignment pyckmeans.io.phylip pyckmeans.knee pyckmeans.ordering pyckmeans.ordination pyckmeans.ordination.utils pyckmeans.utils pyckmeans.utils.plotting pyckmeans.utils.progressbar

MultiCKMeans (class in pyckmeans) (class in pyckmeans.core.multickmeans) MultiCKMeansProgressBars (class in pyckmeans.utils.progressbar) MultiCKmeansResult (class in pyckmeans.core.multickmeans)

N

NegativeEigenvaluesCorrectionError NegativeEigenvaluesWarning norm_elbow (pyckmeans.knee.KneeLocator property) norm_elbow_y (pyckmeans.knee.KneeLocator property)

NucleotideAlignment (class in pyckmeans) (class in pyckmeans.io.nucleotide_alignment) NumpyEncoder (class in pyckmeans.core.utils) (class in pyckmeans.ordination.utils)

O

order() (pyckmeans.core.ckmeans.CKmeansResult method) (pyckmeans.core.multickmeans.MultiCKmeansResult method) (pyckmeans.core.wecr.WECRResult method)

P

p_distance() (in module pyckmeans.distance.c_interop) pcoa() (in module pyckmeans) (in module pyckmeans.ordination) PCOAResult (class in pyckmeans.ordination) plot() (pyckmeans.core.ckmeans.CKmeansResult method) (pyckmeans.core.wecr.WECRResult method) plot_affinity_propagation() (pyckmeans.core.wecr.WECRResult method) plot_ckmeans_result() (in module pyckmeans.utils.plotting) plot_cmatrix() (in module pyckmeans.utils.plotting) plot_metrics() (pyckmeans.core.multickmeans.MultiCKmeansResult method) (pyckmeans.core.wecr.WECRResult method) plot_multickmeans_metrics() (in module pyckmeans.utils.plotting) plot_wecr_result() (in module pyckmeans.utils.plotting) plot_wecr_result_metrics() (in module pyckmeans.utils.plotting) predict() (pyckmeans.CKmeans method) (pyckmeans.core.ckmeans.CKmeans method) (pyckmeans.core.multickmeans.MultiCKMeans method) (pyckmeans.core.wecr.WECR method) (pyckmeans.MultiCKMeans method) (pyckmeans.WECR method) pyckmeans module pyckmeans.core module pyckmeans.core.ckmeans module pyckmeans.core.multickmeans module pyckmeans.core.utils module pyckmeans.core.wecr module

pyckmeans.distance module pyckmeans.distance.c_interop module pyckmeans.io module pyckmeans.io.c_interop module pyckmeans.io.csv module pyckmeans.io.fasta module pyckmeans.io.nucleotide_alignment module pyckmeans.io.phylip module pyckmeans.knee module pyckmeans.ordering module pyckmeans.ordination module pyckmeans.ordination.utils module pyckmeans.utils module pyckmeans.utils.plotting module pyckmeans.utils.progressbar module

R

read_alignment() (in module pyckmeans.io.nucleotide_alignment) read_csv_distmat() (in module pyckmeans.io.csv) read_fasta_alignment() (in module pyckmeans.io.fasta) read_phylip_alignment() (in module pyckmeans.io.phylip) read_phylip_distmat() (in module pyckmeans.io.phylip) recalculate_cluster_memberships() (pyckmeans.core.ckmeans.CKmeansResult method) (pyckmeans.core.wecr.WECRResult method)

rel_extrema_idcs() (in module pyckmeans.knee) reorder() (pyckmeans.core.ckmeans.CKmeansResult method) (pyckmeans.core.multickmeans.MultiCKmeansResult method) (pyckmeans.core.wecr.WECRResult method) reorder_distance() (in module pyckmeans.ordering) reorder_linkage_gw() (in module pyckmeans.ordering)

S

save_km_cls() (pyckmeans.core.ckmeans.CKmeansResult method) (pyckmeans.core.wecr.WECRResult method) shape (pyckmeans.distance.DistanceMatrix property) (pyckmeans.DistanceMatrix property) (pyckmeans.io.nucleotide_alignment.NucleotideAlignment property) (pyckmeans.NucleotideAlignment property)

sort() (pyckmeans.core.ckmeans.CKmeansResult method) (pyckmeans.core.multickmeans.MultiCKmeansResult method) (pyckmeans.core.wecr.WECRResult method)

T

to_csv() (pyckmeans.distance.DistanceMatrix method) (pyckmeans.DistanceMatrix method) to_dict() (pyckmeans.core.ckmeans.CKmeansResult method) (pyckmeans.core.wecr.WECRResult method) (pyckmeans.ordination.PCOAResult method) to_dir() (pyckmeans.core.ckmeans.CKmeansResult method) (pyckmeans.core.wecr.WECRResult method) (pyckmeans.ordination.PCOAResult method)

to_json() (pyckmeans.core.ckmeans.CKmeansResult method) (pyckmeans.core.wecr.WECRResult method) (pyckmeans.ordination.PCOAResult method) to_phylip() (pyckmeans.distance.DistanceMatrix method) (pyckmeans.DistanceMatrix method) transform_y() (pyckmeans.knee.KneeLocator static method)

U

update() (pyckmeans.utils.progressbar.MultiCKMeansProgressBars method)

W

WECR (class in pyckmeans) (class in pyckmeans.core.wecr) WECRResult (class in pyckmeans.core.wecr)

write_csv_distmat() (in module pyckmeans.io.csv) write_phylip_distmat() (in module pyckmeans.io.phylip) wss() (in module pyckmeans.core.ckmeans)