Index

_

__init__() (picasso.build_tree.Picasso method) (picasso.CloneTree.CloneTree method)

A

aggregate_clones() (picasso.CloneTree.CloneTree method)

C

calc_mode() (picasso.CloneTree.CloneTree static method) calc_mode_freq() (picasso.CloneTree.CloneTree static method) character_matrix (picasso.CloneTree.CloneTree attribute) clone_assignments (picasso.CloneTree.CloneTree attribute)

clone_profiles (picasso.CloneTree.CloneTree attribute), [1] clone_profiles_certainty (picasso.CloneTree.CloneTree attribute), [1] clones (picasso.build_tree.Picasso attribute), [1] CloneTree (class in picasso.CloneTree) create_tree_from_paths() (picasso.build_tree.Picasso static method)

D

dataframe_to_itol_colorstrip() (in module picasso.itol_utils) dataframe_to_itol_heatmap() (in module picasso.itol_utils)

dataframe_to_itol_stackedbar() (in module picasso.itol_utils) depth (picasso.build_tree.Picasso attribute), [1]

E

encode_cnvs_as_ternary() (in module picasso.utils)

F

fit() (picasso.build_tree.Picasso method)

G

get_clone_assignments() (picasso.build_tree.Picasso method) get_clone_phylogeny() (picasso.CloneTree.CloneTree method) get_modal_clone_profiles() (picasso.CloneTree.CloneTree method)

get_most_ancestral_clone() (picasso.CloneTree.CloneTree method) get_phylogeny() (picasso.build_tree.Picasso method) get_sample_phylogeny() (picasso.CloneTree.CloneTree method)

I

infer_evolutionary_changes() (picasso.CloneTree.CloneTree method)

L

load_data() (in module picasso.utils)

M

metadata (picasso.CloneTree.CloneTree attribute) module picasso.build_tree picasso.CloneTree picasso.itol_utils picasso.utils

P

Picasso (class in picasso.build_tree) picasso.build_tree module picasso.CloneTree module

picasso.itol_utils module picasso.utils module plot_alterations() (picasso.CloneTree.CloneTree method) plot_clone_sizes() (picasso.CloneTree.CloneTree method)

R

rgba_to_hex() (in module picasso.itol_utils) (picasso.CloneTree.CloneTree static method)

root_tree() (picasso.CloneTree.CloneTree method)

S

split_clone() (picasso.build_tree.Picasso method)

step() (picasso.build_tree.Picasso method)

T

terminal_clones (picasso.build_tree.Picasso attribute), [1]