Index

A

acdeath() (System method), [1] acrenewal() (System method), [1] add_reaction() (System method), [1], [2], [3], [4], [5]

Advantageous (System attribute), [1] advmut() (System method), [1] args (LogLike attribute), [1], [2], [3], [4], [5]

B

bg_internal (Externals_background attribute) branchlen_fly() (in module scPhyloX.tools) (in module scPhyloX.tools.data_factory) BranchLength (class in scPhyloX.estimation.mutation_rate)

bt() (in module scPhyloX.estimation) (in module scPhyloX.estimation.tissue) (in module scPhyloX.simulation), [1] (in module scPhyloX.simulation.haematopoiesis) (in module scPhyloX.simulation.tissue)

C

Cell (class in scPhyloX.simulation), [1], [2] (class in scPhyloX.simulation.haematopoiesis) (class in scPhyloX.simulation.tissue) (class in scPhyloX.simulation.tumor) cell_num (System attribute), [1], [2], [3], [4], [5] cell_number_calc() (in module scPhyloX.tools) (in module scPhyloX.tools.data_factory) cellid (Cell attribute), [1], [2], [3], [4], [5] cellnumber() (in module scPhyloX.estimation), [1], [2] (in module scPhyloX.estimation.haematopoiesis) (in module scPhyloX.estimation.tissue) (in module scPhyloX.estimation.tumor) (in module scPhyloX.simulation) (in module scPhyloX.simulation.tissue)

cellnumber_ac() (in module scPhyloX.estimation) (in module scPhyloX.estimation.tumor) cellnumber_nc() (in module scPhyloX.estimation) (in module scPhyloX.estimation.tumor) celltype (Cell attribute), [1], [2], [3], [4], [5] clade_angles() (in module scPhyloX.tools.PhyloCircular.tree) clade_depth() (in module scPhyloX.tools.PhyloCircular.tree) cmap (Externals_heatmap attribute) colless_index() (in module scPhyloX.tools) (in module scPhyloX.tools.utils) colless_index_corrected() (in module scPhyloX.tools) (in module scPhyloX.tools.utils) combine() (Reaction method), [1], [2], [3], [4], [5] corr_plot() (in module scPhyloX.tools) (in module scPhyloX.tools.utils)

D

data (Externals_heatmap attribute) (Externals_labels attribute) (Externals_patchs attribute) (LogLike attribute), [1], [2], [3], [4], [5], [6] delta (BranchLength attribute) depth (Externals property) Diffcells (System attribute), [1], [2], [3] diffdeath() (System method), [1], [2], [3] diffrenewal() (System method), [1] draw() (Externals method) (Externals_background method) (Externals_heatmap method) (Externals_labels method) (Externals_patchs method)

draw_baseline() (in module scPhyloX.tools.PhyloCircular.tree) draw_clade() (in module scPhyloX.tools.PhyloCircular.tree) draw_depthline() (in module scPhyloX.tools.PhyloCircular.tree) draw_internal_wedge() (in module scPhyloX.tools.PhyloCircular.tree) draw_label() (in module scPhyloX.tools.PhyloCircular.tree) draw_patch() (in module scPhyloX.tools.PhyloCircular.tree)

E

estimate() (GenerationEst method) evolute() (System method), [1], [2], [3], [4], [5] ext_cid() (in module scPhyloX.tools) (in module scPhyloX.tools.utils) ext_gen() (in module scPhyloX.tools) (in module scPhyloX.tools.utils)

Externals (class in scPhyloX.tools.PhyloCircular.externals) Externals_background (class in scPhyloX.tools.PhyloCircular.externals) Externals_heatmap (class in scPhyloX.tools.PhyloCircular.externals) Externals_labels (class in scPhyloX.tools.PhyloCircular.externals) Externals_patchs (class in scPhyloX.tools.PhyloCircular.externals)

F

from_internal() (Externals_background method)

fsize() (Externals method)

G

gen (Cell attribute), [1], [2], [3], [4], [5] generation (GenerationEst attribute) generation_map() (GenerationEst method) GenerationEst (class in scPhyloX.estimation.mutation_rate) get_branchlen() (in module scPhyloX.tools) (in module scPhyloX.tools.data_factory)

get_mutnum() (in module scPhyloX.tools) (in module scPhyloX.tools.data_factory) get_wedge_angles() (Externals_background static method) global_id (System attribute), [1], [2], [3], [4], [5]

I

index (Reaction attribute), [1], [2], [3], [4], [5] initial_depth (Externals attribute) initialize() (Cell method), [1], [2], [3], [4], [5]

internal_clades_angles() (in module scPhyloX.tools.PhyloCircular.tree) is_alive (Cell attribute), [1], [2], [3], [4], [5] itypes (LogLike attribute), [1], [2], [3], [4], [5], [6]

L

label (Externals_heatmap attribute) likelihood (LogLike attribute), [1], [2], [3], [4], [5], [6] likelihood() (BranchLength method) lineage_info (System attribute), [1], [2], [3], [4], [5] log_cells (System attribute), [1], [2], [3], [4], [5] LogLike (class in scPhyloX.estimation), [1], [2] (class in scPhyloX.estimation.haematopoiesis) (class in scPhyloX.estimation.mutation_rate) (class in scPhyloX.estimation.tissue) (class in scPhyloX.estimation.tumor)

lr_dist (GenerationEst attribute) lseq (Cell attribute), [1], [2], [3], [4], [5]

M

make_background() (Externals_background method) max_t (System attribute), [1], [2], [3], [4], [5] mcmc_inference() (in module scPhyloX.estimation), [1], [2] (in module scPhyloX.estimation.haematopoiesis) (in module scPhyloX.estimation.tissue) (in module scPhyloX.estimation.tumor) module scPhyloX scPhyloX.estimation scPhyloX.estimation.haematopoiesis scPhyloX.estimation.mutation_rate scPhyloX.estimation.tissue scPhyloX.estimation.tumor scPhyloX.simulation scPhyloX.simulation.haematopoiesis scPhyloX.simulation.tissue scPhyloX.simulation.tumor scPhyloX.tools scPhyloX.tools.data_factory scPhyloX.tools.PhyloCircular scPhyloX.tools.PhyloCircular.externals scPhyloX.tools.PhyloCircular.tree scPhyloX.tools.utils

mu (BranchLength attribute) (GenerationEst attribute) mut_num (System attribute), [1], [2], [3], [4], [5] mut_num_AC (System attribute), [1] mut_num_DC (System attribute), [1], [2], [3] mut_num_NC (System attribute), [1] mut_num_SC (System attribute), [1], [2], [3] mut_rate (System attribute), [1], [2], [3], [4], [5] mut_time (System attribute), [1], [2], [3], [4], [5] mutate() (System method), [1], [2], [3], [4], [5] mutation_rate_de() (in module scPhyloX.estimation.mutation_rate) mutation_rate_mcmc() (in module scPhyloX.estimation.mutation_rate) mutnum_fly() (in module scPhyloX.tools) (in module scPhyloX.tools.data_factory) my_loglike() (in module scPhyloX.estimation), [1], [2] (in module scPhyloX.estimation.haematopoiesis) (in module scPhyloX.estimation.mutation_rate) (in module scPhyloX.estimation.tissue) (in module scPhyloX.estimation.tumor)

N

nc_sol() (in module scPhyloX.estimation) (in module scPhyloX.estimation.tumor) ncdeath() (System method), [1] ncrenewal() (System method), [1] ncyc() (in module scPhyloX.estimation) (in module scPhyloX.estimation.tissue) Neutral (System attribute), [1] nnc() (in module scPhyloX.estimation) (in module scPhyloX.estimation.tissue)

norm (Externals_heatmap attribute) nstem_num() (in module scPhyloX.estimation) (in module scPhyloX.estimation.haematopoiesis) num_diff (Reaction attribute), [1], [2], [3], [4], [5] num_elements (System attribute), [1], [2], [3], [4], [5] num_lefts (Reaction attribute), [1], [2], [3], [4], [5] num_rights (Reaction attribute), [1], [2], [3], [4], [5]

O

offset (Externals attribute)

otypes (LogLike attribute), [1], [2], [3], [4], [5], [6]

P

p_xi() (in module scPhyloX.estimation), [1], [2] (in module scPhyloX.estimation.haematopoiesis) (in module scPhyloX.estimation.tissue) (in module scPhyloX.estimation.tumor) pad (Externals attribute) para_inference_DE() (in module scPhyloX.estimation), [1], [2] (in module scPhyloX.estimation.haematopoiesis) (in module scPhyloX.estimation.tissue) (in module scPhyloX.estimation.tumor)

perform() (LogLike method), [1], [2], [3], [4], [5], [6] polar_plot() (in module scPhyloX.tools) (in module scPhyloX.tools.PhyloCircular) (in module scPhyloX.tools.PhyloCircular.tree) population_size (in module scPhyloX.tools) (in module scPhyloX.tools.data_factory) prob() (BranchLength method) propensity() (Reaction method), [1], [2], [3], [4], [5]

R

rate (Reaction attribute), [1], [2], [3], [4], [5] Reaction (class in scPhyloX.simulation), [1], [2] (class in scPhyloX.simulation.haematopoiesis) (class in scPhyloX.simulation.tissue) (class in scPhyloX.simulation.tumor)

reactions (System attribute), [1], [2], [3], [4], [5] reconstruct() (in module scPhyloX.tools) (in module scPhyloX.tools.utils) row_order (Externals_heatmap attribute)

S

s1 (GenerationEst attribute) scPhyloX module scPhyloX.estimation module scPhyloX.estimation.haematopoiesis module scPhyloX.estimation.mutation_rate module scPhyloX.estimation.tissue module scPhyloX.estimation.tumor module scPhyloX.simulation module scPhyloX.simulation.haematopoiesis module scPhyloX.simulation.tissue module scPhyloX.simulation.tumor module scPhyloX.tools module scPhyloX.tools.data_factory module scPhyloX.tools.PhyloCircular module

scPhyloX.tools.PhyloCircular.externals module scPhyloX.tools.PhyloCircular.tree module scPhyloX.tools.utils module seq (Cell attribute), [1], [2], [3], [4], [5] set_initial_depth() (Externals method) set_size() (Externals method) simulation() (in module scPhyloX.simulation), [1], [2] (in module scPhyloX.simulation.haematopoiesis) (in module scPhyloX.simulation.tissue) (in module scPhyloX.simulation.tumor) size (Externals attribute) start_t (System attribute), [1], [2], [3], [4], [5] stem_num() (in module scPhyloX.estimation) (in module scPhyloX.estimation.haematopoiesis) stemasym() (System method), [1], [2], [3] Stemcells (System attribute), [1], [2], [3] stemdiff() (System method), [1], [2], [3] stemrenewal() (System method), [1], [2], [3] System (class in scPhyloX.simulation), [1], [2] (class in scPhyloX.simulation.haematopoiesis) (class in scPhyloX.simulation.tissue) (class in scPhyloX.simulation.tumor)

T

tumor_data (in module scPhyloX.tools) (in module scPhyloX.tools.data_factory)

tumor_size (in module scPhyloX.tools) (in module scPhyloX.tools.data_factory)

U

u1 (GenerationEst attribute)

W

wedges_kwargs (Externals_heatmap attribute)