API

Preprocessing

pp.add_depth(tdata[, key_added, tree, copy])

Adds a depth attribute to the tree.

Tools

tl.ancestral_states(tdata, keys[, method, ...])	Reconstructs ancestral states for an attribute.
tl.autocorr(tdata[, keys, connect_key, ...])	Calculate autocorrelation statistic.
tl.clades(tdata[, depth, depth_key, clades, ...])	Marks clades in a tree.
tl.compare_distance(tdata[, dist_keys, ...])	Get pairwise observation distances.
tl.distance(tdata, key[, obs, metric, ...])	Computes distances between observations.
tl.neighbor_distance(tdata[, connect_key, ...])	Aggregates distance to neighboring observations.
tl.sort(tdata, key[, reverse, tree])	Reorders branches based on a node attribute.
tl.tree_distance(tdata[, depth_key, obs, ...])	Computes tree distances between observations.
tl.tree_neighbors(tdata[, n_neighbors, ...])	Identifies neighbors in the tree.
tl.n_extant(tdata[, depth_key, groupby, ...])	Counts extant branches over time.
tl.fitness(tdata[, depth_key, key_added, ...])	Estimates node fitness.
tl.partition_test(tdata, keys[, comparison, ...])	Test for differences between leaf partitions.
tl.expansion_test(tdata[, tree, ...])	Compute expansion p-values on a tree.

Plotting

pl.tree(tdata[, keys, nodes, polar, ...])	Plot a tree with branches, nodes, and annotations.
pl.branches(tdata[, polar, extend_branches, ...])	Plot the branches of a tree.
pl.nodes(tdata[, nodes, color, style, size, ...])	Plot the nodes of a tree.
pl.annotation(tdata[, keys, width, gap, ...])	Plot leaf annotations for a tree.
pl.n_extant(tdata[, color, data, key, ...])	Plot extant branches over time.

Getting elements

get.leaves(tdata[, tree])	Get the leaves of a tree.
get.root(tdata[, tree])	Get the root of a tree.
get.node_df(tdata[, tree])	Get tree node attributes as DataFrame.
get.edge_df(tdata[, tree])	Get tree edge attributes as DataFrame.
get.palette(tdata, key[, custom, cmap, ...])	Get color palette for a given key.

Datasets

datasets.packer19([cache_dir, tree])	C elegans lineage tree with cell state and position [PZH+19].
datasets.yang22([tumors, cache_dir])	Single-cell lineage tracing from KP mouse model [YJN+22].
datasets.koblan25([experiment, cache_dir])	Spatially resolved lineage tracing of 4T1 tumors [KYZ+25].