TreeViz Class

TreeViz

TreeViz(
    tree_data: str | Path | Tree,
    *,
    format: str = "newick",
    outer: bool = True,
    align_leaf_label: bool = True,
    ignore_branch_length: bool = False,
    leaf_label_size: float = 12,
    leaf_label_rmargin: float = 2.0,
    reverse: bool = False,
    ladderize: bool = False,
    line_kws: dict[str, Any] | None = None,
    align_line_kws: dict[str, Any] | None = None,
    label_formatter: Callable[[str], str] | None = None,
    track: Track
)

Phylogenetic Tree Visualization Class

Interface for changing tree properties and adding tree annotations in a track

PARAMETER	DESCRIPTION
tree_data	Tree data (File|File URL|Tree Object|Tree String) TYPE: str | Path | Tree
format	Tree format (newick|phyloxml|nexus|nexml|cdao) TYPE: str DEFAULT: 'newick'
outer	If True, plot tree on outer side. If False, plot tree on inner side. TYPE: bool DEFAULT: True
align_leaf_label	If True, align leaf label. TYPE: bool DEFAULT: True
ignore_branch_length	If True, ignore branch length for plotting tree. TYPE: bool DEFAULT: False
leaf_label_size	Leaf label size TYPE: float DEFAULT: 12
leaf_label_rmargin	Leaf label radius margin TYPE: float DEFAULT: 2.0
reverse	If True, reverse tree TYPE: bool DEFAULT: False
ladderize	If True, ladderize tree TYPE: bool DEFAULT: False
line_kws	Patch properties (e.g. dict(color="red", lw=1, ls="dashed", ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict[str, Any] | None DEFAULT: None
align_line_kws	Patch properties (e.g. dict(lw=1, ls="dotted", alpha=1.0, ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict[str, Any] | None DEFAULT: None
label_formatter	User-defined label text format function to change plot label text content. For example, if you want to change underscore of the label to space, set lambda t: t.replace("_", " "). TYPE: Callable[[str], str] | None DEFAULT: None
track	Track for tree visualization TYPE: Track

track property

track: Track

Track for tree visualization

tree property

tree: Tree

BioPython's Tree Object

leaf_num cached property

leaf_num: int

Leaf number

leaf_labels cached property

leaf_labels: list[str]

Leaf labels

innode_labels cached property

innode_labels: list[str]

Internal node labels

all_node_labels cached property

all_node_labels: list[str]

All node labels

max_tree_depth cached property

max_tree_depth: float

Max tree depth (root -> leaf max branch length)

name2xr cached property

name2xr: dict[str, tuple[float, float]]

Tree node name & node xr coordinate dict

name2rect cached property

name2rect: dict[str, Rectangle]

Tree node name & rectangle dict

load_tree staticmethod

load_tree(data: str | Path | Tree, format: str) -> Tree

Load tree data

PARAMETER	DESCRIPTION
data	Tree data TYPE: str | Path | Tree
format	Tree format TYPE: str

RETURNS	DESCRIPTION
tree	Tree object TYPE: Tree

search_target_node_name

search_target_node_name(query: str | list[str] | tuple[str]) -> str

Search target node name from query

PARAMETER	DESCRIPTION
query	Search query node name(s). If multiple node names are set, MRCA(Most Recent Common Ancester) node is set. TYPE: str | list[str] | tuple[str]

RETURNS	DESCRIPTION
target_node_name	Target node name TYPE: str

get_target_xlim

get_target_xlim(query: str | list[str] | tuple[str]) -> tuple[float, float]

Get target node x limit by query

PARAMETER	DESCRIPTION
query	Search query node name(s) for getting x limit. If multiple node names are set, MRCA(Most Recent Common Ancester) node is set. TYPE: str | list[str] | tuple[str]

RETURNS	DESCRIPTION
xlim	X limit tuple TYPE: tuple[float, float]

show_confidence

show_confidence(
    *,
    size: float = 8,
    orientation: str = "vertical",
    label_formatter: Callable[[float], str] | None = None,
    **kwargs
) -> None

Show confidence value on each internal node of the phylogenetic tree

PARAMETER	DESCRIPTION
size	Text size TYPE: float DEFAULT: 8
orientation	Text orientation (horizontal or vertical) TYPE: str DEFAULT: 'vertical'
label_formatter	User-defined function for label format. TYPE: Callable[[float], str] | None DEFAULT: None
**kwargs	Text properties (e.g. color="red", ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.text.html TYPE: dict DEFAULT: {}

highlight

highlight(
    query: str | list[str] | tuple[str], *, color: str, alpha: float = 0.5, **kwargs
) -> None

Plot highlight for target node

PARAMETER	DESCRIPTION
query	Search query node name(s) for highlight. If multiple node names are set, MRCA(Most Recent Common Ancester) node is set. TYPE: str | list[str] | tuple[str]
color	Highlight color TYPE: str
alpha	Highlight color alpha(transparancy) value TYPE: float DEFAULT: 0.5
**kwargs	Patch properties (e.g. ec="blue", lw=1.0, ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict DEFAULT: {}

marker

marker(
    query: str | list[str] | tuple[str],
    *,
    marker: str = "o",
    size: int = 6,
    descendent: bool = True,
    **kwargs
) -> None

Plot marker on target node(s)

PARAMETER	DESCRIPTION
query	Search query node name(s) for plotting marker. If multiple node names are set, MRCA(Most Recent Common Ancester) node is set. TYPE: str | list[str] | tuple[str]
marker	Marker type (e.g. o, s, D, P, *, x, d, ^, v, <, >) https://matplotlib.org/stable/api/markers_api.html TYPE: str DEFAULT: 'o'
size	Marker size TYPE: int DEFAULT: 6
descendent	If True, plot markers on target node's descendent as well. TYPE: bool DEFAULT: True
**kwargs	Axes.scatter properties (e.g. fc="lime", ec="black", lw=0.5, ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.scatter.html TYPE: dict DEFAULT: {}

set_node_label_props

set_node_label_props(target_node_label: str, **kwargs) -> None

Set tree node label properties

PARAMETER	DESCRIPTION
target_node_label	Target node label name TYPE: str
kwargs	Text properties (e.g. color="red", size=15, ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.text.html TYPE: dict DEFAULT: {}

set_node_line_props

set_node_line_props(
    query: str | list[str] | tuple[str],
    *,
    descendent: bool = True,
    apply_label_color: bool = False,
    **kwargs
) -> None

Set tree node line properties

PARAMETER	DESCRIPTION
query	Search query node name(s) for coloring tree node line. If multiple node names are set, MRCA(Most Recent Common Ancester) node is set. TYPE: str | list[str] | tuple[str]
descendent	If True, set properties on target node's descendent as well. TYPE: bool DEFAULT: True
apply_label_color	If True & descendent=True & kwargs contain color keyword, apply node line color to node label color as well. TYPE: bool DEFAULT: False
**kwargs	Patch properties (e.g. color="blue", lw=2.0, ls="dashed", ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.plot.html TYPE: dict DEFAULT: {}