FeatureTrack Class

FeatureTrack

FeatureTrack(
    name: str,
    seg_name2range: Mapping[str, tuple[int, int]],
    *,
    gv: GenomeViz,
    ratio: float = 1.0,
    space: float | list[float] = 0.01,
    offset: int | TrackAlignType = "left",
    labelsize: float = 20,
    labelmargin: float = 0.01,
    align_label: bool = True,
    label_kws: dict[str, Any] | None = None,
    line_kws: dict[str, Any] | None = None
)

Bases: Track

Feature Track Class

PARAMETER	DESCRIPTION
name	Track name TYPE: str
seg_name2range	Segment name & range dict TYPE: Mapping[str, tuple[int, int]]
gv	Parent GenomeViz instance TYPE: GenomeViz
ratio	Track size ratio TYPE: float DEFAULT: 1.0
space	Space ratio between segments TYPE: float | list[float] DEFAULT: 0.01
offset	Offset int value or TrackAlignType (left|center|right) TYPE: int | TrackAlignType DEFAULT: 'left'
labelsize	Track label size TYPE: float DEFAULT: 20
labelmargin	Track label margin TYPE: float DEFAULT: 0.01
align_label	If True, align track label to the most left position. If False, set track label to first segment start position. TYPE: bool DEFAULT: True
label_kws	Text properties (e.g. dict(size=25, color="red", ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.text.html TYPE: dict[str, Any] | None DEFAULT: None
line_kws	Axes.plot properties (e.g. dict(color="grey", lw=0.5, ls="--", ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.plot.html TYPE: dict[str, Any] | None DEFAULT: None

gv property

gv: GenomeViz

Parent GenomeViz

label property

label: str

Track label (By default, track.label = track.name)

raw_offset property

raw_offset: int | TrackAlignType

Raw offset value

offset property

offset: int

Track offset

segments property

segments: list[FeatureSegment]

Segments

subtracks property

subtracks: list[FeatureSubTrack]

Subtracks

size property

size: int

Total segment size

spaces property

spaces: list[int]

Spaces between segments

plot_size property

plot_size: int

Plot size (track size + sum(spaces))

set_label

set_label(label: str) -> None

Set track label (By default, track.label = track.name)

PARAMETER	DESCRIPTION
label	Track label TYPE: str

set_segment_sep

set_segment_sep(
    sep: bool | list[bool] = True,
    *,
    symbol: str = "//",
    size: float = 20,
    color: str = "grey",
    **kwargs
) -> None

Set segment separator symbol text

PARAMETER	DESCRIPTION
sep	If True, insert separator text between all segments. If list[bool], insert separator text between segments where True. TYPE: bool | list[bool] DEFAULT: True
symbol	Separator symbol text TYPE: str DEFAULT: '//'
size	Separator symbol size TYPE: float DEFAULT: 20
color	Separator symbol color TYPE: str DEFAULT: 'grey'
**kwargs	Text properties https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.text.html TYPE: dict DEFAULT: {}

add_subtrack

add_subtrack(
    name: str | None = None, *, ratio: float = 1.0, ylim: tuple[int, int] = (0, 100)
) -> FeatureSubTrack

Add subtrack for user-defined plot axes

PARAMETER	DESCRIPTION
name	Track name TYPE: str DEFAULT: None
ratio	Subtrack size ratio to feature track TYPE: float DEFAULT: 1.0
ylim	Axes ylim TYPE: tuple[int, int] DEFAULT: (0, 100)

RETURNS	DESCRIPTION
subtrack	Subtrack TYPE: FeatureSubTrack

get_subtrack

get_subtrack(name: str | None = None) -> FeatureSubTrack

Get subtrack by name

If no subtrack found, raise error.

PARAMETER	DESCRIPTION
name	Target subtrack name. If None, first subtrack is returned. TYPE: str | None DEFAULT: None

RETURNS	DESCRIPTION
subtrack	Target subtrack TYPE: FeatureSubTrack

get_segment

get_segment(name: str | None = None) -> FeatureSegment

Get segment by name

PARAMETER	DESCRIPTION
name	Target segment name. If None, first segment is returned. TYPE: str | None DEFAULT: None

RETURNS	DESCRIPTION
segment	Target segment TYPE: FeatureSegment

plot_all

plot_all(fast_render: bool = True) -> None

Plot all objects (Expected to be called in gv.plotfig())

1. Plot track label
2. Plot segment lines
3. Plot segment separator
4. Plot features
5. Plot texts

PARAMETER	DESCRIPTION
fast_render	Enable fast rendering using PatchCollection plot style. TYPE: bool DEFAULT: True