FeatureTrack Class

FeatureTrack

FeatureTrack(
    name: str,
    seg_name2range: Mapping[str, tuple[int, int]],
    *,
    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]]
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

label property

label: str

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

offset property

offset: int

Track offset

segments property

segments: list[FeatureSegment]

Segments

subtracks property

subtracks: list[FeatureSubTrack]

Subtracks

total_seg_size property

total_seg_size: int

Total segment size

spaces property

spaces: list[int]

Spaces between segments

max_track_total_seg_size property

max_track_total_seg_size: int

Max track total segment size (Use space calculation)

plot_size property

plot_size: int

Plot x size (total_seg_size + sum(spaces))

set_max_track_total_seg_size

set_max_track_total_seg_size(max_track_total_seg_size: int) -> None

Set max track total segment size

This method is expected to be called within the GenomeViz instance to update track status. General users should not use this method.

PARAMETER	DESCRIPTION
max_track_total_seg_size	Max track total segment size TYPE: int

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

add_text

add_text(
    x: float,
    text: str,
    *,
    target_seg: str | None = None,
    size: float = 15,
    vpos: VPos = "top",
    hpos: HPos = "left",
    ymargin: float = 0.2,
    rotation: float = 45,
    **kwargs
) -> None

Add text to track segment

PARAMETER	DESCRIPTION
x	Text x coordinate TYPE: float
text	Text content TYPE: str
target_seg	Target segment name. If None, first segment is selected. TYPE: str | None DEFAULT: None
size	Text size TYPE: float DEFAULT: 15
vpos	Vertical position (top|center|bottom) TYPE: str DEFAULT: 'top'
hpos	Horizontal position (left|center|right) TYPE: str DEFAULT: 'left'
ymargin	Y margin TYPE: float DEFAULT: 0.2
rotation	Text rotation TYPE: float DEFAULT: 45
**kwargs	segment.add_text() method keyword arguments (e.g. color="red", ...) TYPE: dict DEFAULT: {}

add_sublabel

add_sublabel(
    text: str | None = None,
    *,
    target_seg: str | None = None,
    size: float = 12,
    pos: str = "bottom-left",
    ymargin: float = 0.2,
    rotation: float = 0,
    **kwargs
) -> None

Add sublabel to corners of the track segment

PARAMETER	DESCRIPTION
text	Text content TYPE: str | None DEFAULT: None
target_seg	Target segment name. If None, first segment is selected. TYPE: str | None DEFAULT: None
size	Text size TYPE: float DEFAULT: 12
pos	Label position ([top|bottom]-[left|center|right]) TYPE: str DEFAULT: 'bottom-left'
ymargin	Y margin TYPE: float DEFAULT: 0.2
rotation	Text rotation TYPE: float DEFAULT: 0
**kwargs	segment.add_text() method keyword arguments (e.g. color="red", ...) TYPE: dict DEFAULT: {}

add_feature

add_feature(
    start: int,
    end: int,
    strand: int = 1,
    *,
    target_seg: str | None = None,
    plotstyle: PlotStyle = "arrow",
    arrow_shaft_ratio: float = 0.5,
    extra_tooltip: dict[str, str] | None = None,
    label: str = "",
    text_kws: dict[str, Any] | None = None,
    **kwargs
) -> None

Add feature

PARAMETER	DESCRIPTION
start	Start position TYPE: int
end	End position TYPE: int
strand	Feature strand TYPE: int DEFAULT: 1
target_seg	Target segment name. If None, first segment is selected. TYPE: str | None DEFAULT: None
plotstyle	Feature plot style (bigarrow|arrow|bigbox|box|bigrbox|rbox) TYPE: PlotStyle DEFAULT: 'arrow'
arrow_shaft_ratio	Arrow shaft size ratio TYPE: float DEFAULT: 0.5
extra_tooltip	Extra tooltip dict for html figure TYPE: dict[str, str] | None DEFAULT: None
label	Feature label TYPE: str DEFAULT: ''
text_kws	segment.add_text() method keyword arguments (e.g. dict(size=12, color="red", ...)) TYPE: dict[str, Any] | None DEFAULT: None
**kwargs	Patch properties (e.g. fc="red", lw=0.5, hatch="//", ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict DEFAULT: {}

add_features

add_features(
    features: SeqFeature | list[SeqFeature],
    *,
    target_seg: str | None = None,
    plotstyle: PlotStyle = "arrow",
    arrow_shaft_ratio: float = 0.5,
    label_type: str | None = None,
    label_handler: Callable[[str], str] | None = None,
    extra_tooltip: dict[str, str] | None = None,
    ignore_outside_range: bool = False,
    text_kws: dict[str, Any] | None = None,
    **kwargs
) -> None

Add features (BioPython SeqFeature)

PARAMETER	DESCRIPTION
features	BioPython SeqFeature or SeqFeature list TYPE: SeqFeature | list[SeqFeature]
target_seg	Target segment name. If None, first segment is selected. TYPE: str | None DEFAULT: None
plotstyle	Feature plot style (bigarrow|arrow|bigbox|box|bigrbox|rbox) TYPE: PlotStyle DEFAULT: 'arrow'
arrow_shaft_ratio	Arrow shaft size ratio TYPE: float DEFAULT: 0.5
label_type	Label type (e.g. gene,protein_id,product,etc...) TYPE: str | None DEFAULT: None
label_handler	Label handler function to customize label display. If None, set label handler to exclude labels containing hypothetical. TYPE: Callable[[str], str] | None DEFAULT: None
extra_tooltip	Extra tooltip dict for html figure TYPE: dict[str, str] | None DEFAULT: None
ignore_outside_range	If True and the feature position is outside the range of the track segment, ignore it without raising an error. TYPE: bool DEFAULT: False
text_kws	segment.add_text() method keyword arguments (e.g. dict(size=12, color="red", ...)) TYPE: dict[str, Any] | None DEFAULT: None
**kwargs	Patch properties (e.g. fc="red", lw=0.5, hatch="//", ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict DEFAULT: {}

add_exon_feature

add_exon_feature(
    locs: list[tuple[int, int]],
    strand: int = 1,
    *,
    target_seg: str | None = None,
    plotstyle: PlotStyle = "arrow",
    arrow_shaft_ratio: float = 0.5,
    label: str = "",
    patch_kws: dict[str, Any] | None = None,
    intron_patch_kws: dict[str, Any] | None = None,
    text_kws: dict[str, Any] | None = None
) -> None

Add exon feature

PARAMETER	DESCRIPTION
locs	Exon locations (e.g. [(0, 100), (200, 300), (350, 400)]) TYPE: list[tuple[int, int]]
strand	Feature strand TYPE: int DEFAULT: 1
target_seg	Target segment name. If None, first segment is selected. TYPE: str | None DEFAULT: None
plotstyle	Feature plot style (bigarrow|arrow|bigbox|box|bigrbox|rbox) TYPE: PlotStyle DEFAULT: 'arrow'
arrow_shaft_ratio	Arrow shaft size ratio TYPE: float DEFAULT: 0.5
label	Feature label TYPE: str DEFAULT: ''
patch_kws	Exon patch properties (e.g. dict(fc="red", lw=0.5, hatch="//", ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict[str, Any] | None DEFAULT: None
intron_patch_kws	Intron patch properties (e.g. dict(color="red", lw=2.0, ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict[str, Any] | None DEFAULT: None
text_kws	segment.add_text() method keyword arguments (e.g. dict(size=12, color="red", ...)) TYPE: dict[str, Any] | None DEFAULT: None

add_exon_features

add_exon_features(
    features: SeqFeature | list[SeqFeature],
    *,
    target_seg: str | None = None,
    plotstyle: PlotStyle = "arrow",
    arrow_shaft_ratio: float = 0.5,
    label_type: str | None = None,
    label_handler: Callable[[str], str] | None = None,
    extra_tooltip: dict[str, str] | None = None,
    ignore_outside_range: bool = False,
    patch_kws: dict[str, Any] | None = None,
    intron_patch_kws: dict[str, Any] | None = None,
    text_kws: dict[str, Any] | None = None
) -> None

Add exon features

PARAMETER	DESCRIPTION
features	BioPython SeqFeature or SeqFeature list TYPE: SeqFeature | list[SeqFeature]
target_seg	Target segment name. If None, first segment is selected. TYPE: str | None DEFAULT: None
plotstyle	Feature plot style (bigarrow|arrow|bigbox|box|bigrbox|rbox) TYPE: PlotStyle DEFAULT: 'arrow'
arrow_shaft_ratio	Arrow shaft size ratio TYPE: float DEFAULT: 0.5
label_type	Label type (e.g. gene,protein_id,product, etc...) TYPE: str | None DEFAULT: None
label_handler	Label handler function to customize label display. If None, set label handler to exclude labels containing hypothetical. TYPE: Callable[[str], str] | None DEFAULT: None
extra_tooltip	Extra tooltip dict for html figure TYPE: dict[str, str] | None DEFAULT: None
ignore_outside_range	If True and the feature position is outside the range of the track segment, ignore it without raising an error. TYPE: bool DEFAULT: False
patch_kws	Exon patch properties (e.g. dict(fc="red", lw=0.5, hatch="//", ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict[str, Any] | None DEFAULT: None
intron_patch_kws	Intron patch properties (e.g. dict(color="red", lw=2.0, ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict[str, Any] | None DEFAULT: None
text_kws	segment.add_text() method keyword arguments (e.g. dict(size=12, color="red", ...)) TYPE: dict[str, Any] | None DEFAULT: None

transform_coord

transform_coord(
    x: int | float | NDArray, *, target_seg: str | None = None
) -> int | float | NDArray[np.float64]

Transform segment-level coordinate to track-level coordinate

PARAMETER	DESCRIPTION
x	Segment-level coordinate(s) TYPE: int | float | NDArray
target_seg	Target segment name. If None, first segment is selected. TYPE: str | None DEFAULT: None

RETURNS	DESCRIPTION
transform_x	Track-level coordinate(s) TYPE: int | float | NDArray[float64]

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