FeatureSegment Class

FeatureSegment

FeatureSegment(name: str, start: int, end: int, feature_track: FeatureTrack)

Feature Segment Class

PARAMETER	DESCRIPTION
name	Segment name TYPE: str
start	Segment start position TYPE: int
end	Segment end position TYPE: int
feature_track	Parent feature track TYPE: FeatureTrack

name property

name: str

Segment name

start property

start: int

Segment start position

end property

end: int

Segment end position

range property

range: tuple[int, int]

Segment (start, end) range

size property

size: int

Segment size

feature_track property

feature_track: FeatureTrack

Parent feature track

track_start property

track_start: int

Segment start position in track

track_end property

track_end: int

Segment end position in track

gid2feature_dict property

gid2feature_dict: dict[str, dict[str, Any]]

gid & feature dict (Sort by start coordinate)

transform_features property

transform_features: list[SeqFeature]

Coordinate transformed features

Segment-level coordinate is transformed to track-level coordinate.

transform_exon_features property

transform_exon_features: list[SeqFeature]

Coordinate transformed exon features

Segment-level coordinate is transformed to track-level coordinate.

transform_ax_method2kws_list property

transform_ax_method2kws_list: dict[AXES_METHOD, list[dict[str, Any]]]

Coordinate transformed axes method & keywords list

is_within_range

is_within_range(pos: int | tuple[int, int]) -> bool

Check target pos is within segment range

transform_coord

transform_coord(x: int) -> int

transform_coord(x: float) -> float

transform_coord(x: NDArray) -> NDArray[np.float64]

transform_coord(x: int | float | NDArray) -> int | float | NDArray[np.float64]

Transform segment-level coordinate to track-level coordinate

PARAMETER	DESCRIPTION
x	Segment level coordinate(s) TYPE: int | float | NDArray

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

add_text

add_text(
    x: float,
    text: str,
    *,
    size: float = 12,
    vpos: VPos = "top",
    hpos: HPos = "left",
    ymargin: float = 0.2,
    rotation: float = 45,
    **kwargs
) -> None

Add text

PARAMETER	DESCRIPTION
x	Text x coordinate TYPE: float
text	Text content TYPE: str
size	Text size TYPE: float DEFAULT: 12
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	Text properties (e.g. color="red", ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.text.html TYPE: dict DEFAULT: {}

add_annotation

add_annotation(
    x: float,
    text: str,
    *,
    y: tuple[float, float] = (1.0, 1.5),
    size: float = 12,
    line_kws: dict[str, Any] | None = None,
    **kwargs
) -> None

Add annotation

PARAMETER	DESCRIPTION
x	Text x coordinate TYPE: float
text	Text content TYPE: str
y	Annotation line y coordinate tuple TYPE: tuple[float, float] DEFAULT: (1.0, 1.5)
size	Text size TYPE: float DEFAULT: 12
line_kws	FancyArrowPatch properties (e.g. color="red", ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.FancyArrowPatch.html TYPE: dict[str, Any] | None DEFAULT: None
**kwargs	Text properties (e.g. color="red", ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.annotate.html TYPE: dict DEFAULT: {}

add_sublabel

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

Add sublabel

PARAMETER	DESCRIPTION
text	Text content. If None, {start:,} - {end:,} bp label is set. 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,
    *,
    plotstyle: PlotStyle = "arrow",
    arrow_shaft_ratio: float = 0.5,
    extra_tooltip: dict[str, str] | None = None,
    annotation: bool = False,
    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
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
annotation	If True, add annotation instead of text TYPE: bool DEFAULT: False
label	Feature label text TYPE: str DEFAULT: ''
text_kws	segment.add_text() or segment.add_annotation() 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],
    *,
    plotstyle: PlotStyle = "arrow",
    arrow_shaft_ratio: float = 0.5,
    label_type: str | None = None,
    label_handler: Callable[[str], str] | None = None,
    annotation: bool = False,
    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]
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
annotation	If True, add annotation instead of text TYPE: bool DEFAULT: False
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() or segment.add_annotation() method keyword arguments (e.g. dict(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,
    *,
    plotstyle: PlotStyle = "arrow",
    arrow_shaft_ratio: float = 0.5,
    label: str = "",
    annotation: 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 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
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: ''
annotation	If True, add annotation instead of text 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() or segment.add_annotation() 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],
    *,
    plotstyle: PlotStyle = "arrow",
    arrow_shaft_ratio: float = 0.5,
    label_type: str | None = None,
    label_handler: Callable[[str], str] | None = None,
    annotation: bool = False,
    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 (BioPython SeqFeature)

PARAMETER	DESCRIPTION
features	BioPython SeqFeature or SeqFeature list TYPE: SeqFeature | list[SeqFeature]
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
annotation	If True, add annotation instead of text TYPE: bool DEFAULT: False
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() or segment.add_annotation() method keyword arguments (e.g. dict(size=12, color="red", ...)) TYPE: dict[str, Any] | None DEFAULT: None

add_lollipop

add_lollipop(
    x: float,
    *,
    y: float = 1.0,
    size: float = 6.0,
    line_kws: dict[str, Any] | None = None,
    point_kws: dict[str, Any] | None = None
) -> None

Add lollipop

PARAMETER	DESCRIPTION
x	X coordinate TYPE: float
y	Y coordinate lollipop height TYPE: float DEFAULT: 1.0
size	Point size TYPE: float DEFAULT: 6.0
line_kws	Axes.vlines properties (e.g. dict(color="red", lw=0.5, ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.vlines.html TYPE: dict[str, Any] | None DEFAULT: None
point_kws	Axes.scatter properties (e.g. dict(fc="red", ec="black", lw=0.5,...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.scatter.html TYPE: dict[str, Any] | None DEFAULT: None

add_promoter

add_promoter(
    x: float,
    length: float = 0.02,
    *,
    y: float = 1.0,
    strand: Strand = 1,
    head_length: float = 1.0,
    head_width: float = 0.5,
    **kwargs
) -> None

Add promoter arrow

PARAMETER	DESCRIPTION
x	X coordinate TYPE: float
length	Arrow length (If 0 < length < 1, it is treated as ratio length) TYPE: float DEFAULT: 0.02
y	Y coordinate promoter height TYPE: float DEFAULT: 1.0
strand	Arrow strand direction (1 or -1) TYPE: Strand DEFAULT: 1
head_length	Arrow head length TYPE: float DEFAULT: 1.0
head_width	Arrow head width TYPE: float DEFAULT: 0.5
kwargs	FancyArrowPatch properties (e.g. color="red", ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.FancyArrowPatch.html TYPE: dict[str, Any] | None DEFAULT: {}

add_highlight

add_highlight(
    x: tuple[float, float],
    *,
    y: tuple[float, float] = (-1, 1),
    color: str = "lime",
    alpha: float = 0.2,
    **kwargs
) -> None

Add highlight

PARAMETER	DESCRIPTION
x	X cooridinate range TYPE: tuple[float, float]
y	Y coordinate range TYPE: tuple[float, float] DEFAULT: (-1, 1)
color	Highlight color TYPE: str DEFAULT: 'lime'
alpha	Color transparency TYPE: float DEFAULT: 0.2
kwargs	Axes.fill_between properties (e.g. lw=1.0, ec="black", ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.fill_between.html TYPE: dict[str, Any] | None DEFAULT: {}