GenomeViz Class

GenomeViz

GenomeViz(
    *,
    fig_width: float = 15,
    fig_track_height: float = 1.0,
    track_align_type: TrackAlignType = "left",
    feature_track_ratio: float = 0.25,
    link_track_ratio: float = 1.0,
    theme: Theme = "light",
    show_axis: bool = False
)

Genome Visualization Class

PARAMETER	DESCRIPTION
fig_width	Figure width TYPE: float DEFAULT: 15
fig_track_height	Figure height = fig_track_height * track number TYPE: float DEFAULT: 1.0
track_align_type	Figure track alignment type (left|center|right) TYPE: TrackAlignType DEFAULT: 'left'
feature_track_ratio	Feature track size ratio TYPE: float DEFAULT: 0.25
link_track_ratio	Link track size ratio TYPE: float DEFAULT: 1.0
theme	light: white background + black text, edge dark: black background + white text, edge TYPE: Theme DEFAULT: 'light'
show_axis	Show axis for debug purpose TYPE: bool DEFAULT: False

figsize property

figsize: tuple[float, float]

Figure size (Width, Height)

feature_tracks property

feature_tracks: list[FeatureTrack]

Feature tracks

link_tracks property

link_tracks: list[LinkTrack]

Link tracks

get_tracks

get_tracks(*, subtrack: bool = True) -> list[Track]

Get tracks

PARAMETER	DESCRIPTION
subtrack	If True, include subtracks in FeatureTrack TYPE: bool DEFAULT: True

RETURNS	DESCRIPTION
tracks	Tracks [FeatureTrack|FeatureSubTrack|LinkTrack] TYPE: list[Track]

add_feature_track

add_feature_track(
    name: str,
    segments: (
        int
        | tuple[int, int]
        | Sequence[int | tuple[int, int]]
        | Mapping[str, int | tuple[int, int]]
    ),
    *,
    space: float | list[float] = 0.02,
    offset: int | TrackAlignType | None = None,
    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
) -> FeatureTrack

Add feature track

Add feature track, and also add link track between feature tracks if other feature tracks already exist.

PARAMETER	DESCRIPTION
name	Track name TYPE: str
segments	Track segments definition. Segment sizes or ranges can be specified. TYPE: int | tuple[int, int] | Sequence[int | tuple[int, int]] | Mapping[str, int | tuple[int, int]]
space	Space ratio between segments. If float, all spaces are set to the same value. If list[float], each space is set to the corresponding value (list size must be len(segments) - 1) TYPE: float | list[float] DEFAULT: 0.02
offset	Offset int value or TrackAlignType (left|center|right) If None, offset is defined by GenomeViz track_align_type argument at initialization. TYPE: int | TrackAlignType | None DEFAULT: None
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

RETURNS	DESCRIPTION
feature_track	Feature track TYPE: FeatureTrack

add_link

add_link(
    target1: tuple[str, int, int] | tuple[str, str | None, int, int],
    target2: tuple[str, int, int] | tuple[str, str | None, int, int],
    color: str = "grey",
    inverted_color: str | None = None,
    alpha: float = 0.8,
    v: float | None = None,
    vmin: float = 0,
    vmax: float = 100,
    size: float = 1.0,
    curve: bool = False,
    filter_length: int = 0,
    ignore_outside_range: bool = False,
    v_tooltip: float | None = None,
    **kwargs
) -> None

Add link patch to link track between adjacent feature tracks

PARAMETER	DESCRIPTION
target1	Target link1 (track_name, start, end) or (track_name, target_segment, start, end) TYPE: tuple[str, int, int] | tuple[str, int | str | None, int, int]
target2	Target link2 (track_name, start, end) or (track_name, target_segment, start, end) TYPE: tuple[str, int, int] | tuple[str, int | str | None, int, int]
color	Link color TYPE: str DEFAULT: 'grey'
inverted_color	Inverted link color. If None, color is set. TYPE: str | None DEFAULT: None
alpha	Color transparency TYPE: float DEFAULT: 0.8
v	Identity value for color interpolation. If None, no color interpolation is done. TYPE: float | None DEFAULT: None
vmin	Min value for color interpolation TYPE: float DEFAULT: 0
vmax	Max value for color interpolation TYPE: float DEFAULT: 100
size	Link vertical size ratio for track TYPE: float DEFAULT: 1.0
curve	If True, bezier curve link is plotted TYPE: bool DEFAULT: False
filter_length	If link length is shorter than filter_length, ignore it. TYPE: int DEFAULT: 0
ignore_outside_range	If True and the link position is outside the range of the target track, ignore it without raising an error. TYPE: bool DEFAULT: False
v_tooltip	Identity value for only tooltip display. If no color interpolation is required, use this option instead of v. TYPE: float | None DEFAULT: None
**kwargs	Patch properties (e.g. ec="black", lw=0.5, hatch="//", ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html DEFAULT: {}

set_scale_bar

set_scale_bar(
    *,
    ymargin: float = 1.0,
    labelsize: float = 15,
    scale_size_label: tuple[int, str] | None = None
) -> None

Set scale bar

PARAMETER	DESCRIPTION
ymargin	Scale bar y margin TYPE: float DEFAULT: 1.0
labelsize	Label size TYPE: float DEFAULT: 15
scale_size_label	Scale bar size & label tuple (e.g. (1000, "1.0 kb")) If None, scale bar size & label are automatically set. TYPE: tuple[int, str] | None DEFAULT: None

set_scale_xticks

set_scale_xticks(
    *,
    ymargin: float = 1.0,
    labelsize: float = 15,
    start: int = 0,
    unit: Unit | None = None
) -> None

Set scale xticks

PARAMETER	DESCRIPTION
ymargin	X ticks y margin TYPE: float DEFAULT: 1.0
labelsize	Label size TYPE: float DEFAULT: 15
start	X ticks start position TYPE: int DEFAULT: 0
unit	Display unit (Gb|Mb|Kb|bp) TYPE: Unit | None DEFAULT: None

set_colorbar

set_colorbar(
    colors: list[str] | None = None,
    *,
    alpha: float = 0.8,
    vmin: float = 0,
    vmax: float = 100,
    bar_height: float = 0.2,
    bar_width: float = 0.01,
    bar_left: float = 1.02,
    bar_bottom: float = 0,
    bar_label: str = "",
    bar_labelsize: float = 15,
    tick_labelsize: float = 10
) -> None

Set colorbar

PARAMETER	DESCRIPTION
colors	Colors for bar TYPE: list[str] | None DEFAULT: None
alpha	Color transparency TYPE: float DEFAULT: 0.8
vmin	Colorbar min value TYPE: float DEFAULT: 0
vmax	Colorbar max value TYPE: float DEFAULT: 100
bar_height	Colorbar height ratio TYPE: float DEFAULT: 0.2
bar_width	Colorbar width ratio TYPE: float DEFAULT: 0.01
bar_left	Colorbar left position TYPE: float DEFAULT: 1.02
bar_bottom	Colorbar bottom position TYPE: float DEFAULT: 0
bar_label	Colorbar label TYPE: str DEFAULT: ''
bar_labelsize	Colorbar label size TYPE: float DEFAULT: 15
tick_labelsize	Colorbar tick label size TYPE: float DEFAULT: 10

plotfig

plotfig(*, dpi: int = 100, fast_render: bool = True) -> Figure

Plot figure

PARAMETER	DESCRIPTION
dpi	DPI TYPE: int DEFAULT: 100
fast_render	Enable fast rendering mode using PatchCollection. Set fast_render=True by default, and set it to False when used in the savefig_html() method. Fast rendering mode cannot generate tooltips for html display. TYPE: bool DEFAULT: True

RETURNS	DESCRIPTION
fig	Plot figure result TYPE: Figure

savefig

savefig(savefile: str | Path, *, dpi: int = 100, pad_inches: float = 0.5) -> None

Save figure to file

PARAMETER	DESCRIPTION
savefile	Save file TYPE: str | Path
dpi	DPI TYPE: int DEFAULT: 100
pad_inches	Padding inches TYPE: float DEFAULT: 0.5

Warnings

To plot a figure that settings a user-defined legend, subtracks, or annotations, call fig.savefig() instead of gv.savefig().

savefig_html

savefig_html(
    html_outfile: str | Path | io.StringIO | io.BytesIO, figure: Figure | None = None
) -> None

Save figure in html format

PARAMETER	DESCRIPTION
html_outfile	Output HTML file (*.html) TYPE: str | Path | StringIO | BytesIO
figure	Save HTML viewer file using user customized figure. Set to output figure including user-specified legend, subtracks, etc. Target figure must be generated by gv.plotfig(fast_render=False). TYPE: Figure | None DEFAULT: None