Track Class

Track

Track(name: str, r_lim: tuple[float, float], r_pad_ratio: float, parent_sector: Sector)

Circos Track Class

PARAMETER	DESCRIPTION
name	Track name TYPE: str
r_lim	Track radius limit region TYPE: tuple[float, float]
r_pad_ratio	Track padding ratio for plot data TYPE: float
parent_sector	Parent sector of track TYPE: Sector

name property

name: str

Track name

size property

size: float

Track size (x coordinate)

start property

start: float

Track start position (x coordinate)

end property

end: float

Track end position (x coordinate)

center property

center: float

Track center position (x coordinate)

r_size property

r_size: float

Track radius size

r_lim property

r_lim: tuple[float, float]

Track radius limit

r_center property

r_center: float

Track center radius

r_plot_size property

r_plot_size: float

Track radius size for plot data (r_size with padding)

r_plot_lim property

r_plot_lim: tuple[float, float]

Track radius limit for plot data (r_lim with padding)

rad_size property

rad_size: float

Track radian size

rad_lim property

rad_lim: tuple[float, float]

Track radian limit

deg_size property

deg_size: float

Track degree size

deg_lim property

deg_lim: tuple[float, float]

Track degree limit

parent_sector property

parent_sector: Sector

Parent sector

clockwise property

clockwise: bool

Track coordinate direction

patches property

patches: list[Patch]

Plot patches

plot_funcs property

plot_funcs: list[Callable[[PolarAxes], None]]

Plot functions

x_to_rad

x_to_rad(x: float, ignore_range_error: bool = False) -> float

Convert x coordinate to radian in track start-end range

PARAMETER	DESCRIPTION
x	X coordinate TYPE: float
ignore_range_error	Ignore x coordinate range error TYPE: bool DEFAULT: False

RETURNS	DESCRIPTION
rad	Radian coordinate TYPE: float

axis

axis(**kwargs) -> None

Plot axis

By default, simple black axis params(fc="none", ec="black", lw=0.5) are set.

PARAMETER	DESCRIPTION
**kwargs	Patch properties (e.g. fc="tomato", ec="blue", hatch="//") https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict DEFAULT: {}

text

text(
    text: str,
    x: float | None = None,
    r: float | None = None,
    *,
    adjust_rotation: bool = True,
    orientation: str = "horizontal",
    ignore_range_error: bool = False,
    **kwargs
) -> None

Plot text

PARAMETER	DESCRIPTION
text	Text content TYPE: str
x	X position. If None, track center x position is set. TYPE: float | None DEFAULT: None
r	Radius position. If None, track center radius position is set. TYPE: float | None DEFAULT: None
adjust_rotation	If True, text rotation is auto set based on x and orientation params. TYPE: bool DEFAULT: True
orientation	Text orientation (horizontal or vertical) If adjust_rotation=True, orientation is used for rotation calculation. TYPE: str DEFAULT: 'horizontal'
ignore_range_error	If True, ignore x position range error (ErrorCase: not track.start <= x <= track.end) TYPE: bool DEFAULT: False
**kwargs	Text properties (e.g. size=12, color="red", va="center", ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.text.html TYPE: dict DEFAULT: {}

rect

rect(
    start: float,
    end: float,
    *,
    r_lim: tuple[float, float] | None = None,
    ignore_pad: bool = False,
    **kwargs
) -> None

Plot rectangle

PARAMETER	DESCRIPTION
start	Start position (x coordinate) TYPE: float
end	End position (x coordinate) TYPE: float
r_lim	Radius limit range. If None, track.r_lim (ignore_pad=False) or track.r_plot_lim (ignore_pad=True) is set. TYPE: tuple[float, float] | None DEFAULT: None
ignore_pad	If True, ignore track padding setting. If r_lim param is set by user, this option not works. TYPE: bool DEFAULT: False
**kwargs	Patch properties (e.g. fc="red", ec="blue", lw=1.0, ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict DEFAULT: {}

arrow

arrow(
    start: float,
    end: float,
    *,
    r_lim: tuple[float, float] | None = None,
    head_length: float = 2,
    shaft_ratio: float = 0.5,
    **kwargs
) -> None

Plot arrow

PARAMETER	DESCRIPTION
start	Start position (x coordinate) TYPE: float
end	End position (x coordinate) TYPE: float
r_lim	Radius limit range. If None, track.r_lim is set. TYPE: tuple[float, float] | None DEFAULT: None
head_length	Arrow head length (Degree unit) TYPE: float DEFAULT: 2
shaft_ratio	Arrow shaft ratio (0 - 1.0) TYPE: float DEFAULT: 0.5
**kwargs	Patch properties (e.g. fc="red", ec="blue", lw=1.0, ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict DEFAULT: {}

xticks

xticks(
    x: list[int] | list[float] | np.ndarray,
    labels: list[str] | None = None,
    *,
    tick_length: float = 2,
    outer: bool = True,
    show_bottom_line: bool = False,
    label_size: float = 8,
    label_margin: float = 0.5,
    label_orientation: str = "horizontal",
    line_kws: dict[str, Any] | None = None,
    text_kws: dict[str, Any] | None = None
) -> None

Plot xticks & labels on user-specified position

If you want to plot xticks and their position labels at regular intervals, it is recommended to use track.xticks_by_interval() instead.

PARAMETER	DESCRIPTION
x	X coordinates TYPE: list[int] | list[float] | ndarray
labels	Labels on xticks. If None, only plot ticks line. TYPE: list[str] | None DEFAULT: None
tick_length	Tick length (Radius unit) TYPE: float DEFAULT: 2
outer	If True, show ticks on outer. If False, show ticks on inner. TYPE: bool DEFAULT: True
show_bottom_line	If True, show bottom line. TYPE: bool DEFAULT: False
label_size	Label size TYPE: float DEFAULT: 8
label_margin	Label margin size TYPE: float DEFAULT: 0.5
label_orientation	Label orientation (horizontal or vertical) TYPE: str DEFAULT: 'horizontal'
line_kws	Patch properties (e.g. dict(ec="red", lw=1, ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict[str, Any] | None DEFAULT: None
text_kws	Text properties (e.g. dict(color="red", alpha=0.5, ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.text.html TYPE: dict[str, Any] | None DEFAULT: None

xticks_by_interval

xticks_by_interval(
    interval: int | float,
    *,
    tick_length: float = 2,
    outer: bool = True,
    show_bottom_line: bool = False,
    show_label: bool = True,
    show_endlabel: bool = True,
    label_size: float = 8,
    label_margin: float = 0.5,
    label_orientation: str = "horizontal",
    label_formatter: Callable[[float], str] | None = None,
    line_kws: dict[str, Any] | None = None,
    text_kws: dict[str, Any] | None = None
) -> None

Plot xticks & position labels by user-specified interval

track.xticks_by_interval() is high-level API function of track.xticks(). If you want to plot xticks and their labels in any position you like, use track.xticks() instead.

PARAMETER	DESCRIPTION
interval	Xticks interval TYPE: int | float
tick_length	Tick length (Radius unit) TYPE: float DEFAULT: 2
outer	If True, show ticks on outer. If False, show ticks on inner. TYPE: bool DEFAULT: True
show_bottom_line	If True, show bottom line. TYPE: bool DEFAULT: False
show_label	If True, show label of xticks interval position. TYPE: bool DEFAULT: True
show_endlabel	If False, no display end xtick label. Used to prevent overlap of start-end xtick labels. TYPE: bool DEFAULT: True
label_size	Label size TYPE: float DEFAULT: 8
label_margin	Label margin size TYPE: float DEFAULT: 0.5
label_orientation	Label orientation (horizontal or vertical) TYPE: str DEFAULT: 'horizontal'
label_formatter	User-defined function for label format. (e.g. 1000 -> '1.0 Kb') TYPE: Callable[[float], str] | None DEFAULT: None
line_kws	Patch properties (e.g. dict(ec="red", lw=1, ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict[str, Any] | None DEFAULT: None
text_kws	Text properties (e.g. dict(color="red", alpha=0.5, ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.text.html TYPE: dict[str, Any] | None DEFAULT: None

yticks

yticks(
    y: list[int] | list[float] | np.ndarray,
    labels: list[str] | None = None,
    *,
    vmin: float = 0,
    vmax: float | None = None,
    side: str = "right",
    tick_length: float = 1,
    label_size: float = 8,
    label_margin: float = 0.5,
    line_kws: dict[str, Any] | None = None,
    text_kws: dict[str, Any] | None = None
) -> None

Plot yticks & labels on user-specified position

PARAMETER	DESCRIPTION
y	Y coordinates TYPE: list[int] | list[float] | ndarray
labels	Labels on yticks. If None, only plot ticks line. TYPE: list[str] | None DEFAULT: None
vmin	Y min value TYPE: float DEFAULT: 0
vmax	Y max value. If None, max(y) is set. TYPE: float | None DEFAULT: None
side	Ticks side position (right or left) TYPE: str DEFAULT: 'right'
tick_length	Tick length (Degree unit) TYPE: float DEFAULT: 1
label_size	Label size TYPE: float DEFAULT: 8
label_margin	Label margin size TYPE: float DEFAULT: 0.5
line_kws	Patch properties (e.g. dict(ec="red", lw=1, ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict[str, Any] | None DEFAULT: None
text_kws	Text properties (e.g. dict(color="red", alpha=0.5, ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.text.html TYPE: dict[str, Any] | None DEFAULT: None

grid

grid(y_grid_num: int | None = 6, x_grid_interval: float | None = None, **kwargs) -> None

Plot grid

By default, color="grey", alpha=0.5, zorder=0 line params are set.

PARAMETER	DESCRIPTION
y_grid_num	Y-axis grid line number. If None, y-axis grid line is not shown. TYPE: int | None DEFAULT: 6
x_grid_interval	X-axis grid line interval. If None, x-axis grid line is not shown. TYPE: float | None DEFAULT: None
**kwargs	Axes.plot properties (e.g. color="red", lw=0.5, ls="--", ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.plot.html TYPE: dict DEFAULT: {}

line

line(
    x: list[float] | np.ndarray,
    y: list[float] | np.ndarray,
    *,
    vmin: float = 0,
    vmax: float | None = None,
    arc: bool = True,
    **kwargs
) -> None

Plot line

PARAMETER	DESCRIPTION
x	X coordinates TYPE: list[float] | ndarray
y	Y coordinates TYPE: list[float] | ndarray
vmin	Y min value TYPE: float DEFAULT: 0
vmax	Y max value. If None, max(y) is set. TYPE: float | None DEFAULT: None
arc	If True, plot arc style line for polar projection. If False, simply plot linear style line. TYPE: bool DEFAULT: True
**kwargs	Axes.plot properties (e.g. color="red", lw=0.5, ls="--", ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.plot.html TYPE: dict DEFAULT: {}

scatter

scatter(
    x: list[float] | np.ndarray,
    y: list[float] | np.ndarray,
    *,
    vmin: float = 0,
    vmax: float | None = None,
    **kwargs
) -> None

Plot scatter

PARAMETER	DESCRIPTION
x	X position list TYPE: list[float] | ndarray
y	Y position list TYPE: list[float] | ndarray
vmin	Y min value TYPE: float DEFAULT: 0
vmax	Y max value. If None, max(y) is set. TYPE: float | None DEFAULT: None
**kwargs	Axes.scatter properties (e.g. ec="black", lw=1.0, ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.scatter.html TYPE: dict DEFAULT: {}

bar

bar(
    x: list[float] | np.ndarray,
    height: list[float] | np.ndarray,
    width: float = 0.8,
    bottom: float | list[float] | np.ndarray = 0,
    align: str = "center",
    *,
    vmin: float = 0,
    vmax: float | None = None,
    **kwargs
) -> None

Plot bar

PARAMETER	DESCRIPTION
x	Bar x coordinates TYPE: list[float] | ndarray
height	Bar heights TYPE: list[float] | ndarray
width	Bar width TYPE: float DEFAULT: 0.8
bottom	Bar bottom(s) TYPE: float | ndarray DEFAULT: 0
align	Bar alignment type (center or edge) TYPE: str DEFAULT: 'center'
vmin	Y min value TYPE: float DEFAULT: 0
vmax	Y max value. If None, np.max(height + bottom) is set. TYPE: float | None DEFAULT: None
**kwargs	Axes.bar properties (e.g. color="tomato", ec="black", lw=0.5, hatch="//") https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.bar.html TYPE: dict DEFAULT: {}

stacked_bar

stacked_bar(
    table_data: str | Path | pd.DataFrame | StackedBarTable,
    *,
    delimiter: str = "\t",
    width: float = 0.6,
    cmap: str | dict[str, str] = "tab10",
    vmax: float | None = None,
    show_label: bool = True,
    label_pos: str = "bottom",
    label_margin: float = 2,
    bar_kws: dict[str, Any] | None = None,
    label_kws: dict[str, Any] | None = None
) -> StackedBarTable

Plot stacked bar from table data

PARAMETER	DESCRIPTION
table_data	Table file or Table DataFrame or StackedBarTable TYPE: str | Path | DataFrame | StackedBarTable
delimiter	Table file delimiter TYPE: str DEFAULT: '\t'
width	Bar width ratio (0.0 - 1.0) TYPE: float DEFAULT: 0.6
cmap	Colormap assigned to each stacked bar. User can set matplotlib's colormap (e.g. tab10, Set3) or col_name -> color dict (e.g. dict(A="red", B="blue", C="green", ...)) TYPE: str | dict[str, str] DEFAULT: 'tab10'
vmax	Stacked bar max value. If None, max value in each row values sum is set. TYPE: float | None DEFAULT: None
show_label	Show table row names as labels TYPE: bool DEFAULT: True
label_pos	Label position (bottom|top) TYPE: str DEFAULT: 'bottom'
label_margin	Label margin size TYPE: float DEFAULT: 2
bar_kws	Axes.bar properties (e.g. dict(ec="black", lw=0.5, hatch="//", ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.bar.html TYPE: dict[str, Any] | None DEFAULT: None
label_kws	Text properties (e.g. dict(size=12, orientation="vertical", ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.text.html TYPE: dict[str, Any] | None DEFAULT: None

RETURNS	DESCRIPTION
sb_table	Stacked bar table TYPE: StackedBarTable

stacked_barh

stacked_barh(
    table_data: str | Path | pd.DataFrame | StackedBarTable,
    *,
    delimiter: str = "\t",
    width: float = 0.6,
    cmap: str | dict[str, str] = "tab10",
    bar_kws: dict[str, Any] | None = None
) -> StackedBarTable

Plot horizontal stacked bar from table data

PARAMETER	DESCRIPTION
table_data	Table file or Table DataFrame or StackedBarTable TYPE: str | Path | DataFrame | StackedBarTable
delimiter	Table file delimiter TYPE: str DEFAULT: '\t'
width	Bar width ratio (0.0 - 1.0) TYPE: float DEFAULT: 0.6
cmap	Colormap assigned to each stacked bar. User can set matplotlib's colormap (e.g. tab10, Set3) or col_name -> color dict (e.g. dict(A="red", B="blue", C="green", ...)) TYPE: str | dict[str, str] DEFAULT: 'tab10'
bar_kws	Patch properties for bar plot (e.g. dict(ec="black, lw=0.2, ...)) TYPE: dict[str, Any] | None DEFAULT: None

RETURNS	DESCRIPTION
sb_table	Stacked bar table TYPE: StackedBarTable

fill_between

fill_between(
    x: list[float] | np.ndarray,
    y1: list[float] | np.ndarray,
    y2: float | list[float] | np.ndarray = 0,
    *,
    vmin: float = 0,
    vmax: float | None = None,
    arc: bool = True,
    **kwargs
) -> None

Fill the area between two horizontal(y1, y2) curves

PARAMETER	DESCRIPTION
x	X coordinates TYPE: list[float] | ndarray
y1	Y coordinates (first curve definition) TYPE: list[float] | ndarray
y2	Y coordinate[s] (second curve definition) TYPE: float | list[float] | ndarray DEFAULT: 0
vmin	Y min value TYPE: float DEFAULT: 0
vmax	Y max value. If None, max(y1 + y2) is set. TYPE: float | None DEFAULT: None
arc	If True, plot arc style line for polar projection. If False, simply plot linear style line. TYPE: bool DEFAULT: True
**kwargs	Axes.fill_between properties (e.g. fc="red", ec="black", lw=0.1, ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.fill_between.html TYPE: dict DEFAULT: {}

heatmap

heatmap(
    data: list | np.ndarray,
    *,
    vmin: float | None = None,
    vmax: float | None = None,
    start: float | None = None,
    end: float | None = None,
    width: float | None = None,
    cmap: str | Colormap = "bwr",
    show_value: bool = False,
    rect_kws: dict[str, Any] | None = None,
    text_kws: dict[str, Any] | None = None
) -> None

Plot heatmap

PARAMETER	DESCRIPTION
data	Numerical list, numpy 1d or 2d array TYPE: list | ndarray
vmin	Min value for heatmap plot. If None, np.min(data) is set. TYPE: float | None DEFAULT: None
vmax	Max value for heatmap plot. If None, np.max(data) is set. TYPE: float | None DEFAULT: None
start	Start position for heatmap plot (x coordinate). If None, track.start is set. TYPE: float | None DEFAULT: None
end	End position for heatmap plot (x coordinate). If None, track.end is set. TYPE: float | None DEFAULT: None
width	Heatmap rectangle x width size. Normally heatmap plots squares of equal width. In some cases, it is necessary to reduce the width of only the last column data square. At that time, width can be set under the following conditions. (col_num - 1) * width < end - start < col_num * width TYPE: float | None DEFAULT: None
cmap	Colormap (e.g. viridis, Spectral, Reds, Greys) https://matplotlib.org/stable/tutorials/colors/colormaps.html TYPE: str | Colormap DEFAULT: 'bwr'
show_value	If True, show data value on heatmap rectangle TYPE: bool DEFAULT: False
rect_kws	Patch properties (e.g. dict(ec="black", lw=0.5, ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict[str, Any] | None DEFAULT: None
text_kws	Text properties (e.g. dict(size=6, color="red", ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.text.html TYPE: dict[str, Any] | None DEFAULT: None

tree

tree(
    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
) -> TreeViz

Plot tree

It is recommended that the track(sector) size be the same as the number of leaf nodes in the tree, to make it easier to combine with bar and heatmap.

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

RETURNS	DESCRIPTION
tv	TreeViz instance TYPE: TreeViz

genomic_features

genomic_features(
    features: SeqFeature | list[SeqFeature],
    *,
    plotstyle: str = "box",
    r_lim: tuple[float, float] | None = None,
    facecolor_handler: Callable[[SeqFeature], str] | None = None,
    **kwargs
) -> None

Plot genomic features

PARAMETER	DESCRIPTION
features	Biopython's SeqFeature or SeqFeature list TYPE: SeqFeature | list[SeqFeature]
plotstyle	Plot style (box or arrow) TYPE: str DEFAULT: 'box'
r_lim	Radius limit range. If None, track.r_plot_lim is set. TYPE: tuple[float, float] | None DEFAULT: None
facecolor_handler	User-defined function to handle facecolor TYPE: Callable[[SeqFeature], str] | None DEFAULT: None
**kwargs	Patch properties (e.g. fc="red", ec="blue", lw=1.0, ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict DEFAULT: {}