FeatureTrack Class

FeatureTrack

FeatureTrack(
    name: str,
    size: int,
    start_pos: int = 0,
    labelsize: int = 20,
    labelcolor: str = "black",
    labelmargin: float = 0.01,
    linewidth: int = 1,
    linecolor: str = "black",
    spines: bool = False,
    ratio: float = 1.0,
)

Bases: Track

FeatureTrack Class

PARAMETER	DESCRIPTION
name	Track name TYPE: str
size	Track size TYPE: int
start_pos	Track start position. Track start-end range is defined as (start_pos, start_pos + size). TYPE: int DEFAULT: 0
labelsize	Track label size TYPE: int DEFAULT: 20
labelcolor	Track label color TYPE: str DEFAULT: 'black'
labelmargin	Track label margin TYPE: float DEFAULT: 0.01
linewidth	Track line width TYPE: int DEFAULT: 1
linecolor	Track line color TYPE: str DEFAULT: 'black'
spines	Display track spines TYPE: bool DEFAULT: False
ratio	Track height ratio TYPE: float DEFAULT: 1.0

add_feature

add_feature(
    start: int,
    end: int,
    strand: LiteralTypes.STRAND = 1,
    label: str = "",
    labelsize: int = 15,
    labelcolor: str = "black",
    plotstyle: LiteralTypes.PLOTSTYLE = "bigarrow",
    facecolor: str = "orange",
    edgecolor: str = "black",
    linewidth: float = 0,
    labelrotation: int = 45,
    labelvpos: LiteralTypes.LABELVPOS = "strand",
    labelhpos: LiteralTypes.LABELHPOS = "center",
    labelha: LiteralTypes.LABELHA = "left",
    arrow_shaft_ratio: float = 0.5,
    size_ratio: float = 1.0,
    patch_kws: dict[str, Any] | None = None,
) -> None

Add feature to track

PARAMETER	DESCRIPTION
start	Featrue start position TYPE: int
end	Feature end position TYPE: int
strand	Feature strand TYPE: int DEFAULT: 1
label	Feature label TYPE: str DEFAULT: ''
labelsize	Feature label size TYPE: int DEFAULT: 15
labelcolor	Feature label color TYPE: str DEFAULT: 'black'
plotstyle	Feature plot style (bigarrow|arrow|bigbox|box|bigrbox|rbox) TYPE: str DEFAULT: 'bigarrow'
facecolor	Feature facecolor TYPE: str DEFAULT: 'orange'
edgecolor	Feature edgecolor TYPE: str DEFAULT: 'black'
linewidth	Feature edge linewidth TYPE: float DEFAULT: 0
labelrotation	Feature label rotation TYPE: int DEFAULT: 45
labelvpos	Feature label vertical position (top|center|bottom|strand) If 'strand' is set, 'top' or 'bottom' is auto selected by strand. TYPE: str DEFAULT: 'strand'
labelhpos	Feature label horizontal position (left|center|right) TYPE: str DEFAULT: 'center'
labelha	Feature label horizontal alignment (left|center|right) TYPE: str DEFAULT: 'left'
arrow_shaft_ratio	Feature arrow shaft ratio TYPE: float DEFAULT: 0.5
size_ratio	Feature size ratio to track TYPE: float DEFAULT: 1.0
patch_kws	Patch properties (e.g. fc="red", ec="black", lw=0.5, ...) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict[str, Any] | None DEFAULT: None

add_exon_feature

add_exon_feature(
    exon_regions: list[tuple[int, int]],
    strand: LiteralTypes.STRAND = 1,
    label: str = "",
    labelsize: int = 15,
    labelcolor: str = "black",
    plotstyle: LiteralTypes.PLOTSTYLE = "bigarrow",
    facecolor: str = "orange",
    edgecolor: str = "black",
    linewidth: float = 0,
    labelrotation: int = 45,
    labelvpos: LiteralTypes.LABELVPOS = "strand",
    labelhpos: LiteralTypes.LABELHPOS = "center",
    labelha: LiteralTypes.LABELHA = "left",
    arrow_shaft_ratio: float = 0.5,
    size_ratio: float = 1.0,
    exon_labels: list[str] | None = None,
    exon_label_kws: dict[str, Any] | None = None,
    patch_kws: dict[str, Any] | None = None,
    intron_patch_kws: dict[str, Any] | None = None,
) -> None

Add exon feature to track

PARAMETER	DESCRIPTION
exon_regions	Exon feature start-end postion list TYPE: list[tuple[int, int]]
strand	Feature strand TYPE: int DEFAULT: 1
label	Feature label TYPE: str DEFAULT: ''
labelsize	Feature label size TYPE: int DEFAULT: 15
labelcolor	Feature label color TYPE: str DEFAULT: 'black'
plotstyle	Feature plot style (bigarrow|arrow|bigbox|box|bigrbox|rbox) TYPE: str DEFAULT: 'bigarrow'
facecolor	Feature facecolor TYPE: str DEFAULT: 'orange'
edgecolor	Feature edgecolor TYPE: str DEFAULT: 'black'
linewidth	Feature edge linewidth TYPE: float DEFAULT: 0
labelrotation	Feature label rotation TYPE: int DEFAULT: 45
labelvpos	Feature label vertical position (top|center|bottom|strand) If 'strand' is set, 'top' or 'bottom' is auto selected by strand. TYPE: str DEFAULT: 'strand'
labelhpos	Feature label horizontal position (left|center|right) TYPE: str DEFAULT: 'center'
labelha	Feature label horizontal alignment (left|center|right) TYPE: str DEFAULT: 'left'
arrow_shaft_ratio	Feature arrow shaft ratio TYPE: float DEFAULT: 0.5
size_ratio	Feature size ratio to track TYPE: float DEFAULT: 1.0
exon_labels	Exon labels. Array length must be same as exon_regions. TYPE: list[str] | None DEFAULT: None
exon_label_kws	Text properties (e.g. dict(size=12, color="red", ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.text.html TYPE: dict[str, Any] | None DEFAULT: None
patch_kws	Exon patch properties (e.g. dict(fc="red", ec="black", lw=0.5, ...)) 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(ec="red", lw=2, ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict[str, Any] | None DEFAULT: None

add_features

add_features(
    features: list[SeqFeature],
    label_type: str | None = None,
    label_handle_func: Callable[[str], str] | None = None,
    labelsize: int = 15,
    labelcolor: str = "black",
    plotstyle: LiteralTypes.PLOTSTYLE = "bigarrow",
    facecolor: str = "orange",
    edgecolor: str = "black",
    linewidth: float = 0,
    labelrotation: int = 45,
    labelvpos: LiteralTypes.LABELVPOS = "strand",
    labelhpos: LiteralTypes.LABELHPOS = "center",
    labelha: LiteralTypes.LABELHA = "left",
    arrow_shaft_ratio: float = 0.5,
    size_ratio: float = 1.0,
    patch_kws: dict[str, Any] | None = None,
) -> None

Add features (BioPython's SeqFeature list)

PARAMETER	DESCRIPTION
features	BioPython's SeqFeature list TYPE: str
label_type	Label type (e.g. gene,protein_id,product,etc...) TYPE: str | None DEFAULT: None
label_handle_func	User defined function to handle label. Useful for filtering out unnecesary labels such as hypothetical ~~~, omitting labels with long characters, etc. TYPE: Callable[[str], str] | None DEFAULT: None
labelsize	Feature label size TYPE: int DEFAULT: 15
labelcolor	Feature label color TYPE: str DEFAULT: 'black'
plotstyle	Feature plot style (bigarrow|arrow|bigbox|box|bigrbox|rbox) TYPE: str DEFAULT: 'bigarrow'
facecolor	Feature facecolor. If Genbank qualifiers has facecolor key (e.g. /facecolor="red"), facecolor key value is applied preferentially. TYPE: str DEFAULT: 'orange'
edgecolor	Feature edgecolor TYPE: str DEFAULT: 'black'
linewidth	Feature edge linewidth TYPE: float DEFAULT: 0
labelrotation	Feature label rotation TYPE: int DEFAULT: 45
labelvpos	Feature label vertical position (top|center|bottom|strand) If 'strand' is set, 'top' or 'bottom' is auto selected by strand. TYPE: str DEFAULT: 'strand'
labelhpos	Feature label horizontal position (left|center|right) TYPE: str DEFAULT: 'center'
labelha	Feature label horizontal alignment (left|center|right) TYPE: str DEFAULT: 'left'
arrow_shaft_ratio	Feature arrow shaft ratio TYPE: float DEFAULT: 0.5
size_ratio	Feature size ratio to track TYPE: float DEFAULT: 1.0
patch_kws	Patch properties (e.g. dict(fc="red", ec="black", lw=0.5, ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict[str, Any] | None DEFAULT: None

add_genbank_features

add_genbank_features(
    gbk: Genbank,
    feature_type: str = "CDS",
    label_type: str | None = None,
    label_handle_func: Callable[[str], str] | None = None,
    allow_partial: bool = False,
    pseudogene: bool = False,
    labelsize: int = 15,
    labelcolor: str = "black",
    plotstyle: LiteralTypes.PLOTSTYLE = "bigarrow",
    facecolor: str = "orange",
    facecolor_handle_func: Callable[[SeqFeature], str] | None = None,
    edgecolor: str = "black",
    linewidth: float = 0,
    labelrotation: int = 45,
    labelvpos: LiteralTypes.LABELVPOS = "strand",
    labelhpos: LiteralTypes.LABELHPOS = "center",
    labelha: LiteralTypes.LABELHA = "left",
    arrow_shaft_ratio: float = 0.5,
    size_ratio: float = 1.0,
    patch_kws: dict[str, Any] | None = None,
) -> None

Add features from genbank record

PARAMETER	DESCRIPTION
gbk	Genbank object TYPE: Genbank
feature_type	Feature type (e.g. CDS,rRNA,tRNA,etc...) TYPE: str DEFAULT: 'CDS'
label_type	Label type (e.g. gene,protein_id,product,etc...) TYPE: str | None DEFAULT: None
label_handle_func	User defined function to handle label. Useful for filtering out unnecesary labels such as hypothetical ~~~, omitting labels with long characters, etc. TYPE: Callable[[str], str] | None DEFAULT: None
allow_partial	If True, features that are partially included in range are also extracted TYPE: bool DEFAULT: False
pseudogene	If True and feature_type='CDS', only add CDS features with /pseudo or /pseudogene qualifiers. TYPE: bool DEFAULT: False
labelsize	Feature label size TYPE: int DEFAULT: 15
labelcolor	Feature label color TYPE: str DEFAULT: 'black'
plotstyle	Feature plot style (bigarrow|arrow|bigbox|box|bigrbox|rbox) TYPE: str DEFAULT: 'bigarrow'
facecolor	Feature facecolor. If Genbank qualifiers has facecolor key (e.g. /facecolor="red"), facecolor key value is applied preferentially. TYPE: str DEFAULT: 'orange'
facecolor_handle_func	User defined function to handle feature facecolor. TYPE: Callable[[SeqFeature], str] | None DEFAULT: None
edgecolor	Feature edgecolor TYPE: str DEFAULT: 'black'
linewidth	Feature edge linewidth TYPE: float DEFAULT: 0
labelrotation	Feature label rotation TYPE: int DEFAULT: 45
labelvpos	Feature label vertical position (top|center|bottom|strand) If 'strand' is set, 'top' or 'bottom' is auto selected by strand. TYPE: str DEFAULT: 'strand'
labelhpos	Feature label horizontal position (left|center|right) TYPE: str DEFAULT: 'center'
labelha	Feature label horizontal alignment (left|center|right) TYPE: str DEFAULT: 'left'
arrow_shaft_ratio	Feature arrow shaft ratio TYPE: float DEFAULT: 0.5
size_ratio	Feature size ratio to track TYPE: float DEFAULT: 1.0
patch_kws	Patch properties (e.g. dict(fc="red", ec="black", lw=0.5, ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict[str, Any] | None DEFAULT: None

add_gff_features

add_gff_features(
    gff: Gff,
    feature_type: str = "CDS",
    parse_exon_intron: bool = False,
    label_type: str | None = None,
    label_handle_func: Callable[[str], str] | None = None,
    labelsize: int = 15,
    labelcolor: str = "black",
    plotstyle: LiteralTypes.PLOTSTYLE = "bigarrow",
    facecolor: str = "orange",
    facecolor_handle_func: Callable[[SeqFeature], str] | None = None,
    edgecolor: str = "black",
    linewidth: float = 0,
    labelrotation: int = 45,
    labelvpos: LiteralTypes.LABELVPOS = "strand",
    labelhpos: LiteralTypes.LABELHPOS = "center",
    labelha: LiteralTypes.LABELHA = "left",
    arrow_shaft_ratio: float = 0.5,
    size_ratio: float = 1.0,
    patch_kws: dict[str, Any] | None = None,
    intron_patch_kws: dict[str, Any] | None = None,
) -> None

Add features from GFF record

PARAMETER	DESCRIPTION
gff	GFF object TYPE: Gff
feature_type	Feature type (e.g. CDS,gene,mRNA,etc...) TYPE: str DEFAULT: 'CDS'
parse_exon_intron	If True, try to parse and add exon-intron structured feature (Expected to be used for eukaryote with feature_type=mRNA|ncRNA) TYPE: bool DEFAULT: False
label_type	Label type in attributes column (e.g. ID,Name,product,etc...) TYPE: str | None DEFAULT: None
label_handle_func	User defined function to handle label. Useful for filtering out unnecesary labels such as hypothetical ~~~, omitting labels with long characters, etc. TYPE: Callable[[str], str] | None DEFAULT: None
labelsize	Feature label size TYPE: int DEFAULT: 15
labelcolor	Feature label color TYPE: str DEFAULT: 'black'
plotstyle	Feature plot style (bigarrow|arrow|bigbox|box|bigrbox|rbox) TYPE: str DEFAULT: 'bigarrow'
facecolor	Feature facecolor. If GFF attributes column has facecolor tag (e.g. facecolor=red;), facecolor tag value is applied preferentially. TYPE: str DEFAULT: 'orange'
facecolor_handle_func	User defined function to handle feature facecolor. TYPE: Callable[[SeqFeature], str] | None DEFAULT: None
edgecolor	Feature edgecolor TYPE: str DEFAULT: 'black'
linewidth	Feature edge linewidth TYPE: float DEFAULT: 0
labelrotation	Feature label rotation TYPE: int DEFAULT: 45
labelvpos	Feature label vertical position (top|center|bottom|strand) If 'strand' is set, 'top' or 'bottom' is auto selected by strand. TYPE: str DEFAULT: 'strand'
labelhpos	Feature label horizontal position (left|center|right) TYPE: str DEFAULT: 'center'
labelha	Feature label horizontal alignment (left|center|right) TYPE: str DEFAULT: 'left'
arrow_shaft_ratio	Feature arrow shaft ratio TYPE: float DEFAULT: 0.5
size_ratio	Feature size ratio to track TYPE: float DEFAULT: 1.0
patch_kws	Patch properties (e.g. dict(fc="red", ec="black", lw=0.5, ...)) 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(ec="red", lw=0.5, ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html TYPE: dict[str, Any] | None DEFAULT: None

add_subtrack

add_subtrack(
    name: str | None = None, ratio: float = 1.0, position: str = "below"
) -> None

Add subtrack to feature track

PARAMETER	DESCRIPTION
name	Subtrack name. If None, subtrack name is automatically set. TYPE: str | None DEFAULT: None
ratio	Subtrack size ratio to feature track TYPE: float DEFAULT: 1.0
position	Subtrack position (above|below) TYPE: str DEFAULT: 'below'

get_subtrack

get_subtrack(name: str) -> FeatureSubTrack

Get subtrack by name

PARAMETER	DESCRIPTION
name	Target subtrack name TYPE: str

RETURNS	DESCRIPTION
subtrack	Target subtrack TYPE: FeatureSubTrack

set_sublabel

set_sublabel(
    text: str | None = None,
    size: int = 15,
    color: str = "black",
    position: str = "bottom-left",
    ymargin: float = 0.2,
    sublabel_kws: dict[str, Any] | None = None,
) -> None

Set sublabel to feature track

PARAMETER	DESCRIPTION
text	Sublabel text. If None, {start} - {end} bp label text is set. TYPE: str | None DEFAULT: None
size	Sublabel size TYPE: int DEFAULT: 15
color	Sublabel color TYPE: str DEFAULT: 'black'
position	Sublabel position ([top|bottom]-[left|center|right]) TYPE: str DEFAULT: 'bottom-left'
ymargin	Sublabel y-margin TYPE: float DEFAULT: 0.2
sublabel_kws	Text properties (e.g. dict(size=12, color="red", ...)) https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.text.html TYPE: dict[str, Any] | None DEFAULT: None