trackc.pl.bed_track#

trackc.pl.bed_track(ax: Axes | None = None, bed: DataFrame | str | None = None, regions: Sequence[str] | str | None = None, style: str | None = 'bar', primary_col: Sequence[str] | None = '#3271B2', secondary_col: Sequence[str] | None = '#FBD23C', cmap: Colormap | str | None = None, intervals: int | None = 1, alpha: float | None = 1, invert_y: bool | None = False, label: str | None = None, label_fontsize: int | None = 12, label_rotation: int | None = 0, vmin: float | None = None, vmax: float | None = None, tick_fontsize: int | None = 8, tick_fl: str | None = '%0.2f', score_label_size: int | None = 7)[source]#

Plot bed track, support for multiple or reverse genome regions. support bed3 and bed5, the fields after the column5 will be ignored, should be sorted py chromStart if style is line

Parameters:

  • ax (matplotlib.axes.Axes object) –

  • bed (pd.DataFrame | str) –

    If bed if a filepath, the file should have no headers.

    Here is bed formats:
    column1: chrom

    The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).

    column2: chromStart

    The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.

    column3: chromEnd

    The ending position of the feature in the chromosome or scaffold.

    column4: name

    Defines the name of the BED line. Either “.” (=no name), or other string

    column5: score

    Defines the name of the BED line. if nessasary, can be set as ., if track_type/style is one of bar/line

    column6: strand

    Defines the strand. Either “.” (=no strand) or “+” or “-“.

    if the input data have 4 columns, then default input is bedGraph format: [chrom start end score]

  • regions (str | str list) –

    The genome regions to plot. e.g. "chr6:1000000-2000000" or ["chr6:1000000-2000000", "chr3:5000000-4000000"]

    The start can be larger than the end (e.g. "chr6:2000000-1000000"), which means you want to get the reverse region

  • style (str) – bed blocks style, opions in [‘line’, ‘bar’, ‘link’, ‘tri’, ‘rec’]

  • primary_col (str) – the color of line/tri/rec, if color is color list, the block color will set by regions

  • secondary_col (str) – the color of line/tri/rec for negative values

  • cmap (str | matplotlib.colors.Colormap) – the colormap of the plot except style:line

  • intervals (int) – if style is one of [tri, rec], the row number distribution for triangle or rectangle blocks

  • alpha (float) – alpha of plot color

  • invert_y (bool) – whether reverse the y-axis

  • label (str) – the title of the track, will show on the left

  • label_fontsize (int) – the label text fontsize

  • label_rotation (int) – the label text rotation

  • vmin (float) – the minimum range of values used to define the ylim

  • vmax (float) – the maximum range of values used to define the ylim

  • tick_fontsize (int) – values range ticks text fontsize

  • tick_fl (str) – values range ticks retains a few decimal places

  • score_label_size (int) – score colorbar label fontsize