trackc.pl.zoomin#

trackc.pl.zoomin(ax: Axes | None = None, raw_regions: Sequence[str] | str | None = None, zoomin_regions: Sequence[str] | str | None = None, colors: Sequence[str] | None = None, alpha: float = 1, line_on: bool = False, fill: bool = True)[source]#

Plot zoomin track, support for multiple or reverse genome regions.

Parameters:

  • ax (matplotlib.axes.Axes object) –

  • raw_regions (str | str list) –

    The raw genome regions, some of these regions will be selected to zoom in. e.g. "chr6:1000000-2000000" or ["chr6:1000000-2000000", "chr3:5000000-4000000", "chr5"]

    The start can be larger than the end (eg. "chr6:2000000-1000000"), which means the reverse region

  • zoomin_regions (str | str list) – regions to be zoomin, The format is the same as raw_regions. the regions of zoomin_regions should be located in the raw_regions

  • colors (str list) – the colors of the zoomin_regions

  • alpha (float) – alpha of plot color

  • line_on (bool) – Whether to display the line of zoomin plots

  • fill (bool) – Whether to fill the zoomin plots

Example

>>> full_regions = "chr18:45000000-78077248"
>>> zoom_regions = ['chr18:47400000-48280000', 'chr18:75280000-74030000']
>>> neo_domain_regions = ['chr18:47950000-48280000', 'chr18:75280000-74850000']

>>> ten = tc.tenon(figsize=(8,1))
>>> ten.add(pos='bottom', height=1, hspace=0.1)
>>> ten.add(pos='bottom', height=1, hspace=0.1)

>>> tc.pl.zoomin(ax=ten.axs(0), raw_regions=full_regions, zoomin_regions=zoom_regions, line_on=True, fill=False, alpha=0.5)
>>> tc.pl.zoomin(ax=ten.axs(1), raw_regions=zoom_regions, zoomin_regions=neo_domain_regions, line_on=False, fill=True, alpha=0.5)
>>> tc.savefig('trackc_zoomin_track.pdf')