trackc.pl.virtual4C#

trackc.pl.virtual4C(clr: ~cooler.api.Cooler | str, ax: ~matplotlib.axes._axes.Axes | None = None, balance: bool = False, target: str | None = None, regions: ~typing.Sequence[str] | str | None = None, track_type: str | None = 'line', color: str | None = 'tab:blue', cmap: ~typing.Sequence[~matplotlib.colors.Colormap] | str | None = <matplotlib.colors.LinearSegmentedColormap object>, target_color: str | None = None, target_name: str | None = None, logdata: bool = False, trim_range: float = 0.98, minrange: float | None = None, maxrange: float | None = None, label: str | None = None, label_rotation: int | None = 0, label_fontsize: int | None = 12)[source]#

Plot virtual4C track, support for multiple or reverse genome regions.

Parameters:

  • ax (matplotlib.axes.Axes object) –

  • clr (cooler.Cooler | str) – cool format Hi-C matrix (open2c/cooler) or cool file path cooler.Cooler e.g. GM12878=cooler.Cooler(‘./GM12878.chr18.mcool::/resolutions/50000’) str e.g. ‘GM12878.chr18.mcool::/resolutions/50000’ or ‘GM12878.chr18.cool’

  • balance (bool) – The 'balance' parameters of coolMat.matrix(balance=False).fetch('chr6:119940450-123940450')

  • target (str) – Coordinates of the viewpoint. e.g. ‘chr8:127735434-127735435’

  • regions (str | str list) – The genome regions, which contact to the viewpoint 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 you want to get the reverse region contacts

  • track_type (str) – virtual4C types, you can choose one of [‘line’, ‘bar’, ‘heatmap’]

  • color (str) – line or bar type virtual4C color

  • cmap (str | matplotlib.colors.Colormap) – if track_type set heatmap, the cmap

  • target_color (str) – virtual4C viewpoint color

  • target_name (str) – viewpoint label

  • logdata (bool) – do you want to log the data before plotting

  • trim_range (float) – remove the extreme values by trimming the counts.[0,1]

  • minrange (float) – the minimum range of values used to define the ylim or color palette

  • maxrange (float) – the maximum range of values used to define the ylim or color palette

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

  • label_rotation (int) – the label text rotation

  • label_fontsize (int) – the label text fontsize

Example

>>> import trackc as tc
>>> regions = ['chr8:127000000-129200000', 'chr14:96500000-99300000']
>>> MYC_TSS = 'chr8:127735434-127735435'
>>> ten = tc.tenon(figsize=(8,1))
>>> ten.add(pos='bottom', height=1, hspace=0.1)
>>> AML_1360 = cooler.Cooler('./GSM4604287_1360.iced.mcool::/resolutions/10000')
>>> tc.pl.virtual4C(ax=ten.axs(0), clr=AML_1360, target=MYC_TSS, regions=regions,
            track_type='line', label='Virtual 4C', target_color='r')
>>> tc.savefig('trackc_virtual4c.pdf')