trackc.pl.bdgmat_track

trackc.pl.bdgmat_track(ax: ~matplotlib.axes._axes.Axes | None = None, bed: ~pandas.core.frame.DataFrame | str | None = None, regions: ~typing.Sequence[str] | str | None = None, style: str | None = 'heatmap', logdata: bool = False, minrange: float | None = None, maxrange: float | None = None, color: ~typing.Sequence[str] | None = 'silver', cmap: ~matplotlib.colors.Colormap | str | None = <matplotlib.colors.LinearSegmentedColormap object>, alpha: float | None = 1, label: str | None = None, label_fontsize: int | None = 8, ticks_on: bool = True, tick_fontsize: int | None = 7, tick_fl: str | None = '%0.2f', line_lg_ncol: int | None = 1)

Plot bedGraph matrix track, support for multiple or reverse genome regions. bedgraph matrix file like bedgraph, columns from 4th are values bedgraph matrix should be sorted by chrom, start

Parameters

If bed if a filepath, the file should have headers, The first three columns are [chrom start end] bedGraph matrix format: [chrom start end scorename1 scorename2 …]

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 (eg. "chr6:2000000-1000000"),

which means you want to get the reverse region

style: str

heatmap or line, default heatmap

logdata: bool | bool list

whether log the data before plotting

minrange: float | float list

the minimum range of values used to show

maxrange: float | float list

the maximum range of values used to show

color: str or list

the color of the plot for style: line, if color is a list, the line color will be set by matrix columns order

cmap: str | matplotlib.colors.Colormap

the colormap of the plot for style: heatmap

alpha: float

alpha of plot color

label: str

the title of the track, will show on the left

label_fontsize: int

the label text fontsize

ticks_on: bool

whether show the ticks

tick_fontsize: int

ticks text fontsize

tick_fl: str

ticks retains a few decimal places

line_lg_ncol: int

the number of columns of legend for style: line