grnet.plot package

Module contents

GRN plotting function

Parameters

data: Union[pandas.DataFrame, grnet.abstract.Estimator, grnet.clusters.CellClasses]: data source for plotting GRN (GRN matrix, pretrained Estimator, or CellClasses)
ax: matplotlib.pyplot.Axes, default: None: axes to plot the GRN (if None, axes will be newly generated)
id: Union[int, str]: index or name of the cell class in CellClasses. if data is not a CellClasses, id will always be ignored.
**kwargs: arguments for plot aethetics

grnet.plot.planetplot(subjective: ~grnet.abstract._estimator.Estimator | ~grnet.clusters._cellclasses.CellClasses, objective: ~grnet.clusters._cellclasses.CellClasses, metric: ~typing.Callable = <function d_asterisk>, ax: ~matplotlib.axes._axes.Axes | None = None, id: int | str | None = None, **kwargs) → None

function for planet plot

Parameters

subjective: Union[grnet.abstract.Estimator, grnet.clusters.CellClasses]: data source for the GRNet model of the subjective cell class (Estimator, or CellClasses)
objective: grnet.clusters.CellClasses: data source for the GRNs of the objective cell classes
metric: Callable, deafult: grnet.evaluations.d_asterisk: evaluation function for the similarities of cell classes
ax: matplotlib.pyplot.Axes, default: None: axes to plot (if None, axes will be newly generated)
id: Union[int, str]: index or name of the cell class in CellClasses. if subjective is not a CellClasses, id will always be ignored.
**kwargs: arguments for plot aethetics

References

see also our original article for further information on planet plots * original article: https://doi.org/10.1016/j.stemcr.2022.10.015