harissa.utils module#

harissa.utils#

Various utility functions.

Functions#

`build_pos`	Compute node layout given an interaction matrix.
`plot_network`	Plot a gene regulatory network.
`binarize`	Return a binarized version of the data using gene-specific thresholds derived from the data-calibrated mechanistic model.

harissa.utils.build_pos(inter, method=None)[source]#: Compute node layout given an interaction matrix.

harissa.utils.plot_network(inter, pos, width=1.0, height=1.0, scale=1.0, names=None, vdict=None, tol=None, root=False, axes=None, nodes=None, n0=True, file=None, verb=False, fontsize=None, vcolor=None, nodesize=1.0, bend=0.14, bend_all=False, alpha=None, hide_isolated_genes=False, hide_stimulus_leaves=False)[source]#

Plot a gene regulatory network.

Parameters:

hide_isolated_genes (bool) – Hide genes that have no neighbors.
hide_stimulus_leaves (bool) – Hide genes whose only neighbor is the stimulus.

harissa.utils.binarize(data)[source]#: Return a binarized version of the data using gene-specific thresholds derived from the data-calibrated mechanistic model.