simba.pl.node_similarity

simba.pl.node_similarity(adata, bins=20, log=True, show_cutoff=True, cutoff=None, n_edges=5000, fig_size=(5, 3), pad=1.08, w_pad=None, h_pad=None, save_fig=None, fig_path=None, fig_name='plot_node_similarity.pdf')[source]

Plot similarity scores of nodes

Parameters:

  • adata (Anndata) – Annotated data matrix.

  • bins (int, optional (default: 20)) – The number of equal-width bins in the given range for histogram plot.

  • log (bool, optional (default: True)) – If True, log scale will be used for y axis.

  • show_cutoff (bool, optional (default: True)) – If True, cutoff on scores will be shown

  • cutoff (int, optional (default: None)) – Cutoff used to select edges

  • n_edges (int, optional (default: 5000)) – The number of edges to select.

  • pad (float, optional (default: 1.08)) – Padding between the figure edge and the edges of subplots, as a fraction of the font size.

  • h_pad (float, optional (default: None)) – Padding (height/width) between edges of adjacent subplots, as a fraction of the font size. Defaults to pad.

  • w_pad (float, optional (default: None)) – Padding (height/width) between edges of adjacent subplots, as a fraction of the font size. Defaults to pad.

  • fig_size (tuple, optional (default: (5,8))) – figure size.

  • save_fig (bool, optional (default: False)) – if True,save the figure.

  • fig_path (str, optional (default: None)) – If save_fig is True, specify figure path.

  • fig_name (str, optional (default: ‘plot_node_similarity.pdf’)) – if save_fig is True, specify figure name.

Return type:

None