simba.pl.entity_barcode

simba.pl.entity_barcode(adata_cmp, entities, anno_ref=None, layer='softmax', palette=None, alpha=0.8, linewidths=1, show_cutoff=False, cutoff=0.5, min_rank=None, max_rank=None, fig_size=(6, 2), fig_ncol=1, save_fig=None, fig_path=None, fig_name='plot_barcode.pdf', pad=1.08, w_pad=None, h_pad=None, **kwargs)[source]

Plot query entity barcode

Parameters:

  • adata_cmp (AnnData) – Anndata object from compare_entities

  • entities (list) – Entity names to plot.

  • anno_ref (str) – Annotation used for reference entity

  • layer (str, optional (default: ‘softmax’)) – Layer to use make barcode plots

  • palette (dict, optional (default: None)) – Color palette used for anno_ref

  • alpha (float, optional (default: 0.8)) – 0.0 transparent through 1.0 opaque

  • linewidths (int, optional (default: 1)) – The width of each line.

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

  • cutoff (float, optional (default: 0.5)) – Cutoff value for y axis

  • min_rank (int, optional (default: None)) – Specify the minimum rank of observations to show. If None, min_rank is set to 0.

  • max_rank (int, optional (default: None)) – Specify the maximum rank of observations to show. If None, max_rank is set to the number of observations.

  • fig_size (tuple, optional (default: (6,2))) – figure size.

  • fig_ncol (int, optional (default: 1)) – the number of columns of the figure panel

  • 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_barcode.pdf’)) – if save_fig is True, specify figure name.

  • **kwargs (dict, optional) – Other keyword arguments are passed through to mpl.collections.LineCollection

Return type:

None