simba.pl.pcs_features

simba.pl.pcs_features(adata, log=False, size=3, show_cutoff=True, pad=1.08, w_pad=None, h_pad=None, fig_size=(3, 3), fig_ncol=3, save_fig=None, fig_path=None, fig_name='plot_pcs_features.pdf', **kwargs)[source]

Plot features that contribute to the top PCs.

Parameters:

  • adata (Anndata) – Annotated data matrix.

  • log (bool, optional (default: True)) – If True, variance_ratio will be log-transformed.

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

  • size (int, optional (default: 3)) – The marker size

  • 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: (3,3))) – figure size.

  • fig_ncol (int, optional (default: 3)) – 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_pcs_features.pdf’)) – if save_fig is True, specify figure name.

  • **kwargs (dict, optional) – Other keyword arguments are passed through to plt.scatter

Return type:

None