simba.pl.variable_genes

simba.pl.variable_genes(adata, show_texts=False, n_texts=10, size=8, text_size=10, pad=1.08, w_pad=None, h_pad=None, fig_size=(4, 4), save_fig=None, fig_path=None, fig_name='plot_variable_genes.pdf', **kwargs)[source]

Plot highly variable genes.

Parameters:

  • adata (Anndata) – Annotated data matrix.

  • show_texts (bool, optional (default: False)) – If True, text annotation will be shown.

  • n_texts (int, optional (default: 10)) – The number of texts to plot.

  • size (int, optional (default: 8)) – The marker size

  • text_size (int, optional (default: 10)) – The text 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.

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

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

Return type:

None