simba.pl.pca_variance_ratio
- simba.pl.pca_variance_ratio(adata, log=True, show_cutoff=True, fig_size=(4, 4), save_fig=None, fig_path=None, fig_name='plot_variance_ratio.pdf', pad=1.08, w_pad=None, h_pad=None, **kwargs)[source]
Plot the variance ratio.
- 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
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_variance_ratio.pdf’)) – if save_fig is True, specify figure name.
**kwargs (dict, optional) – Other keyword arguments are passed through to
plt.plot
- Return type:
None