simba.pl.svd_nodes

simba.pl.svd_nodes(adata, comp1=1, comp2=2, color=None, dict_palette=None, cutoff=None, n_edges=5000, size=8, drawing_order='random', dict_drawing_order=None, fig_size=(4, 4), fig_ncol=3, fig_legend_ncol=1, fig_legend_order=None, alpha=1, pad=1.08, w_pad=None, h_pad=None, save_fig=None, fig_path=None, fig_name='plot_svd_nodes.pdf', vmin=None, vmax=None, **kwargs)[source]

Plot SVD coordinates

Parameters:

  • adata (Anndata) – Annotated data matrix.

  • comp1 (int, optional (default: 1)) – Component used for x axis.

  • comp2 (int, optional (default: 2)) – Component used for y axis.

  • color (list, optional (default: None)) – A list of variables that will produce points with different colors. e.g. color = [‘anno1’, ‘anno2’]

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

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

  • dict_palette (dict,optional (default: None)) – A dictionary of palettes for different variables in color. Only valid for categorical/string variables e.g. dict_palette = {‘ann1’: {},’ann2’: {}}

  • drawing_order (str (default: ‘random’)) – The order in which values are plotted, This can be one of the following values - ‘original’: plot points in the same order as in input dataframe - ‘sorted’ : plot points with higher values on top. - ‘random’ : plot points in a random order

  • dict_drawing_order (dict,optional (default: None)) – A dictionary of drawing_order for different variables in color. Only valid for categorical/string variables e.g. dict_drawing_order = {‘ann1’: ‘original’,’ann2’: ‘sorted’}

  • size (int (default: 8)) – Point size.

  • fig_size (tuple, optional (default: (4, 4))) – figure size.

  • fig_ncol (int, optional (default: 3)) – the number of columns of the figure panel

  • fig_legend_order (dict,optional (default: None)) – Specified order for the appearance of the annotation keys. Only valid for categorical/string variable e.g. fig_legend_order = {‘ann1’:[‘a’,’b’,’c’],’ann2’:[‘aa’,’bb’,’cc’]}

  • fig_legend_ncol (int, optional (default: 1)) – The number of columns that the legend has.

  • vmin (float, optional (default: None)) – The min and max values are used to normalize continuous values. If None, the respective min and max of continuous values is used.

  • vmax (float, optional (default: None)) – The min and max values are used to normalize continuous values. If None, the respective min and max of continuous values is used.

  • alpha (float, optional (default: 1)) – 0.0 transparent through 1.0 opaque

  • 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.

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

Return type:

None