pyVIA.plotting_via.plot_scatter

pyVIA.plotting_via.plot_scatter(embedding, labels, cmap='rainbow', s=5, alpha=0.3, edgecolors='None', title='', text_labels=True, color_dict=None, via_object=None, sc_index_terminal_states=None, true_labels=[], show_legend=True, hide_axes_ticks=True, color_labels_reverse=False)[source]

General scatter plotting tool for numeric and categorical labels on the single-cell level

Parameters:

  • embedding (ndarray) – ndarray n_samples x 2

  • labels (list) – list single cell labels list of number or strings

  • cmap – str default = ‘rainbow’

  • s – int size of scatter dot

  • alpha – float with 0 transparent to 1 opaque default =0.3

  • edgecolors –

  • title (str) – str

  • text_labels (bool) – bool default =True

  • via_object –

  • sc_index_terminal_states (list) – list of integers corresponding to one cell in each of the terminal states

  • color_dict – {‘true_label_group_1’: #COLOR,’true_label_group_2’: #COLOR2,….} where the dictionary keys correspond to the provided labels

  • true_labels (list) – list of single cell labels used to annotate the terminal states

Returns:

matplotlib pyplot fig, ax