trisicell.pl.dendro_tree

trisicell.pl.dendro_tree(tree, width=1200, height=500, dpi=300, cell_info=None, label_color='group_color', line_size=0.4, tiplab_size=2.5, inner_node_type='nmuts', inner_node_size=2, distance_labels_to_bottom=4, annotation=None, output_file=None)

Draw the tree in dendro fromat.

Parameters

• tree (networkx.DiGraph) – The input tree.

• width (int, optional) – Width of the figure, by default 8

• height (int, optional) – Height of the figure, by default 3

• dpi (int, optional) – The resolution, by default 300

• cell_info (pandas.DataFrame, optional) – Information about cells such as color, expression values of genes and etc, by default None

• label_color (str, optional) – The column name in which colors of cells are stored in the dataframe provided as cell_info, by default “group_color”

• line_size (float, optional) – Line size of the tree, by default 0.4

• tiplab_size (float, optional) – Cell name size in the tree, by default 2.5

• inner_node_type (str, optional) –

  The format of the inner nodes (i.e. mutations), by default “nmuts” Values are:

  • nmuts: only number of mutations

  • nodeid: only node id

  • both: both number of mutations and node id

• inner_node_size (int, optional) – Size of the inner nodes (i.e. mutations), by default 2

• distance_labels_to_bottom (int, optional) – Distance cell names to the bottom of the figure, by default 4

• annotation (list, optional) – List of gene names provided in the column dataframe of cell_info in to be annotated in the bottom of the tree, by default []

• output_file (str, optional) – Path to a file for saving the tree in, by default None

Returns

Return type

None

Note

The cell names in the tree must be identical to the index of cell_info dataframe if it was provided.