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)[source]
Draw the tree in dendro fromat.
- Parameters
tree (
networkx.DiGraph
) – The input tree.width (
int
, optional) – Width of the figure, by default 8height (
int
, optional) – Height of the figure, by default 3dpi (
int
, optional) – The resolution, by default 300cell_info (
pandas.DataFrame
, optional) – Information about cells such as color, expression values of genes and etc, by default Nonelabel_color (
str
, optional) – The column name in which colors of cells are stored in the dataframe provided ascell_info
, by default “group_color”line_size (
float
, optional) – Line size of the tree, by default 0.4tiplab_size (
float
, optional) – Cell name size in the tree, by default 2.5inner_node_type (
str
, optional) –The format of the inner nodes (i.e. mutations), by default “nmuts” Values are:
nmuts
: only number of mutationsnodeid
: only node idboth
: both number of mutations and node id
inner_node_size (
int
, optional) – Size of the inner nodes (i.e. mutations), by default 2distance_labels_to_bottom (
int
, optional) – Distance cell names to the bottom of the figure, by default 4annotation (
list
, optional) – List of gene names provided in the column dataframe ofcell_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
Note
The cell names in the tree must be identical to the index of
cell_info
dataframe if it was provided.