cospar.pl.visualize_tree

cospar.pl.visualize_tree(input_tree, color_coding=None, mode='r', width=60, height=60, dpi=300, data_des='tree', figure_path='.', line_width=0, marker_size_internal=5, marker_size_leaf=5)

Visualize a tree structured in ete3 style.

We provide the option to color code the leaf of the tree. For example, if the leaf nodes represent single cells, and some are more similar than others according to other information, we may impose the same color for these similar cells. Then, visualization with this color setting will allow us see how the tree structure recaptulate the similarity of these cells. If so, similar colors tend to cluster together.

This function will require a full installation of the ete3 packages (which are not part of the default cospar installation), including ete3, ete_toolchain, PyQt5, QtPy. Please run the following to install.

`bash conda install -c etetoolkit ete3 ete_toolchain pip install PyQt5 pip install QtPy `

Parameters

input_tree

A tree stored in ete3 style. This can be the output from running cs.tl.fate_hierarchy(adata, source=”X_clone”), where the resulting tree will be stored at my_tree = adata.uns[“fate_hierarchy_X_clone”][“tree”].

color_coding : dict, None

A dictionary for mapping the leaf names to a specific color. An example color_coding will be {‘node_1’:”#e5f5f9”,’node_2’:”#99d8c9”,…}. ‘node_1’ and ‘node_2’ will be the leaf node names.

mode

The mode of plotting. {‘r’, ‘c’}. ‘c’ is the circular mode, and ‘r’ is the rectangular mode.

width

Width of the tree plot.

height

Height of the tree plot.

dpi

Resolution of the tree plot.

data_des

Label for saving the figure, i.e., figure name.

figure_path

Figure directory.