def get_tree_style(**kwargs): style = TreeStyle() style.layout_fn = layout style.allow_face_overlap = True style.branch_vertical_margin = 5 style.complete_branch_lines_when_necessary = False style.draw_aligned_faces_as_table = False style.scale = 1500 style.scale_length = 0.05 style.show_branch_support = False style.show_leaf_name = False for key, value in kwargs.items(): if value == "True": value = True else: try: value = float(value) except ValueError: pass setattr(style, key, value) return style
def make_cluster_tree(tree_file: str, matrix: str, out_file: str, outgroup: Optional[List[str]] = None) -> None: """Draw a tree with cluster absence/presence information from an existing tree file and absence/presence matrix, and save it as an image under the supplied file name. Arguments: tree_file: the name of the file containing the tree to annotate matrix: a comma- or tab-separated absence/presence matrix out_file: the name under which to save the resulting image outgroup: the organism(s) to use as an outgroup, if any """ # ClusterTree needs tab-separated, but that can't be exported cleanly matrix = matrix.replace(",", "\t") # tree with clustering analysis tree = ClusterTree(tree_file, text_array=matrix) # rerooting the tree if outgroup: ancestor = tree.get_common_ancestor(outgroup) tree.set_outgroup(ancestor) tree.ladderize(direction=1) # set drawing line width to 2 my_node_style = NodeStyle() my_node_style["vt_line_width"] = 2 my_node_style["hz_line_width"] = 2 my_node_style["size"] = 5 # layout function def sel_mylayout(node): node.set_style(my_node_style) if node.is_leaf(): # add names in larger font + italics species_name = AttrFace("name", fsize=12, fstyle="italic") add_face_to_node(species_name, node, column=0, position="branch-right") # add absence/presence matrix for i, value in enumerate(getattr(node, "profile", [])): if value > 0: color = "#FF0000" else: color = "#EEEEEE" my_face = CircleFace(8, color, style="circle") my_face.margin_right = 3 my_face.margin_bottom = 3 add_face_to_node(my_face, node, position="aligned", column=i) # Use my layout to visualize the tree my_tree_style = TreeStyle() # Add header for j, name in enumerate(tree.arraytable.colNames): name_face = TextFace(name, fsize=11) name_face.rotation = -90 name_face.hz_align = 1 name_face.vt_align = 1 name_face.margin_bottom = 10 my_tree_style.aligned_header.add_face(name_face, column=j) my_tree_style.scale_length = 0.1 # myTreeStyle.show_branch_support = True # don't auto-show leaf names, since we dealt with that above my_tree_style.show_leaf_name = False # set layout function for my_tree_style my_tree_style.layout_fn = sel_mylayout #tree.render(out_file, w=183, units="mm", dpi=600, tree_style=my_tree_style) tree.render(out_file, dpi=600, tree_style=my_tree_style)